What We're Reading

This is a lightly curated list from our Zotero group, which is public (with closed membership) and viewable here: https://www.zotero.org/groups/2308144/iasge. You can download this list as BibTex in our GitLab Repository.

2019

Martin Klein and Van de Sompel. An Institutional Perspective to Rescue Scholarly Orphans. May 2019. URL: https://vimeo.com/337332089 (visited on 2019-06-27).
[BibTeX▼]

@misc{klein_institutional_2019,
    author = "Klein, Martin and de Sompel, Van",
    title = "An {Institutional} {Perspective} to {Rescue} {Scholarly} {Orphans}",
    url = "https://vimeo.com/337332089",
    urldate = "2019-06-27",
    month = "May",
    year = "2019"
}

Martin Klein and Herbert Van de Sompel. An Institutional Perspective to Rescue Scholarly Orphans. April 2019. URL: https://www.cni.org/topics/digital-preservation/an-institutional-perspective-to-rescue-scholarly-orphans (visited on 2019-06-27).
[BibTeX▼]

@misc{noauthor_institutional_2019,
    author = "Klein, Martin and de Sompel, Herbert Van",
    title = "An {Institutional} {Perspective} to {Rescue} {Scholarly} {Orphans}",
    url = "https://www.cni.org/topics/digital-preservation/an-institutional-perspective-to-rescue-scholarly-orphans",
    language = "en-US",
    urldate = "2019-06-27",
    journal = "CNI: Coalition for Networked Information",
    month = "April",
    year = "2019"
}

Michael Hirsch; Tom Klaver. Pyzenodo3: Pure Python 3 wrapper for the Zenodo REST API. 2019. URL: https://github.com/scivision/pyzenodo3 (visited on 2019-07-08).
[BibTeX▼]

@misc{klaver_pyzenodo3:_2019,
    author = "Klaver, Michael Hirsch; Tom",
    title = "pyzenodo3: {Pure} {Python} 3 wrapper for the {Zenodo} {REST} {API}",
    url = "https://github.com/scivision/pyzenodo3",
    urldate = "2019-07-08",
    year = "2019"
}

Chris Holdgraf. Binder with Zenodo - Jupyter Blog. 2019. URL: https://blog.jupyter.org/binder-with-zenodo-af68ed6648a6 (visited on 2019-07-08).
[abstract▼] [BibTeX▼]

@misc{holdgraf_binder_2019,
    author = "Holdgraf, Chris",
    title = "Binder with {Zenodo} - {Jupyter} {Blog}",
    url = "https://blog.jupyter.org/binder-with-zenodo-af68ed6648a6",
    language = "en",
    urldate = "2019-07-08",
    journal = "Medium",
    year = "2019"
}

Elizabeth Lawley. Publication and Evaluation Challenges in Games & Interactive Media. Presentations and other scholarship, August 2019. URL: https://scholarworks.rit.edu/other/919.
[BibTeX▼]

@article{lawley_publication_2019,
    author = "Lawley, Elizabeth",
    title = "Publication and {Evaluation} {Challenges} in {Games} \\& {Interactive} {Media}",
    url = "https://scholarworks.rit.edu/other/919",
    journal = "Presentations and other scholarship",
    month = "August",
    year = "2019"
}

Wagner Felidré, Leonardo Furtado, Daniel da Costa, Bruno Cartaxo, and Gustavo Pinto. Continuous Integration Theater. arXiv, July 2019. URL: http://arxiv.org/abs/1907.01602 (visited on 2019-07-07).
[abstract▼] [BibTeX▼]

Background: Continuous Integration (CI) systems are now the bedrock of several software development practices. Several tools such as TravisCI, CircleCI, and Hudson, that implement CI practices, are commonly adopted by software engineers. However, the way that software engineers use these tools could lead to what we call "Continuous Integration Theater", a situation in which software engineers do not employ these tools effectively, leading to unhealthy CI practices. Aims: The goal of this paper is to make sense of how commonplace are these unhealthy continuous integration practices being employed in practice. Method: By inspecting 1,270 open-source projects that use TravisCI, the most used CI service, we quantitatively studied how common is to use CI (1) with infrequent commits, (2) in a software project with poor test coverage, (3) with builds that stay broken for long periods, and (4) with builds that take too long to run. Results: We observed that 748 (\$sim\$60\%) projects face infrequent commits, which essentially makes the merging process harder. Moreover, we were able to find code coverage information for 51 projects. The average code coverage was 78\%, although Ruby projects have a higher code coverage than Java projects (86\% and 63\%, respectively). However, some projects with very small coverage (\$sim\$4\%) were found. Still, we observed that 85\% of the studied projects have at least one broken build that take more than four days to be fixed. Interestingly, very small projects (up to 1,000 lines of code) are the ones that take the longest to fix broken builds. Finally, we noted that, for the majority of the studied projects, the build is executed under the 10 minutes rule of thumb. Conclusions: Our results are important to an increasing community of software engineers that employ CI practices on daily basis but may not be aware of bad practices that are eventually employed.
```
@article{felidre_continuous_2019,
    author = "Felidré, Wagner and Furtado, Leonardo and da Costa, Daniel and Cartaxo, Bruno and Pinto, Gustavo",
    title = "Continuous {Integration} {Theater}",
    url = "http://arxiv.org/abs/1907.01602",
    language = "English",
    urldate = "2019-07-07",
    journal = "arXiv",
    month = "July",
    year = "2019"
}
```
Delphix Corp., Chris Patton, Eric Noah Schrock, Matthew Benjamin Amdur, and Zubair Kahn. Version Control of Applications. June 2019. URL: https://patentimages.storage.googleapis.com/83/6e/91/175bdab95b3358/US20190187980A1.pdf.
[abstract▼] [BibTeX▼]

An application development system allows developers of software system to manage infrastructure resources during the development and testing process . The application devel opment system allows users to define application containers that comprise components including source code , binaries , and virtual databases used for the application . An applica tion container can be associated with policies that control various aspects of the actions taken using the application container including constraints and access control . The application development system enforces the policies for actions taken by users for the application containers . The encapsulation of policies with the application containers allows users of the application containers to take actions including creating virtual databases , provisioning virtual databases , and the like without requiring system adminis trators to manage resource issues.
```
@misc{delphix_corp._version_2019,
    author = "Corp., Delphix and Patton, Chris and Schrock, Eric Noah and Amdur, Matthew Benjamin and Kahn, Zubair",
    title = "Version {Control} of {Applications}",
    url = "https://patentimages.storage.googleapis.com/83/6e/91/175bdab95b3358/US20190187980A1.pdf",
    language = "English",
    publisher = "United States Patent Application Publication",
    month = "June",
    year = "2019"
}
```
Sara B Donevant, Erik R Svendsen, Jane V Richter, Abbas S Tavakoli, Jean B r Craig, Nicholas D Boltin, Homayoun Valafar, Salvatore Robert DiNardi, and Joan M Culley. Designing and executing a functional exercise to test a novel informatics tool for mass casualty triage. Journal of the American Medical Informatics Association, June 2019. URL: https://doi.org/10.1093/jamia/ocz087 (visited on 2019-07-05), doi:10.1093/jamia/ocz087.
[abstract▼] [BibTeX▼]

The testing of informatics tools designed for use during mass casualty incidents presents a unique problem as there is no readily available population of victims or identical exposure setting. The purpose of this article is to describe the process of designing, planning, and executing a functional exercise to accomplish the research objective of validating an informatics tool specifically designed to identify and triage victims of irritant gas syndrome agents.During a 3-year time frame, the research team and partners developed the Emergency Department Informatics Computational Tool and planned a functional exercise to test it using medical records data from 298 patients seen in 1 emergency department following a chlorine gas exposure in 2005.The research team learned valuable lessons throughout the planning process that will assist future researchers with developing a functional exercise to test informatics tools. Key considerations for a functional exercise include contributors, venue, and information technology needs (ie, hardware, software, and data collection methods).Due to the nature of mass casualty incidents, testing informatics tools and technology for these incidents is challenging. Previous studies have shown a functional exercise as a viable option to test informatics tools developed for use during mass casualty incidents.Utilizing a functional exercise to test new mass casualty management technology and informatics tools involves a painstaking and complex planning process; however, it does allow researchers to address issues inherent in studying informatics tools for mas casualty incidents.
```
@article{donevant_designing_2019,
    author = "Donevant, Sara B and Svendsen, Erik R and Richter, Jane V and Tavakoli, Abbas S and Craig, Jean B r and Boltin, Nicholas D and Valafar, Homayoun and DiNardi, Salvatore Robert and Culley, Joan M",
    title = "Designing and executing a functional exercise to test a novel informatics tool for mass casualty triage",
    issn = "1527-974X",
    url = "https://doi.org/10.1093/jamia/ocz087",
    doi = "10.1093/jamia/ocz087",
    language = "English",
    urldate = "2019-07-05",
    journal = "Journal of the American Medical Informatics Association",
    month = "June",
    year = "2019"
}
```
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, and Anthony Gitter. Open collaborative writing with Manubot. PLOS Computational Biology, 15(6):e1007128, June 2019. URL: https://doi.org/10.1371/journal.pcbi.1007128, doi:10.1371/journal.pcbi.1007128.
[abstract▼] [BibTeX▼]

Author summary Traditionally, scholarly manuscripts have been written in private by a predefined team of collaborators. But now the internet enables realtime open science, where project communication occurs online in a public venue and anyone is able to contribute. Dispersed teams of online contributors require new tools to jointly prepare manuscripts. Existing tools fail to scale beyond tens of authors and struggle to support iterative refinement of proposed changes. Therefore, we created a system called Manubot for writing manuscripts based on collaborative version control. Manubot adopts the workflow from open source software development, which has enabled hundreds of contributors to simultaneously develop complex codebases such as Python and Linux, and applies it to open collaborative writing. Manubot also addresses other shortcomings of current publishing tools. Specifically, all changes to a manuscript are tracked, enabling transparency and better attribution of credit. Manubot automates many tasks, including creating the bibliography and deploying the manuscript as a webpage. Manubot webpages preserve old versions and provide a simple yet interactive interface for reading. As such, Manubot is a suitable foundation for next-generation preprints. Manuscript readers have ample opportunity to not only provide public peer review but also to contribute improvements, before and after journal publication.
```
@article{himmelstein_open_2019,
    author = "Himmelstein, Daniel S. and Rubinetti, Vincent and Slochower, David R. and Hu, Dongbo and Malladi, Venkat S. and Greene, Casey S. and Gitter, Anthony",
    title = "Open collaborative writing with {Manubot}",
    volume = "15",
    url = "https://doi.org/10.1371/journal.pcbi.1007128",
    doi = "10.1371/journal.pcbi.1007128",
    number = "6",
    journal = "PLOS Computational Biology",
    month = "June",
    year = "2019",
    pages = "e1007128"
}
```
Andy Jackson. A New Release of Heritrix 3. 2019. URL: https://netpreserveblog.wordpress.com/2019/02/19/a-new-release-of-heritrix-3/ (visited on 2019-06-29).
[abstract▼] [BibTeX▼]

By Andy Jackson, Web Archiving Technical Lead at the British Library One of the outcomes of the Online Hours meetings has been an increase in activity around Heritrix 3. Most of us rely on Heritrix…
```
@misc{jackson_new_2019,
    author = "Jackson, Andy",
    title = "A {New} {Release} of {Heritrix} 3",
    url = "https://netpreserveblog.wordpress.com/2019/02/19/a-new-release-of-heritrix-3/",
    language = "en",
    urldate = "2019-06-29",
    year = "2019"
}
```
Jörg Rapp, Melanie Platz, and Engelbert Niehaus. One Health and Space Technology—Application of Open Community Approach. In Annette Froehlich, editor, Embedding Space in African Society: The United Nations Sustainable Development Goals 2030 Supported by Space Applications, Southern Space Studies, pages 237–253. Springer International Publishing, Cham, 2019. URL: https://doi.org/10.1007/978-3-030-06040-4_14 (visited on 2019-07-17), doi:10.1007/978-3-030-06040-4_14.
[abstract▼] [BibTeX▼]

"‘One Health’ is an approach to designing and implementing programmes, policies, legislation and research in which multiple sectors communicate and work together to achieve better public health outcomes." (World Health Organization (2017). One Health, http://www.who.int/features/qa/one-health/en/, retreived 17 July 2018). One health and space technology are linked in terms of satellite navigation, remote sensing and satellite communication. Global navigation systems allow users to detect their current geolocation. The geolocation can be used to provide tailored information to the user via mobile devices. Satellite communication can be used among others for tele-health applications and health service delivery in remote areas. Open Educational Resources (OER) and educational justice contribute to capacity building. These OER can be tailored to the current geolocation of a user and to the profile of e.g. staff members and health services providers, especially in rural areas.
```
@incollection{rapp_one_2019,
    author = "Rapp, Jörg and Platz, Melanie and Niehaus, Engelbert",
    editor = "Froehlich, Annette",
    address = "Cham",
    series = "Southern {Space} {Studies}",
    title = "One {Health} and {Space} {Technology}—{Application} of {Open} {Community} {Approach}",
    isbn = "978-3-030-06040-4",
    url = "https://doi.org/10.1007/978-3-030-06040-4\_14",
    language = "en",
    urldate = "2019-07-17",
    booktitle = "Embedding {Space} in {African} {Society}: {The} {United} {Nations} {Sustainable} {Development} {Goals} 2030 {Supported} by {Space} {Applications}",
    publisher = "Springer International Publishing",
    year = "2019",
    doi = "10.1007/978-3-030-06040-4\_14",
    pages = "237--253"
}
```
Tsung-Wei Huang, Chun-Xun Lin, Guannan Guo, and Martin D. F. Wong. INVITED: Essential Building Blocks for Creating an Open-sourceEDA Project. 2019. URL: https://tsung-wei-huang.github.io/papers/dac19-invited.pdf (visited on 2019-07-17).
[abstract▼] [BibTeX▼]

Open source has started energizing both industrial and academicresearch and development in electronic design automation (EDA)systems. By moving to open source, we can speed up our effortand work with others who are working toward the same goals,while reducing costs and improving end products. However, build-ing an open-source project is much more than placing the code-base on the web. In this paper, we will talk about essential buildingblocks to create an impactful open-source project, including sourcerepository, project landing page, documentation, and continuousintegration. We will also cover the use of web-based frameworksto design a showcase project to bring community’s attention. Wewill then share our experience in developing an open-sourcetim-ing analyzer (OpenTimer) and a parallel task programming library(Cpp-Taskflow), both of which are being used in many industrialand academic EDA research projects.
```
@misc{tsung-wei_huang_invited:_2019,
    author = "{Tsung-Wei Huang} and {Chun-Xun Lin} and {Guannan Guo} and {Martin D. F. Wong}",
    title = "{INVITED}: {Essential} {Building} {Blocks} for {Creating} an {Open}-{sourceEDA} {Project}",
    url = "https://tsung-wei-huang.github.io/papers/dac19-invited.pdf",
    urldate = "2019-07-17",
    year = "2019"
}
```
Richard Glassey. Adopting Git/Github Within Teaching: A Survey of Tool Support. In Proceedings of the ACM Conference on Global Computing Education, CompEd '19, 143–149. New York, NY, USA, 2019. ACM. URL: http://doi.acm.org/10.1145/3300115.3309518 (visited on 2019-07-17), doi:10.1145/3300115.3309518.
[abstract▼] [BibTeX▼]

The adoption and use of Git and Github within computer science education is growing in popularity. The motivation for this shift is strong: it combines a robust system for managing student coursework, sophisticated collaboration and communication tools for students and teaching staff, and an authentic experience of an important software engineering skill. Whilst previous literature has reported upon experience and benefits, there still exists a technical barrier to overcome in adopting Git and Github within an educational context. In response, both the community of teachers using Git/Github and the Github organisation itself have developed tool support to help solve the challenge of adoption, however these efforts are somewhat isolated and relatively unstudied. This work aims to provide an overview of these tools, identify the commonalities and differences, and develop a framework for comparison to assist teachers when looking for solutions for their own courses.
```
@inproceedings{glassey_adopting_2019,
    author = "Glassey, Richard",
    address = "New York, NY, USA",
    series = "{CompEd} '19",
    title = "Adopting {Git}/{Github} {Within} {Teaching}: {A} {Survey} of {Tool} {Support}",
    isbn = "978-1-4503-6259-7",
    url = "http://doi.acm.org/10.1145/3300115.3309518",
    doi = "10.1145/3300115.3309518",
    language = "en",
    urldate = "2019-07-17",
    booktitle = "Proceedings of the {ACM} {Conference} on {Global} {Computing} {Education}",
    publisher = "ACM",
    year = "2019",
    pages = "143--149"
}
```
Jeffrey Perkel. Resources to accompany Nature Toolbox article on Science on GitHub: jperkel/Science-on-GitHub. May 2019. URL: https://github.com/jperkel/Science-on-GitHub (visited on 2019-07-17).
[abstract▼] [BibTeX▼]

Science on GitHub As an accompaniment to Jeffrey Perkel's article for Nature on researchers using GitHub to store data, we have compiled this list of projects as a table of comma-separated values (a CSV file). To view the file, just click the link ("Science on GitHub.csv). Feel free to suggest others via the issues tab at the top of the page. Or, to suggest changes directly in GitHub, click file, then click the pencil icon in the toolbar at the upper right. When you're done, click "commit changes" at the bottom of the page. To get a sense of how GitHub tracks changes, click the file "README.md", and click the History button in the toolbar. Each line represents a single change to that file. If you click the specific commit identifier at the right of a given line (eg: 7135e43), you can view exactly what that change entailed. Lines highlighted in green are additions, while lines in red have been deleted.
```
@misc{perkel_resources_2019,
    author = "Perkel, Jeffrey",
    title = "Resources to accompany {Nature} {Toolbox} article on {Science} on {GitHub}: jperkel/{Science}-on-{GitHub}",
    copyright = "CC0-1.0",
    url = "https://github.com/jperkel/Science-on-GitHub",
    urldate = "2019-07-17",
    month = "May",
    year = "2019"
}
```
Xiaoju (Julie) Chen, Matthew R. Marsteller, Sarah Young, and Jessica Benner. Understanding the Research Practices and Service Needs of Civil and Environmental Engineering Researchers – a Grounded Theory Approach. In Making an Impact: Building Support with Data and Design, 16. Tampa, FL, June 2019. URL: https://www.asee.org/public/conferences/140/papers/26350/view.
[abstract▼] [BibTeX▼]

Background Researchers from different disciplines have different behaviors and needs during the life cycle of their research. Understanding the behavior and needs related to a suite of research-related activities can help librarians develop a deeper knowledge about the subject fields in which their users are involved. It is important for subject librarians and information specialists to understand the research life cycle within the disciplines. Purpose In this study, we aim to understand the research practices and needs of Civil and Environmental Engineering (CEE) scholars. The research questions driving this project are "What are the research supports needed by CEE researchers during the whole research lifecycle?" and "What can academic libraries do to improve services to meet these needs?" Method We used qualitative research methods with a grounded theory guided approach to address the problem. We recruited representative CEE researchers in our institution aiming to balance gender and years of experience in our sample. We ultimately interviewed nine out of 27 possible researchers. Recruited researchers participated in a 60-minute interview. The semi-structured interview protocol was designed by Ithaka S+R, a research institution with which we collaborated for this study. After transcribing the interviews, we conducted two rounds of analysis. First, each team member coded all interviews and generated open codes. Next, we discussed our codes and collated them into a set of four themes. Each team member then coded each interview for one of the four themes. After the two rounds of coding, we summarized the results and provided recommendations accordingly.
```
@inproceedings{chen_understanding_2019,
    author = "Chen, Xiaoju (Julie) and Marsteller, Matthew R. and Young, Sarah and Benner, Jessica",
    address = "Tampa, FL",
    title = "Understanding the {Research} {Practices} and {Service} {Needs} of {Civil} and {Environmental} {Engineering} {Researchers} – a {Grounded} {Theory} {Approach}",
    url = "https://www.asee.org/public/conferences/140/papers/26350/view",
    language = "en",
    booktitle = "Making an {Impact}: {Building} {Support} with {Data} and {Design}",
    month = "June",
    year = "2019",
    pages = "16"
}
```
Egon Willighagen, Nina Jeliazkova, and Rajarshi Guha. Journal of Cheminformatics, ORCID, and GitHub. Journal of Cheminformatics, 11(1):44, July 2019. URL: https://doi.org/10.1186/s13321-019-0365-4 (visited on 2019-07-15), doi:10.1186/s13321-019-0365-4.
[abstract▼] [BibTeX▼]

Two years ago, Rajarshi Guha and Egon Willighagen took over the Editor-in-Chief roles for the Journal of Cheminformatics from Christoph Steinbeck and David Wild [1]. This year our journal reached the age of 10: on 17 March 2009, Wild welcomed us to a new journal for cheminformatics [2], a 100\% open access journal, which was still very new for chemistry at the time. In those 10 years, the journal published 939 papers, of which 286 are research papers and 110 are software papers. To help us with the handling of all submissions, we were joined by Nina Jeliazkova as our first Associate Editor in 2018. When Guha and Willighagen took over, they set out to further the field in its transition to Open Science [1]. The first thing we did was to start a Twitter account, where we have since been tweeting the articles, as an alternative to the RSS feed of new articles. The Twitter account currently has more than 700 followers. The second thing we did was start encouraging more authors to provide their ORCID identifiers [3]. We started requesting the corresponding author to provide their ORCID identifier and we updated our Editorial Board page with ORCID identifiers for our board members (https://jcheminf.biomedcentral.com/about/editorial-board).
```
@article{willighagen_journal_2019,
    author = "Willighagen, Egon and Jeliazkova, Nina and Guha, Rajarshi",
    title = "Journal of {Cheminformatics}, {ORCID}, and {GitHub}",
    volume = "11",
    issn = "1758-2946",
    url = "https://doi.org/10.1186/s13321-019-0365-4",
    doi = "10.1186/s13321-019-0365-4",
    number = "1",
    urldate = "2019-07-15",
    journal = "Journal of Cheminformatics",
    month = "July",
    year = "2019",
    pages = "44"
}
```
Simon Larsén and Richard Glassey. RepoBee: Developing Tool Support for Courses Using Git/GitHub. In Proceedings of the 2019 ACM Conference on Innovation and Technology in Computer Science Education, ITiCSE '19, 534–540. Aberdeen, Scotland Uk, July 2019. ACM. URL: http://doi.acm.org/10.1145/3304221.3319784 (visited on 2019-07-15), doi:10.1145/3304221.3319784.
[abstract▼] [BibTeX▼]

The use of version control systems within computing education is growing in popularity. However, this is challenging because such systems are not particularly well designed to support educational situations, nor are they easy to use with confidence in teaching, as specialist knowledge and experience is required. This experience paper reports the development of the open source tool RepoBee, which assists in the use of Git/GitHub in an educational context. The tool provides a straightforward interface for managing batch tasks such as repository generation and cloning for setting and gathering assignments, opening and closing of issues to communicate with students, as well as facilitating peer reviews. Parts of RepoBee are open to integration with third party tools for additional tasks, such as running unit tests or static analysis on student repositories. We also include the perspectives of both teachers and teaching assistants who have been using the tool as part of a first year course for computer scientists.
```
@inproceedings{larsen_repobee:_2019,
    author = "Larsén, Simon and Glassey, Richard",
    address = "Aberdeen, Scotland Uk",
    series = "{ITiCSE} '19",
    title = "{RepoBee}: {Developing} {Tool} {Support} for {Courses} {Using} {Git}/{GitHub}",
    isbn = "978-1-4503-6301-3",
    url = "http://doi.acm.org/10.1145/3304221.3319784",
    doi = "10.1145/3304221.3319784",
    language = "English",
    urldate = "2019-07-15",
    booktitle = "Proceedings of the 2019 {ACM} {Conference} on {Innovation} and {Technology} in {Computer} {Science} {Education}",
    publisher = "ACM",
    month = "July",
    year = "2019",
    pages = "534--540"
}
```
Giovanni Colavizza, Iain Hrynaszkiewicz, Isla Staden, Kirstie Whitaker, and Barbara McGillivray. The citation advantage of linking publications to research data. arXiv, July 2019. URL: http://arxiv.org/abs/1907.02565, doi:arXiv:1907.02565v1.
[abstract▼] [BibTeX▼]

Efforts to make research results open and reproducible are increasingly reflected by journal policies encouraging or mandating authors to provide data availability statements. As a consequence of this, there has been a strong uptake of data availability statements in recent literature. Nevertheless, it is still unclear what proportion of these statements actually contain well-formed links to data, for example via a URL or permanent identifier, and if there is an added value in providing them. We consider \$531,889\$ journal articles published by PLOS and BMC which are part of the PubMed Open Access collection, categorize their data availability statements according to their content and analyze the citation advantage of different statement categories via regression. We find that, following mandated publisher policies, data availability statements have become common by now, yet statements containing a link to a repository are still just a fraction of the total. We also find that articles with these statements, in particular, can have up to 25.36\% higher citation impact on average: an encouraging result for all publishers and authors who make the effort of sharing their data. All our data and code are made available in order to reproduce and extend our results.
```
@article{colavizza_citation_2019,
    author = "Colavizza, Giovanni and Hrynaszkiewicz, Iain and Staden, Isla and Whitaker, Kirstie and McGillivray, Barbara",
    title = "The citation advantage of linking publications to research data",
    url = "http://arxiv.org/abs/1907.02565",
    doi = "arXiv:1907.02565v1",
    language = "English",
    journal = "arXiv",
    month = "July",
    year = "2019"
}
```
Courtney Rivard. Turning Archives into Data: Archival Rhetorics and Digital Literacy in the Composition Classroom. College Composition and Communication, June 2019. URL: http://www.ncte.org/library/NCTEFiles/Resources/Journals/CCC/0704-jun2019/CCC0704Jun19Turning.pdf (visited on 2019-07-15).
[abstract▼] [BibTeX▼]

Using assignments drawn from a first-year composition course that centers the Southern Life Histories Collection, part of the New Deal’s Federal Writers’ Project, this paper argues for a pedagogical approach that teaches students digital literacy through archival rhetorics by converting archival texts into data.
```
@article{rivard_turning_2019,
    author = "Rivard, Courtney",
    title = "Turning {Archives} into {Data}: {Archival} {Rhetorics} and {Digital} {Literacy} in the {Composition} {Classroom}",
    volume = "70",
    url = "http://www.ncte.org/library/NCTEFiles/Resources/Journals/CCC/0704-jun2019/CCC0704Jun19Turning.pdf",
    language = "English",
    number = "4",
    urldate = "2019-07-15",
    journal = "College Composition and Communication",
    month = "June",
    year = "2019"
}
```
Charon A. Pierson. Data Ownership and Data Sharing Practices. In Deborah C Poff and Alex C. Michalos, editors, Encyclopedia of Business and Professional Ethics, pages 1–3. Springer International Publishing, Cham, March 2019. URL: https://doi.org/10.1007/978-3-319-23514-1_315-1 (visited on 2019-07-15), doi:10.1007/978-3-319-23514-1_315-1.
[abstract▼] [BibTeX▼]

Research-generated data are generally regarded asintellectual property and entitled to legal protec-tion or copyright; however, ownership of thoserights may be governed by institutional policies.Implicit in the idea of ownership of data is theconcept of stewardship of data, including access,creation, modification, sale, storage, and the abil-ity to assign or license any of these privileges toothers. Open data and open science promote shar-ing research data gathered by scientists to verifyscientificfindings, reduce thefinancial burden ofconducting research, and improve the reproduc-ibility of scientific studies (Editorial2018). It isalso widely held that open data decrease thecost of research by fostering multiple projectsfrom one data source, although there are costsassociated with transforming and maintainingdata in a repository where others can have access.In contrast, funding agencies that review, approve,and fund competing research grants can claimownership of the data generated by a researcher;this is especially common in pharmaceutical ordevice companies that fund a researcher in aninstitution. The USA and other governments andphilanthropic organizations that fund researchersfor scientific projects usually award the grants toan institution and not an individual, thus makingthe institution the owner of the data and furthercomplicating the issues. Data ownership policiesand guarantees of data integrity are necessary forproper allocation of rights and privileges andfor data sharing to be of any benefit. The FAIRData Principles (Wilkinson et al.2016) are aguide to maximizing the value of shared data bymaking itFindable,Accessible,Interoperable, andReusable.
```
@incollection{pierson_data_2019,
    author = "Pierson, Charon A.",
    editor = "Poff, Deborah C and Michalos, Alex C.",
    address = "Cham",
    title = "Data {Ownership} and {Data} {Sharing} {Practices}",
    isbn = "978-3-319-23514-1",
    url = "https://doi.org/10.1007/978-3-319-23514-1\_315-1",
    language = "English",
    urldate = "2019-07-15",
    booktitle = "Encyclopedia of {Business} and {Professional} {Ethics}",
    publisher = "Springer International Publishing",
    month = "March",
    year = "2019",
    doi = "10.1007/978-3-319-23514-1\_315-1",
    pages = "1--3"
}
```

Jessica Meyerson. Episode 4: Software in Digital/Scholarly Communications – Saving Software Together. May 2019. URL: https://www.softwarepreservationnetwork.org/blog/spn-webinar-2018-ep4/ (visited on 2019-07-15).
[BibTeX▼]

@misc{jessica_meyerson_episode_2019,
    author = "{Jessica Meyerson}",
    title = "Episode 4: {Software} in {Digital}/{Scholarly} {Communications} – {Saving} {Software} {Together}",
    url = "https://www.softwarepreservationnetwork.org/blog/spn-webinar-2018-ep4/",
    language = "en-US",
    urldate = "2019-07-15",
    collaborator = "{James Howison} and {Veronica Ikeshoji-Orlati} and {Neil Chue Hong}",
    month = "May",
    year = "2019"
}

TIND. TIND Preservation White Paper. 2019. URL: https://info.tind.io/preservation-white-paper (visited on 2019-07-15).
[BibTeX▼]

@misc{tind_tind_2019,
    author = "TIND",
    title = "{TIND} {Preservation} {White} {Paper}",
    url = "https://info.tind.io/preservation-white-paper",
    language = "en",
    urldate = "2019-07-15",
    year = "2019"
}

Stephan Druskat. Citation File Format (CFF). 2019. URL: https://citation-file-format.github.io/ (visited on 2019-07-15).
[abstract▼] [BibTeX▼]

Landing page for the Citation File Format (CFF), a YAML 1.2-based format for providing citation metadata for (research/scientific) software.
```
@misc{druskat_citation_2019,
    author = "Druskat, Stephan",
    title = "Citation {File} {Format} ({CFF})",
    url = "https://citation-file-format.github.io/",
    language = "en",
    urldate = "2019-07-15",
    journal = "Citation File Format (CFF)",
    year = "2019"
}
```

OAP. How to make your own work open access - Harvard Open Access Project. June 2019. URL: https://cyber.harvard.edu/hoap/How_to_make_your_own_work_open_access#Deposit_in_an_OA_repository_.28.22green.22_OA.29 (visited on 2019-07-14).
[BibTeX▼]

@misc{noauthor_how_2019,
    author = "OAP",
    title = "How to make your own work open access - {Harvard} {Open} {Access} {Project}",
    url = "https://cyber.harvard.edu/hoap/How\_to\_make\_your\_own\_work\_open\_access\#Deposit\_in\_an\_OA\_repository\_.28.22green.22\_OA.29",
    urldate = "2019-07-14",
    month = "June",
    year = "2019"
}

Samvera. Samvera - an open source repository solution for digital content. 2019. URL: https://samvera.org/ (visited on 2019-07-09).
[abstract▼] [BibTeX▼]

Samvera is a versatile and feature rich repository solution that is being used by institutions worldwide to provide access to their digital content.
```
@misc{samvera_samvera_2019,
    author = "{Samvera}",
    title = "Samvera - an open source repository solution for digital content",
    url = "https://samvera.org/",
    language = "en-US",
    urldate = "2019-07-09",
    journal = "Samvera",
    year = "2019"
}
```
Huaimin Wang, Gang Yin, Tao Wang, and Yue Yu. Crowd-Based Methodology of Software Development in the Internet Era. In Brian Fitzgerald, Audris Mockus, and Minghui Zhou, editors, Towards Engineering Free/Libre Open Source Software (FLOSS) Ecosystems for Impact and Sustainability: Communications of NII Shonan Meetings, pages 135–156. Springer Singapore, Singapore, July 2019. URL: https://doi.org/10.1007/978-981-13-7099-1_9, doi:10.1007/978-981-13-7099-1_9.
[abstract▼] [BibTeX▼]

In today’s Internet era, software has infiltrated all aspects of people’s lives, the trend of software-defined everything is essentially unstoppable. The classical methodologies in software engineering are expected to produce software at a low cost and with strong functionality by guiding the development process using industrialization methods and principles. However, as the complexity of software application scenarios and operating environments continues to increase, especially in the Internet era, prominent bottlenecks remain in improving the efficiency and quality of software development. Compared to the engineering methods, open source can attract tens of thousands of contributors to participate in the software creation process. This methodology is more deferential to each developer’s individuality and aims to create a liberal, diverse, and democratic environment, thus stimulating the enthusiasm and creative inspiration of contributors on a large scale and ultimately generating greater collective wisdom. But the challenges in the diversification of individual interest concerns, the unevenness of contribution capabilities, and the unpredictable results of group collaboration make it unable to fully fulfill the tasks of clear and organized software manufacturing. In this chapter, we propose a crowd-based methodology that integrates the software creation process into the software manufacturing process, link a small-scale but well-organized core team with self-organized but large-scale crowd contributors, and transform a software opus to products in a timely fashion. Based on the crowd-based methodology, we design and implement the TRUSTIE environment to support the construction of software ecosystem. We illustrate the framework and key technologies and present typical application practices in both proprietary companies and online communities.
```
@incollection{wang_crowd-based_2019,
    author = "Wang, Huaimin and Yin, Gang and Wang, Tao and Yu, Yue",
    editor = "Fitzgerald, Brian and Mockus, Audris and Zhou, Minghui",
    address = "Singapore",
    title = "Crowd-{Based} {Methodology} of {Software} {Development} in the {Internet} {Era}",
    isbn = "978-981-13-7099-1",
    url = "https://doi.org/10.1007/978-981-13-7099-1\_9",
    language = "English",
    booktitle = "Towards {Engineering} {Free}/{Libre} {Open} {Source} {Software} ({FLOSS}) {Ecosystems} for {Impact} and {Sustainability}: {Communications} of {NII} {Shonan} {Meetings}",
    publisher = "Springer Singapore",
    month = "July",
    year = "2019",
    doi = "10.1007/978-981-13-7099-1\_9",
    pages = "135--156"
}
```
Raula Gaikovina Kula and Gregorio Robles. The Life and Death of Software Ecosystems. In Brian Fitzgerald, Audris Mockus, and Minghui Zhou, editors, Towards Engineering Free/Libre Open Source Software (FLOSS) Ecosystems for Impact and Sustainability: Communications of NII Shonan Meetings, pages 97–105. Springer Singapore, Singapore, 2019. URL: https://doi.org/10.1007/978-981-13-7099-1_6, doi:10.1007/978-981-13-7099-1_6.
[abstract▼] [BibTeX▼]

Software ecosystems have gained a lot of attention in recent times. Industry and developers gather around technologies and collaborate to their advancement; when the boundaries of such an effort go beyond certain amount of projects, we are witnessing the appearance of Free/Libre and Open Source Software (FLOSS) ecosystems. In this chapter, we explore two aspects that contribute to a healthy ecosystem, related to the attraction (and detraction) and the death of ecosystems. To function and survive, ecosystems need to attract people, get them onboarded, and retain them. In Section One, we explore possibilities with provocative research questions for attracting and detracting contributors (and users): the lifeblood of FLOSS ecosystems. Then, in the Section Two, we focus on the death of systems, exploring some presumed to be dead systems and their state in the afterlife.
```
@incollection{kula_life_2019,
    author = "Kula, Raula Gaikovina and Robles, Gregorio",
    editor = "Fitzgerald, Brian and Mockus, Audris and Zhou, Minghui",
    address = "Singapore",
    title = "The {Life} and {Death} of {Software} {Ecosystems}",
    isbn = "978-981-13-7099-1",
    url = "https://doi.org/10.1007/978-981-13-7099-1\_6",
    booktitle = "Towards {Engineering} {Free}/{Libre} {Open} {Source} {Software} ({FLOSS}) {Ecosystems} for {Impact} and {Sustainability}: {Communications} of {NII} {Shonan} {Meetings}",
    publisher = "Springer Singapore",
    year = "2019",
    doi = "10.1007/978-981-13-7099-1\_6",
    pages = "97--105"
}
```
Claudia Hilderbrand, Christopher Perdriau, Lara Letaw, Jillian Emard, Zoe Steine-Hanson, Margaret Burnett, and Anita Sarma. Engineering Gender-Inclusivity into Software: Tales from the Trenches. arXiv, May 2019. URL: http://arxiv.org/abs/1905.10361 (visited on 2019-07-11).
[abstract▼] [BibTeX▼]

Although the need for gender-inclusivity in software itself is gaining attention among both SE researchers and SE practitioners, and methods have been published to help, little has been reported on how to make such methods work in real-world settings. For example, how do busy software practitioners use such methods in low-cost ways? How do they endeavor to maximize benefits from using them? How do they avoid the controversies that can arise in talking about gender? To find out how teams were handling these and similar questions, we turned to 10 real-world software teams. We present these teams experiences "in the trenches," in the form of 12 practices and 3 potential pitfalls, so as to provide their insights to other real-world software teams trying to engineer gender-inclusivity into their software products.
```
@article{hilderbrand_engineering_2019,
    author = "Hilderbrand, Claudia and Perdriau, Christopher and Letaw, Lara and Emard, Jillian and Steine-Hanson, Zoe and Burnett, Margaret and Sarma, Anita",
    title = "Engineering {Gender}-{Inclusivity} into {Software}: {Tales} from the {Trenches}",
    url = "http://arxiv.org/abs/1905.10361",
    language = "English",
    urldate = "2019-07-11",
    journal = "arXiv",
    month = "May",
    year = "2019"
}
```
Xiangyang Liu, Haixia Hu, Juan Bao, and Juan Bao. Research on the Strategy of Constructing Ecological Classroom of Basic Computer Education in Medical Colleges. In 2019 4th International Conference on Humanities Science and Society Development (ICHSSD 2019). Xiamen, China, July 2019. Atlantis Press. URL: https://www.atlantis-press.com/article/125911638.
[abstract▼] [BibTeX▼]

With the continuous integration of new technologies in the medical field, the computer literacy of medical posts puts forward higher requirements. Practical research at home and abroad shows that the theory of ecological classroom has a significant effect on improving the teaching of courses. The research analyses the ecological imbalance of basic education of computer public courses from the aspects of classroom teaching environment, classroom teaching subject, teaching objectives and teaching methods. Through designing teaching research experiments to verify the teaching effect, this paper expounds the effective way to construct the basic ecological classroom of computer. The research can be used for reference in the teaching reform of computer basic education.
```
@inproceedings{xiangyang_liu_research_2019,
    author = "{Xiangyang Liu} and {Haixia Hu} and {Juan Bao} and {Juan Bao}",
    address = "Xiamen, China",
    title = "Research on the {Strategy} of {Constructing} {Ecological} {Classroom} of {Basic} {Computer} {Education} in {Medical} {Colleges}",
    url = "https://www.atlantis-press.com/article/125911638",
    booktitle = "2019 4th {International} {Conference} on {Humanities} {Science} and {Society} {Development} ({ICHSSD} 2019)",
    publisher = "Atlantis Press",
    month = "July",
    year = "2019"
}
```

Žiga Avsec, Roman Kreuzhuber, Johnny Israeli, Nancy Xu, Jun Cheng, Avanti Shrikumar, Abhimanyu Banerjee, Daniel S. Kim, Thorsten Beier, Lara Urban, Anshul Kundaje, Oliver Stegle, and Julien Gagneur. The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nature Biotechnology, 37(6):592–600, June 2019. URL: https://doi.org/10.1038/s41587-019-0140-0, doi:10.1038/s41587-019-0140-0.
[BibTeX▼]

@article{avsec_kipoi_2019,
    author = "Avsec, Žiga and Kreuzhuber, Roman and Israeli, Johnny and Xu, Nancy and Cheng, Jun and Shrikumar, Avanti and Banerjee, Abhimanyu and Kim, Daniel S. and Beier, Thorsten and Urban, Lara and Kundaje, Anshul and Stegle, Oliver and Gagneur, Julien",
    title = "The {Kipoi} repository accelerates community exchange and reuse of predictive models for genomics",
    volume = "37",
    issn = "1546-1696",
    url = "https://doi.org/10.1038/s41587-019-0140-0",
    doi = "10.1038/s41587-019-0140-0",
    language = "English",
    number = "6",
    journal = "Nature Biotechnology",
    month = "June",
    year = "2019",
    pages = "592--600"
}

Margaret Heller. Community technology projects: making them work. ALA Editions, Chicago, IL, 2019. ISBN 978-0-8389-1837-1.
[abstract▼] [BibTeX▼]

"This book is a guide for people who want to get started with community technology projects, understand what their options are, learn how to find and create communities, and decide which skills to learn. For those who are already engaged with communities, it will be a guide to creating a welcoming community for new people and maintaining a motivated community in challenging times. I want everyone to be inspired to make better library technology communities"--
```
@book{heller_community_2019,
    author = "Heller, Margaret",
    address = "Chicago, IL",
    title = "Community technology projects: making them work",
    isbn = "978-0-8389-1837-1",
    language = "English",
    publisher = "ALA Editions",
    year = "2019"
}
```
William B. Langdon, Zhen Yu Ding, Shin Hwei Tan, Westly Weimer, Yiwei Lyu, Kevin Leach, Christopher Timperley, Nicolas Chausseau, Yu Huang, Oliver Krauss, Eric Schulte, and Gabin An. Research Note: The State and Future of Genetic Improvement. In Genetic Improvement workshop,GI-2019 @ ICSE,, 8. UCL Department of Computer Science, June 2019. URL: http://www-dept.cs.ucl.ac.uk/staff/w.langdon/ftp/public/public/papers/gi2019_discussion.pdf (visited on 2019-07-10).
[abstract▼] [BibTeX▼]

We report the discussion session at the sixth international Genetic Improvement workshop,GI-2019 @ ICSE, which was held as part of the41stACM/IEEE International Conference onSoftware Engineering on Tuesday 28thMay 2019. Topics included GI representations, themaintainability of evolved code, automated software testing, future areas of GI research, suchas co-evolution, and existing GI tools and benchmarks.
```
@inproceedings{langdon_research_2019,
    author = "Langdon, William B. and Ding, Zhen Yu and Tan, Shin Hwei and Weimer, Westly and Lyu, Yiwei and Leach, Kevin and Timperley, Christopher and Chausseau, Nicolas and Huang, Yu and Krauss, Oliver and Schulte, Eric and An, Gabin",
    title = "Research {Note}: {The} {State} and {Future} of {Genetic} {Improvement}",
    url = "http://www-dept.cs.ucl.ac.uk/staff/w.langdon/ftp/public/public/papers/gi2019\_discussion.pdf",
    language = "English",
    urldate = "2019-07-10",
    booktitle = "Genetic {Improvement} workshop,{GI}-2019 @ {ICSE},",
    publisher = "UCL Department of Computer Science",
    month = "June",
    year = "2019",
    pages = "8"
}
```

Kees Teszelsky. Web Archiving Down Under: Relaunch of the Web Curator Tool at the IIPC conference, Wellington, New Zealand - Open Preservation Foundation. 2019. URL: https://openpreservation.org/blog/2018/12/20/wctrelaunch/ (visited on 2019-04-19).
[BibTeX▼]

@misc{teszelsky_web_nodate,
    author = "Teszelsky, Kees",
    title = "Web {Archiving} {Down} {Under}: {Relaunch} of the {Web} {Curator} {Tool} at the {IIPC} conference, {Wellington}, {New} {Zealand} - {Open} {Preservation} {Foundation}",
    url = "https://openpreservation.org/blog/2018/12/20/wctrelaunch/",
    urldate = "2019-04-19",
    year = "2019"
}

Software Heritage. You can “save code now”! 2019. URL: https://www.softwareheritage.org/2019/01/10/save_code_now/ (visited on 2019-04-21).
[abstract▼] [BibTeX▼]

Software Heritage is now open for your source code submissions! Search engines use something called a Web crawler to systematically “crawl,” or look through, the Web in order to create indexes that can be searched through. In order to populate the Software Heritage Archive we also use a crawler, but unfortunately, unlike for usual […]
```
@misc{software_heritage_you_2019,
    author = "{Software Heritage}",
    title = "You can “save code now”!",
    url = "https://www.softwareheritage.org/2019/01/10/save\_code\_now/",
    language = "en-US",
    urldate = "2019-04-21",
    year = "2019"
}
```
Niels Ole1 Finnemann. Web Archive. Knowledge Organization, 46(1):47–70, 2019. URL: https://www.nomos-elibrary.de/10.5771/0943-7444-2019-1-47/web-archive-volume-46-2019-issue-1 (visited on 2019-04-15), doi:10.5771/0943-7444-2019-1-47.
[abstract▼] [BibTeX▼]

This article deals with the function of general web archives within the emerging organization of fastgrowing digital knowledge resources. It opens with a brief overview of reasons why general web archives are needed. Sections two and three present major, long term web archive initiatives and discuss the purposes and possible functions and unknown future needs, demands and concerns. Section four analyses three main principles for the selection of materials to be preserved in contemporary web archiving strategies, topic-centric, domain-centric and time-centric archiving strategies and how to combine these to provide a broad and rich archive. Section five is concerned with inherent limitations and why web archives are always flawed. The last section deals with the question whether and how web archives may be considered a new type of knowledge organization system (KOS) necessary to preserve web materials, to allow for the development of a range of new methodologies, to analyze these particular corpora in long term and long tail perspectives, and to build a bridge towards the rapidly expanding but fragmented landscape of digital archives, libraries, research infrastructures and other sorts of digital repositories.
```
@article{finnemann_web_2019,
    author = "Finnemann, Niels Ole1",
    title = "Web {Archive}",
    volume = "46",
    issn = "09437444",
    url = "https://www.nomos-elibrary.de/10.5771/0943-7444-2019-1-47/web-archive-volume-46-2019-issue-1",
    doi = "10.5771/0943-7444-2019-1-47",
    number = "1",
    urldate = "2019-04-15",
    journal = "Knowledge Organization",
    year = "2019",
    pages = "47--70"
}
```
Apache Foundation. The Apache® Software Foundation Expands Infrastructure with GitHub Integration. April 2019. URL: https://blogs.apache.org/foundation/entry/the-apache-software-foundation-expands (visited on 2019-04-29).
[abstract▼] [BibTeX▼]

Wakefield, MA —29 April 2019— The Apache® Software Foundation (ASF), the all-volunteer developers, stewards, and incubators of more than 350 Open Source projects and initiatives, announced today it has completed its Infrastructure support expansion by migrating its Git service to GitHub.
```
@misc{noauthor_apache_2019-1,
    author = "Foundation, Apache",
    type = "Blog",
    title = "The {Apache}® {Software} {Foundation} {Expands} {Infrastructure} with {GitHub} {Integration}",
    url = "https://blogs.apache.org/foundation/entry/the-apache-software-foundation-expands",
    language = "English",
    urldate = "2019-04-29",
    journal = "The Apache Software Foundation Blog",
    month = "April",
    year = "2019"
}
```

Julie Meloni. A Gentle Introduction to Version Control. March 2019. URL: https://www.chronicle.com/blogs/profhacker/a-gentle-introduction-to-version-control/23064 (visited on 2018-04-25).
[BibTeX▼]

@misc{meloni_gentle_2019,
    author = "Meloni, Julie",
    type = "News",
    title = "A {Gentle} {Introduction} to {Version} {Control}",
    url = "https://www.chronicle.com/blogs/profhacker/a-gentle-introduction-to-version-control/23064",
    language = "English",
    urldate = "2018-04-25",
    journal = "ProfHacker: Teaching, tech, and productivity.",
    month = "March",
    year = "2019"
}

Digital Preservation Coalition. Tools - Digital Preservation Handbook. 2019. URL: https://dpconline.org/handbook/technical-solutions-and-tools/tools (visited on 2019-03-26).
[BibTeX▼]

@misc{digital_preservation_coalition_tools_nodate,
    author = "{Digital Preservation Coalition}",
    title = "Tools - {Digital} {Preservation} {Handbook}",
    url = "https://dpconline.org/handbook/technical-solutions-and-tools/tools",
    urldate = "2019-03-26",
    year = "2019"
}

Rockefeller Archive Center. The Rockefeller Archive Center - Digital Preservation Policy. 2019. URL: https://rockarch.org/programs/digital/DigPresPolicy.php (visited on 2019-04-01).
[BibTeX▼]

@misc{rockefeller_archive_center_rockefeller_nodate,
    author = "{Rockefeller Archive Center}",
    title = "The {Rockefeller} {Archive} {Center} - {Digital} {Preservation} {Policy}",
    url = "https://rockarch.org/programs/digital/DigPresPolicy.php",
    urldate = "2019-04-01",
    year = "2019"
}

Institut national de recherche en informatique et en automatique. Paris Call: Software Source Code as Heritage for Sustainable Development. 2019. URL: https://unesdoc.unesco.org/ark:/48223/pf0000366715.locale=fr (visited on 2019-04-04).
[BibTeX▼]

@misc{institut_national_de_recherche_en_informatique_et_en_automatique_paris_2019,
    author = "{Institut national de recherche en informatique et en automatique}",
    title = "Paris {Call}: {Software} {Source} {Code} as {Heritage} for {Sustainable} {Development}",
    url = "https://unesdoc.unesco.org/ark:/48223/pf0000366715.locale=fr",
    language = "eng",
    urldate = "2019-04-04",
    publisher = "UNESCO",
    year = "2019"
}

Alex Thurman. List of Web archiving initiatives. 2019. URL: https://en.wikipedia.org/w/index.php?title=List_of_Web_archiving_initiatives&oldid=892173167 (visited on 2019-05-05).
[abstract▼] [BibTeX▼]

This page contains a list of Web archiving initiatives worldwide. For easier reading, the information is divided in three tables: web archiving initiatives, archived data, and access methods. This Wikipedia page was originally generated from the results obtained for the research paper A survey on web archiving initiatives published by the Arquivo.pt (the Portuguese web-archive) team.
```
@misc{thurman_list_2019,
    author = "Thurman, Alex",
    title = "List of {Web} archiving initiatives",
    copyright = "Creative Commons Attribution-ShareAlike License",
    url = "https://en.wikipedia.org/w/index.php?title=List\_of\_Web\_archiving\_initiatives\&oldid=892173167",
    language = "en",
    urldate = "2019-05-05",
    journal = "Wikipedia",
    year = "2019"
}
```

Abbie Grotke. FEATURE: Web Archiving at the Library of Congress. 2019. URL: http://www.infotoday.com/cilmag/dec11/Grotke.shtml (visited on 2019-05-17).
[BibTeX▼]

@misc{grotke_feature:_nodate,
    author = "Grotke, Abbie",
    title = "{FEATURE}: {Web} {Archiving} at the {Library} of {Congress}",
    url = "http://www.infotoday.com/cilmag/dec11/Grotke.shtml",
    urldate = "2019-05-17",
    year = "2019"
}

Cathy Outten. Research Guides: Scholarly Communication: Institutional Repositories. 2019. URL: https://csulb.libguides.com/c.php?g=39245&p=250108.
[abstract▼] [BibTeX▼]

@misc{outten_research_nodate,
    author = "Outten, Cathy",
    title = "Research {Guides}: {Scholarly} {Communication}: {Institutional} {Repositories}",
    copyright = "Copyright California State University, Long Beach 2019",
    url = "https://csulb.libguides.com/c.php?g=39245\&p=250108",
    language = "en",
    date = "2019-06-13",
    year = "2019"
}

Christine Fruin. LibGuides: Scholarly Communication Toolkit: Repositories. 2019. URL: //acrl.libguides.com/scholcomm/toolkit/repositories (visited on 2019-06-13).
[abstract▼] [BibTeX▼]

@misc{fruin_libguides:_nodate,
    author = "Fruin, Christine",
    title = "{LibGuides}: {Scholarly} {Communication} {Toolkit}: {Repositories}",
    copyright = "Copyright ACRL 2019",
    url = "//acrl.libguides.com/scholcomm/toolkit/repositories",
    language = "en",
    urldate = "2019-06-13",
    year = "2019"
}

Fábio Perez, Sandra Avila, and Eduardo Valle. Solo or Ensemble?Choosing a CNN Architecture for Melanoma Classification. arXiv, April 2019. URL: https://arxiv.org/pdf/1904.12724.pdf.
[abstract▼] [BibTeX▼]

Convolutional neural networks (CNNs) deliver excep-tional results for computer vision, including medical imageanalysis. With the growing number of available architec-tures, picking one over another is far from obvious. Ex-isting art suggests that, when performing transfer learn-ing, the performance of CNN architectures on ImageNetcorrelates strongly with their performance on target tasks.We evaluate that claim for melanoma classification, over 9CNNs architectures, in 5 sets of splits created on the ISICChallenge 2017 dataset, and 3 repeated measures, result-ing in 135 models. The correlations we found were, tobegin with, much smaller than those reported by existingart, and disappeared altogether when we considered onlythe top-performing networks: uncontrolled nuisances (i.e.,splits and randomness) overcome any of the analyzed fac-tors. Whenever possible, the best approach for melanomaclassification is still to create ensembles of multiple mod-els. We compared two choices for selecting which models toensemble: picking them at random (among a pool of high-quality ones) vs. using the validation set to determine whichones to pick first. For small ensembles, we found a slightadvantage on the second approach but found that randomchoice was also competitive. Although our aim in this pa-per was not to maximize performance, we easily reachedAUCs comparable to the first place on the ISIC Challenge2017.
```
@article{perez_solo_2019,
    author = "Perez, Fábio and Avila, Sandra and Valle, Eduardo",
    title = "Solo or {Ensemble}?{Choosing} a {CNN} {Architecture} for {Melanoma} {Classification}",
    url = "https://arxiv.org/pdf/1904.12724.pdf",
    language = "English",
    journal = "arXiv",
    month = "April",
    year = "2019"
}
```
Tim Ribaric. Git It Done with GitHub: Digital Scholarship with Open Tools. June 2019. URL: http://hdl.handle.net/10464/14144 (visited on 2019-06-09).
[abstract▼] [BibTeX▼]

Presentation material from Lightning Talk done at Digital Odyssey, 2019. Held in North York Central Library. Event sponsored and organized by Ontario Library and Information Technology (OLITA), a division of Ontario Library Association (OLA)
```
@misc{noauthor_git_2019,
    author = "Ribaric, Tim",
    address = "North York Central Library Ontario, NY",
    title = "Git {It} {Done} with {GitHub}: {Digital} {Scholarship} with {Open} {Tools}",
    url = "http://hdl.handle.net/10464/14144",
    language = "English",
    urldate = "2019-06-09",
    month = "June",
    year = "2019"
}
```
M. Assante, L. Candela, D. Castelli, R. Cirillo, G. Coro, L. Frosini, L. Lelii, F. Mangiacrapa, P. Pagano, G. Panichi, and F. Sinibaldi. Enacting open science by D4science. Future Generation Computer Systems, May 2019. URL: http://www.sciencedirect.com/science/article/pii/S0167739X1831464X, doi:10.1016/j.future.2019.05.063.
[abstract▼] [BibTeX▼]

The open science movement is promising to revolutionise the way science is conducted with the goal to make it more fair, solid and democratic. This revolution is destined to remain just a wish if it is not supported by changes in culture and practices as well as in enabling technologies. This paper describes the D4Science offerings to enact open science-friendly Virtual Research Environments. In particular, the paper describes how complete solutions suitable for realising open science practices can be achieved by integrating a social networking collaborative environment with a shared workspace, an open data analytics platform, and a catalogue enabling to effectively find, access and reuse every research artefact.
```
@article{assante_enacting_2019,
    author = "Assante, M. and Candela, L. and Castelli, D. and Cirillo, R. and Coro, G. and Frosini, L. and Lelii, L. and Mangiacrapa, F. and Pagano, P. and Panichi, G. and Sinibaldi, F.",
    title = "Enacting open science by {D}4Science",
    issn = "0167-739X",
    url = "http://www.sciencedirect.com/science/article/pii/S0167739X1831464X",
    doi = "10.1016/j.future.2019.05.063",
    language = "English",
    journal = "Future Generation Computer Systems",
    month = "May",
    year = "2019"
}
```
E. Teiniker, G. Seuchter, and W. Farrelly. Engaging Part-Time Students in Software Security by Inductive Learning. In 2019 IEEE Global Engineering Education Conference (EDUCON), 491–499. Dubai, United Arab Emirates, April 2019. URL: https://ieeexplore.ieee.org/abstract/document/8725029, doi:10.1109/EDUCON.2019.8725029.
[abstract▼] [BibTeX▼]

Software problems are a considerable challenge in computer security. Implementation bugs and design flaws cause numerous security problems in software driven systems. An effective measure to optimize software security is to improve the education of software engineers. In this paper we present a combination of inductive learning approaches to engage part-time students in software security. We describe which types of examples we used to teach core practices of secure software development and which inductive learning styles fit best into that education concept. These examples combined with a virtual laboratory based on Linux and open source tools have been published on GitHub as an Open Educational Resource (OER).
```
@inproceedings{e._teiniker_engaging_2019,
    author = "{E. Teiniker} and {G. Seuchter} and {W. Farrelly}",
    address = "Dubai, United Arab Emirates",
    title = "Engaging {Part}-{Time} {Students} in {Software} {Security} by {Inductive} {Learning}",
    isbn = "2165-9567",
    url = "https://ieeexplore.ieee.org/abstract/document/8725029",
    doi = "10.1109/EDUCON.2019.8725029",
    language = "English",
    booktitle = "2019 {IEEE} {Global} {Engineering} {Education} {Conference} ({EDUCON})",
    month = "April",
    year = "2019",
    pages = "491--499"
}
```
Heather S. Packer, Adriane Chapman, and Leslie Carr. GitHub2prov: Provenance for Supporting Software Project Management. In 11th International Workshop on Theory and Practice of Provenance (TaPP 2019), 8. Philadelphia, PA, 2019. USENIX Association. URL: https://www.usenix.org/conference/tapp2019/presentation/packer.
[abstract▼] [BibTeX▼]

Software project management is a complex task that requires accurate information and experience to inform the decision-making process. In the real world software project managers rarely have access to perfect nformation. In order to support them, we propose leveraging information from Version Control Systems and their repositories to support decision-making. In this paper, we propose a ROV model GitHub2PROV, which xtends Git2PROV with details about GitHub commits and issues from GitHub repositories. We discuss how this model supports project anagement decisions in agile evelopment, specifically in terms of Control Schedule Reviews and workload.
```
@inproceedings{packer_github2prov:_2019,
    author = "Packer, Heather S. and Chapman, Adriane and Carr, Leslie",
    address = "Philadelphia, PA",
    title = "{GitHub}2PROV: {Provenance} for {Supporting} {Software} {Project} {Management}",
    url = "https://www.usenix.org/conference/tapp2019/presentation/packer",
    language = "English",
    booktitle = "11th {International} {Workshop} on {Theory} and {Practice} of {Provenance} ({TaPP} 2019)",
    publisher = "USENIX Association",
    year = "2019",
    pages = "8"
}
```
Nadia Eghbal. The rise of few-maintainer projects. May 2019. URL: https://increment.com/open-source/the-rise-of-few-maintainer-projects/?mc_cid=05100f64e2&mc_eid=6fb5ad943a (visited on 2019-05-30).
[abstract▼] [BibTeX▼]

When a developer named Ayrton Sparling disclosed the presence of malicious code in a popular npm module, event-stream, the response was disbelief—not because the code existed, but because of the way it got there. The code, intended to steal users’ bitcoin wallets, had been injected by an unknown developer with the username right9ctrl. That person had gained commit access from event-stream’s author, Dominic Tarr, simply by asking for it. To many angry users, this was the equivalent of opening one’s front door to the first stranger who knocked, then grabbing one’s coat and leaving for the day. Right9ctrl, in response, did exactly what one might have expected: He headed straight for the valuables.
```
@misc{eghbal_rise_2019,
    author = "Eghbal, Nadia",
    type = "news",
    title = "The rise of few-maintainer projects",
    url = "https://increment.com/open-source/the-rise-of-few-maintainer-projects/?mc\_cid=05100f64e2\&mc\_eid=6fb5ad943a",
    language = "English",
    urldate = "2019-05-30",
    journal = "increment",
    month = "May",
    year = "2019"
}
```
Gowtham Kaki, KC Sivaramakrishnan, and Suresh Jagannathan. Version Control Is for Your Data Too. ACM, pages 19, May 2019. URL: http://gowthamk.github.io/docs/snapl19.pdf, doi:10.4230/LIPIcs.SNAPL.2019.8.
[abstract▼] [BibTeX▼]

Programmers regularly use distributed version control systems (DVCS) such as Git to facilitatecollaborative software development. The primary purpose of a DVCS is to maintain integrity ofsource code in the presence of concurrent, possibly conflicting edits from collaborators. In addition tosafely merging concurrent non-conflicting edits, a DVCS extensively tracks source code provenanceto help programmers contextualize and resolve conflicts. Provenance also facilitates debugging byletting programmers see diffs between versions and quickly find those edits that introduced theoffending conflict (e.g., viagit blame).In this paper, we posit that analogous workflows to collaborative software development also arisein distributed software execution; we argue that the characteristics that make a DVCS an ideal fitfor the former also make it an ideal fit for the latter. Building on this observation, we propose adistributed programming model, calledcarmotthat views distributed shared state as an entityevolving in time, manifested as a sequence of persistent versions, and relies on an explicitly definedmerge semanticsto reconcile concurrent conflicting versions. We show examples demonstrating howcarmotsimplifies distributed programming, while also enabling novel workflows integral to modernapplications such as blockchains. We also describe a prototype implementation ofcarmotthat weuse to evaluate its practicality.
```
@article{kaki_version_2019,
    author = "Kaki, Gowtham and Sivaramakrishnan, KC and Jagannathan, Suresh",
    title = "Version {Control} {Is} for {Your} {Data} {Too}",
    url = "http://gowthamk.github.io/docs/snapl19.pdf",
    doi = "10.4230/LIPIcs.SNAPL.2019.8",
    month = "May",
    year = "2019",
    journal = "ACM",
    pages = "19"
}
```
Mia Partlow, Theresa Quill, and Mireille Djenno. An open source solution to a common collection problem: the Africa image and map portal. Library Hi Tech News, pages 000–000, May 2019. URL: https://doi.org/10.1108/LHTN-01-2019-0004 (visited on 2019-05-30), doi:10.1108/LHTN-01-2019-0004.
[abstract▼] [BibTeX▼]

Purpose The purpose of this paper is to provide an overview of the Africa image and map portal (AIMP) project?s origins and development, along with its applications to date. This paper includes methods and a step-by-step appendix so that the project can be reproduced at other institutions. Design/methodology/approach AIMP was created with a suite of free and open source software, including QGIS, Mapbox.js and GitHub. Built around the concept of an interactive index map, AIMP allows for geographic searching of maps, posters and images from Indiana University?s (IU) African Studies collections. This paper presents a case study for the use of this geographic discovery tool at an academic library. Findings AIMP has allowed comparison of collection strengths with research interests of IU African Studies affiliates and to make strategic collection development decisions that will best serve the authors? patrons. The instruction applications of AIMP are also full of potential. To date, the Librarian for African Studies has used the portal to familiarize faculty, as well as undergraduate and graduate students, with the range of image and map resources available to them, in a variety of settings. Social implications AIMP allows researchers around the world to discover materials through a geographic search, dramatically connecting and increasing access to and discoverability of these important collections. The use of free and open source geospatial software (foss4g) means that the interface does not rely on an institution?s proprietary software-licensing agreements, making it replicable for other institutions. This use of foss4g widens access to maps, spatial data, images and posters of Africa held by IUL to a global audience. Originality/value While interactive index maps are popular among map libraries, AIMP uniquely acts as a discovery portal for a variety of media, including images and posters. In this way, AIMP works to overcome institutional silos and increase discoverability of these important collections to a global audience.
```
@article{partlow_open_2019,
    author = "Partlow, Mia and Quill, Theresa and Djenno, Mireille",
    title = "An open source solution to a common collection problem: the {Africa} image and map portal",
    issn = "0741-9058",
    url = "https://doi.org/10.1108/LHTN-01-2019-0004",
    doi = "10.1108/LHTN-01-2019-0004",
    language = "English",
    urldate = "2019-05-30",
    journal = "Library Hi Tech News",
    month = "May",
    year = "2019",
    pages = "000--000"
}
```
Wouter van Atteveldt, drew margolin, Cuihua Shen, Damian Trilling, and René Weber. A Roadmap for Computational Communication Research. SocArXiv, May 2019. URL: https://osf.io/preprints/socarxiv/4dhfk/, doi:10.31235/osf.io/4dhfk.
[abstract▼] [BibTeX▼]

Computational Communication Research (CCR) is a new open access journal dedicated to publishing high quality computational research in communication science. This editorial introduction describes the role that we envision for the journal. First, we explain what computational communication science is and why a new journal is needed for this subfield. Then, we elaborate on the type of research this journal seeks to publish, and stress the need for transparent and reproducible science. The relation between theoretical development and computational analysis is discussed, and we argue for the value of null-findings and risky research in additive science. Subsequently, the (experimental) two-phase review process is described. In this process, after the first double-blind review phase, an editor can signal that they intend to publish the article conditional on satisfactory revisions. This starts the second review phase, in which authors and reviewers are no longer required to be anonymous and the authors are encouraged to publish a preprint to their article which will be linked as working paper from the journal. Finally, we introduce the four articles that, together with this Introduction, form the inaugural issue.
```
@article{van_atteveldt_roadmap_2019,
    author = "van Atteveldt, Wouter and margolin, drew and Shen, Cuihua and Trilling, Damian and Weber, René",
    title = "A {Roadmap} for {Computational} {Communication} {Research}",
    url = "https://osf.io/preprints/socarxiv/4dhfk/",
    doi = "10.31235/osf.io/4dhfk",
    language = "English",
    journal = "SocArXiv",
    month = "May",
    year = "2019"
}
```

Michael T. Eismann. More Than a Paper. Optical Engineering, 58(5):1–2, May 2019. URL: https://doi.org/10.1117/1.OE.58.5.050101, doi:10.1117/1.OE.58.5.050101.
[abstract▼] [BibTeX▼]

@article{michael_t._eismann_more_2019,
    author = "{Michael T. Eismann}",
    title = "More {Than} a {Paper}",
    volume = "58",
    url = "https://doi.org/10.1117/1.OE.58.5.050101",
    doi = "10.1117/1.OE.58.5.050101",
    language = "English",
    number = "5",
    journal = "Optical Engineering",
    month = "May",
    year = "2019",
    pages = "1--2"
}

Mariam El Mezouar, Feng Zhang, and Ying Zou. An empirical study on the teams structures in social coding using GitHub projects. Empirical Software Engineering, pages 1–34, May 2019. URL: https://doi.org/10.1007/s10664-019-09700-1, doi:10.1007/s10664-019-09700-1.
[abstract▼] [BibTeX▼]

Social coding enables collaborative software development in virtual and distributed communities. Social coding platforms (e.g., GitHub) provide the pull request feature that allows developers to clone a project, make code changes, and request the project owners to review and integrate the code changes to the main stream of a project. The pull request feature has been widely adopted by a large number of GitHub projects, as it minimizes the risk of exposing the projects to the open communities. The efficiency of the pull requests review process depends both on technical (e.g., the code quality) and social (e.g., the connection of a contributor to the project maintainer) factors. However, it is still unclear which social factors have the most impact on the efficiency of the review process. To identify the social factors, we study the team structures formed by the developers within the projects that adopt the pull-based development model. We build the pull-based networks, where two developers are linked if one has integrated a pull request submitted by the other. We investigate the 7,850 most popular projects on GitHub that are developed in ten programming languages. We identify the network metrics that have a significant association with the speed of processing the pull requests. Specifically, maintaining a strong core of contributors and denser interactions among the developers is associated with faster response and processing of the pull requests. We further find that more than 90\% of the studied projects follow 8 dominant team structures out of 18 possible team structures. In the larger projects, only a set of developers is granted review and integration privileges of the pull requests, reflecting a strict decision making process. The small to medium projects are characterized by a small number of core contributors who maintain repeated interactions, and are able to process the incoming pull requests more efficiently. The evolution of the team structures of projects over time reveals that only a low percentage of the projects witnesses a change towards team structures associated to faster pull requests processing (e.g., stronger centralization).
```
@article{el_mezouar_empirical_2019,
    author = "El Mezouar, Mariam and Zhang, Feng and Zou, Ying",
    title = "An empirical study on the teams structures in social coding using {GitHub} projects",
    issn = "1573-7616",
    url = "https://doi.org/10.1007/s10664-019-09700-1",
    doi = "10.1007/s10664-019-09700-1",
    language = "English",
    journal = "Empirical Software Engineering",
    month = "May",
    year = "2019",
    pages = "1--34"
}
```
Shangwen Wang, Xiaoguang Mao, and Xin Yi. Dissection on Java Organs in GitHub Repositories. Volume PP. IEEE, May 2019. URL: https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8716735, doi:10.1109/ACCESS.2019.2917330.
[abstract▼] [BibTeX▼]

Organ transplantation has brought convenience for software reuse and evolution since it was proposed. However, studies about mature, high-quality organs are still insufficient. It is still unclear about the detailed characteristics of organs in open-source environment. In this paper, we look deep into organs obtained from software evolution processes of ten large-scale Java repositories hosted on GitHub, aiming at providing practical information for utilizing organs in open-source environment. We found that 1) commits use add as a keyword in their comments possess the most organs, occupying 38\% of the total amount, but commits with the keyword fix possess the highest locating accuracy (about 57\%); 2) developers prefer to add new classes when they bring new functionalities to the projects in that the proportion of Class Level Organs is 40\%, more than Statement Level Organs’ and Function Level Organs’ (35\% and 25\%, respectively); 3) nearly 70\% of the total amount are cross-file organs with the median of the number of files each organ spans reaching 3 and the average of this value being around 4; 4) a small number (0.55\%) of organs are multicommit; 5) more than 40\% of code reuse in open-source software can be finished by organ transplantation. Based on our findings, we highlight implications for future studies and design the mode of using organs to conduct code reuse.
```
@book{wang_dissection_2019,
    author = "Wang, Shangwen and Mao, Xiaoguang and Yi, Xin",
    title = "Dissection on {Java} {Organs} in {GitHub} {Repositories}",
    volume = "PP",
    url = "https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8716735",
    language = "English",
    publisher = "IEEE",
    month = "May",
    year = "2019",
    doi = "10.1109/ACCESS.2019.2917330"
}
```
Alexandra Chassanoff and Micah Altman. Curation as “Interoperability With the Future”: Preserving Scholarly Research Software in Academic Libraries. Journal of the Association for Information Science and Technology, 2019. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/asi.24244, doi:10.1002/asi.24244.
[abstract▼] [BibTeX▼]

This article considers the problem of preserving research software within the wider realm of digital curation, academic research libraries, and the scholarly record. We conducted a pilot study to understand the ecosystem in which research software participates, and to identify significant characteristics that have high potential to support future scholarly practices. A set of topical curation dimensions were derived from the extant literature and applied to select cases of institutionally significant research software. This approach yields our main contribution, a curation model and decision framework for preserving research software as a scholarly object. The results of our study highlight the unique characteristics and challenges at play in building curation services in academic research libraries.
```
@article{chassanoff_curation_nodate,
    author = "Chassanoff, Alexandra and Altman, Micah",
    title = "Curation as “{Interoperability} {With} the {Future}”: {Preserving} {Scholarly} {Research} {Software} in {Academic} {Libraries}",
    volume = "0",
    url = "https://onlinelibrary.wiley.com/doi/abs/10.1002/asi.24244",
    doi = "10.1002/asi.24244",
    number = "0",
    journal = "Journal of the Association for Information Science and Technology",
    year = "2019"
}
```
Shawn P. Gilroy and Brent A. Kaplan. Furthering Open Science in Behavior Analysis: An Introduction and Tutorial for Using GitHub in Research. Perspectives on Behavior Science, pages 1–17, May 2019. URL: https://doi.org/10.1007/s40614-019-00202-5, doi:10.1007/s40614-019-00202-5.
[abstract▼] [BibTeX▼]

Open and transparent practices in scholarly research are increasingly encouraged by academic journals and funding agencies. Various elements of behavior analytic research are communicated transparently, though it is not common practice to archive study materials to support future replications. This tutorial presents a review of the Transparent and Open Practices guidelines provided by the Open Science Foundation and provides instructions on how behavior analysts can use GitHub transparency in research across multiple levels. GitHub is presented as a service that can be used to publicly archive various elements of research and is uniquely suited to research that is technical, data driven, and collaborative. The GitHub platform is reviewed, and the steps necessary to create an account, initialize repositories, archive study files, and synchronize changes to remote repositories are described in several examples. Implications of increased calls for transparency and modern statistical methods are discussed with regard to behavior analysis, and archiving platforms such as GitHub are reviewed as one means of supporting transparent research.
```
@article{gilroy_furthering_2019,
    author = "Gilroy, Shawn P. and Kaplan, Brent A.",
    title = "Furthering {Open} {Science} in {Behavior} {Analysis}: {An} {Introduction} and {Tutorial} for {Using} {GitHub} in {Research}",
    issn = "2520-8977",
    url = "https://doi.org/10.1007/s40614-019-00202-5",
    doi = "10.1007/s40614-019-00202-5",
    language = "English",
    journal = "Perspectives on Behavior Science",
    month = "May",
    year = "2019",
    pages = "1--17"
}
```
James Blythe, Emilio Ferrara, Di Huang, Kristina Lerman, Goran Muric, Anna Sapienza, Alexey Tregubov, Diogo Pacheco, John Bollenbacher, Alessandro Flammini, Pik-Mai Hui, and Filippo Mencze. The DARPA SocialSim Challenge: Massive Multi-AgentSimulations of the Github Ecosystem. In Proceedings of the 18th International Conference on Autonomous Agents and MultiAgent Systems, 1835–1837. Montreal QC, Canada, May 2019. International Foundation for Autonomous Agents and Multiagent Systems. URL: https://dl.acm.org/citation.cfm?id=3331935&preflayout=flat.
[abstract▼] [BibTeX▼]

We model the evolution of GitHub, a large collaborative software-development ecosystem, using massive multi-agent simulations asa part of DARPA’s SocialSim program. Our best performing modelsand our agent-based simulation framework are described here. Sixdifferent agent models were tested based on a variety of machinelearning and statistical methods. The most successful models arebased on sampling from a stationary probability distribution ofactions and repositories for each agent
```
@inproceedings{blythe_darpa_2019,
    author = "Blythe, James and Ferrara, Emilio and Huang, Di and Lerman, Kristina and Muric, Goran and Sapienza, Anna and Tregubov, Alexey and Pacheco, Diogo and Bollenbacher, John and Flammini, Alessandro and Hui, Pik-Mai and Mencze, Filippo",
    address = "Montreal QC, Canada",
    title = "The {DARPA} {SocialSim} {Challenge}: {Massive} {Multi}-{AgentSimulations} of the {Github} {Ecosystem}",
    isbn = "978-1-4503-6309-9",
    url = "https://dl.acm.org/citation.cfm?id=3331935\&preflayout=flat",
    language = "English",
    publisher = "International Foundation for Autonomous Agents and Multiagent Systems",
    month = "May",
    year = "2019",
    booktitle = "Proceedings of the 18th International Conference on Autonomous Agents and MultiAgent Systems",
    pages = "1835--1837"
}
```
Yao Lu, Xinjun Mao, Tao Wang, Gang Yin, Zude Li, and Wanyuan Wang. Studying in the “Bazaar”: an Exploratory Study of Crowdsourced Learning in GitHub. IEEE Access, 1(1):99, May 2019. URL: https://www.researchgate.net/publication/332947736_Studying_in_the_Bazaar_an_Exploratory_Study_of_Crowdsourced_Learning_in_GitHub (visited on 2019-05-22), doi:10.1109/ACCESS.2019.2915247.
[abstract▼] [BibTeX▼]

In recent years, GitHub, the most popular social coding site, has been increasingly employed for managing learning content, sharing knowledge, imparting experience, and requesting and contributing learning resources in a crowdsourced way. We thus refer to this type of e-learning practices in which people perform learning-related tasks with open calls in an online community to gain knowledge or skills in specific areas as crowdsourced learning (CL). To understand this emerging phenomenon in GitHub, we investigate the popularity of the learning projects and learners’ CL activities, first on the extracted GHTorrent learning projects and then on a selected sample of 105 popular learning projects. We then conduct an online survey of 301 learners to qualitatively understand their practices and perceptions of CL in GitHub. Our main findings reveal that the learner’ CL practices show some different characteristics from those of open source development, e.g., the learning projects have very few long-term contributors (less than 5\% of all contributors). Moreover, although the learners benefit from conducting personalized learning with the high-quality content and contributions made by the community, they encounter challenges in maintaining initiatives to conduct continuous unsupervised learning and in ensuring the quality of content and contributions. Based on the findings, we discuss the reasons behind the growth of CL and provide implications on the CL platform design.
```
@article{lu_studying_2019,
    author = "Lu, Yao and Mao, Xinjun and Wang, Tao and Yin, Gang and Li, Zude and Wang, Wanyuan",
    title = "Studying in the “{Bazaar}”: an {Exploratory} {Study} of {Crowdsourced} {Learning} in {GitHub}",
    volume = "1",
    issn = "2169-3536",
    url = "https://www.researchgate.net/publication/332947736\_Studying\_in\_the\_Bazaar\_an\_Exploratory\_Study\_of\_Crowdsourced\_Learning\_in\_GitHub",
    doi = "10.1109/ACCESS.2019.2915247",
    language = "English",
    number = "1",
    urldate = "2019-05-22",
    journal = "IEEE Access",
    month = "May",
    year = "2019",
    pages = "99"
}
```
Martha Stuit, Rebecca Welzenbach, and Rachel Woodbrook. Take Control of Your Scholarly Identity withDeep Blue. May 2019. URL: https://deepblue.lib.umich.edu/handle/2027.42/149125.
[abstract▼] [BibTeX▼]

If the CV is the table of contents to a scholarly career, repositories help make the fuller story available by providing direct access to the rich content deposited in them. This extends beyond articles to teaching materials, conference materials (papers, slides, posters), data, code, images, and other resources. This session will engage attendees in identifying the breadth of their research outputs, and exploring how repositories can help add depth to online scholarly identities by making these outputs more visible and available. It will focus on the Deep Blue repositories (Deep Blue Documents and Deep Blue Data) stewarded by the University of Michigan Library as venues for exposing this work, and will be most useful for those in faculty and staff roles, but applicable for anyone building out their scholarly identity online. Breadth of representation becomes ever more important as more people engage in public scholarship or other types of work not traditionally captured in conversations around scholarship and promotion. Attendees will leave the session with a list of their own scholarly accomplishments to explore making available online, and a framework to use in determining the best platform(s) for their work. The session will also include a chance for participants to interact with Deep Blue and Deep Blue Data, and learn about repositories in general as well as the services available to them as members of the University of Michigan. The session will complement Enriching Scholarship sessions “Managing your scholarly presence online” and “Visualize public engagement with scholarly research using Altmetric Explorer”.
```
@misc{stuit_take_2019,
    author = "Stuit, Martha and Welzenbach, Rebecca and Woodbrook, Rachel",
    address = "Ann Arbor, MI",
    type = "Slides",
    title = "Take {Control} of {Your} {Scholarly} {Identity} {withDeep} {Blue}",
    url = "https://deepblue.lib.umich.edu/handle/2027.42/149125",
    language = "English",
    month = "May",
    year = "2019"
}
```
Rute Correia, Jorge Vieira, and Manuela Aparicio. Community radio stations sustainability model: An open-source solution. Radio Journal: International Studies in Broadcast & Audio Media, 17(1):29–45, April 2019. URL: http://www.ingentaconnect.com/content/intellect/rj/2019/00000017/00000001/art00003, doi:10.1386/rjao.17.1.29_1.
[abstract▼] [BibTeX▼]

Abstract: Community radio stations are important social-inclusion structures, empowering communities through media access and production, reinforcing their ties with the wider civil society. The free and open-source software movement has been established since the 1980s, founded on the freedom to use, to study, to share and to improve a software's source code. It focuses on sharing knowledge, enabling action within a community towards a common goal. With millions of projects and market dominance in specific areas of IT, open source is one of the most successful community movements of our time. In this article, we argue that theoretical frameworks and other insights drawn from the open-source movement can be valuable tools for understanding and critically analysing the designated community radio sphere in terms of technology, content creation and community management to provide a sustainable broadcast practice, expanding already-existing inclusive environments and potentiating empowerment through participation.
```
@article{correia_community_2019,
    author = "Correia, Rute and Vieira, Jorge and Aparicio, Manuela",
    title = "Community radio stations sustainability model: {An} open-source solution.",
    volume = "17",
    url = "http://www.ingentaconnect.com/content/intellect/rj/2019/00000017/00000001/art00003",
    language = "English",
    number = "1",
    journal = "Radio Journal: International Studies in Broadcast \\& Audio Media",
    doi = "10.1386/rjao.17.1.29\_1",
    month = "April",
    year = "2019",
    pages = "29--45"
}
```
Jirateep Tantisuwankulb, Yusuf Sulistyo Nugrohoa, Raula Gaikovina Kulaa, Hideaki Hataa, Arnon Rungsawangb, Pattara Leelapruteb, and Kenichi Matsumoto. A Topological Analysis of Communication Channels forKnowledge Sharing in Contemporary GitHub Projects. The Journal of Systems and Software, pages 27, May 2019. URL: https://arxiv.org/abs/1905.03593v1, doi:arXiv:1905.03593 [cs.SE].
[abstract▼] [BibTeX▼]

With over 28 million developers, success of GitHub collaborative platform ishighlighted through the abundance of communication channels among con-temporary software projects. Knowledge is broken into two forms and itstransfer (through communication channels) can be described as externaliza-tion or combination by the SECI model of knowledge transfer of an organiza-tion. Over the years, such platforms have revolutionized the way developerswork, introducing new channels to share knowledge in the form of pull re-quests, issues and wikis. It is unclear how these channels capture and shareknowledge. In this research, our goal is to analyze how communication chan-nels share knowledge over projects. First, using the SECI model, we are ableto map how knowledge is transferred through the communication channels.Then in a large-scale topology analysis of seven library package platforms, weextracted insights of how knowledge is shared by different library ecosystemswithin GitHub. Using topology data analysis, we show that (i) channels tendto evolve over time and (ii) library ecosystems consistently have channels tocapture new knowledge (i.e., externalization). Results from the study aid inunderstanding what channels are important sources of knowledge, also withinsights into how projects can attract and sustain developer contributions.
```
@article{tantisuwankulb_topological_2019,
    author = "Tantisuwankulb, Jirateep and Nugrohoa, Yusuf Sulistyo and Kulaa, Raula Gaikovina and Hataa, Hideaki and Rungsawangb, Arnon and Leelapruteb, Pattara and Matsumoto, Kenichi",
    title = "A {Topological} {Analysis} of {Communication} {Channels} {forKnowledge} {Sharing} in {Contemporary} {GitHub} {Projects}",
    url = "https://arxiv.org/abs/1905.03593v1",
    doi = "arXiv:1905.03593 [cs.SE]",
    language = "English",
    journal = "The Journal of Systems and Software",
    month = "May",
    year = "2019",
    pages = "27"
}
```
Daniel German, Bram Adams, and Kate Stewart. Cregit: Token-level blame information in git version control repositories. Empirical Software Engineering, May 2019. URL: https://link.springer.com/article/10.1007/s10664-019-09704-x#citeas, doi:https://doi.org/10.1007/s10664-019-09704-x.
[abstract▼] [BibTeX▼]

The blame feature of version control systems is widely used—both by practitioners and researchers—to determine who has last modified a given line of code, and the commit where this contribution was made. The main disadvantage of blame is that, when a line is modified several times, it only shows the last commit that modified it—occluding previous changes to other areas of the same line. In this paper, we developed a method to increase the granularity of blame in git: instead of tracking lines of code, this method is capable of tracking tokens in source code. We evaluate its effectiveness with an empirical study in which we compare the accuracy of blame in git (per line) with our proposed blame-per-token method. We demonstrate that, in 5 large open source systems, blame-per-token is capable of properly identifying the commit that introduced a token with an accuracy between 94.5\% and 99.2\%, while blame-per-line can only achieve an accuracy between 75\% and 91\% (with a margin of error of +/-5\% and a confidence interval of 95\%). We also classify the reasons why either blame method fails, highlighting each method’s weaknesses. The blame-per-token method has been implemented in an open source tool called cregit, which is currently in use by the Linux Foundation to identify the persons who have contributed to the source code of the Linux kernel.
```
@article{german_cregit:_2019,
    author = "German, Daniel and Adams, Bram and Stewart, Kate",
    title = "cregit: {Token}-level blame information in git version control repositories",
    issn = "1573-7616",
    url = "https://link.springer.com/article/10.1007/s10664-019-09704-x\#citeas",
    doi = "https://doi.org/10.1007/s10664-019-09704-x",
    language = "English",
    journal = "Empirical Software Engineering",
    month = "May",
    year = "2019"
}
```
Joel Ross. Introduction to Programming. April 2019. URL: https://infx511.github.io/ (visited on 2019-05-12).
[abstract▼] [BibTeX▼]

This book covers the fundamentals of computer programming as used for data science. It will introduce programming concepts such as syntax, data referencing, control structures, functions, data structures, abstraction, and debugging, as well as development tools and technologies (such as the command-line and version control). The goal is to develop skills in algorithmic thinking, abstraction, and debugging. It assumes no previous programming background. These materials were developed for the INFX 511: Introduction to Programming for Data Science and Visualization course taught at the University of Washington Information School; however they have been structured to be an online resource for anyone who wishes to learn programming.
```
@misc{ross_introduction_2019,
    author = "Ross, Joel",
    type = "Textbook",
    title = "Introduction to {Programming}",
    url = "https://infx511.github.io/",
    language = "English",
    urldate = "2019-05-12",
    journal = "Introduction to Programming",
    month = "April",
    year = "2019"
}
```

George Cushen. Why you should create your personal website with Academic and Hugo. February 2019. URL: https://georgecushen.com/create-your-website-with-hugo/ (visited on 2019-05-12).
[BibTeX▼]

@misc{cushen_why_2019,
    author = "Cushen, George",
    type = "Blog",
    title = "Why you should create your personal website with {Academic} and {Hugo}",
    url = "https://georgecushen.com/create-your-website-with-hugo/",
    language = "English",
    urldate = "2019-05-12",
    journal = "George Cushen",
    month = "February",
    year = "2019"
}

Aaron Williams. Scripting versus Point-and-Click, a Slack Debate. April 2019. URL: https://medium.com/@urban_institute/scripting-versus-point-and-click-a-slack-debate-6947923f1b9e (visited on 2019-05-10).
[abstract▼] [BibTeX▼]

Back in February, the Data@Urban editors were making comments on an early draft of the post "Why The Urban Institute Visualizes Data with ggplot2." Author Aaron Williams made the statement: "Point-and-click tools for data visualization are popular, but they are neither reproducible nor scalable." Which prompted quite the lively debate among our editors. As interesting as it may have been to publish the full transcript of our “track changes” comment threads, we thought it might be more useful to record our thoughts via a live conversation.
```
@misc{williams_scripting_2019,
    author = "Williams, Aaron",
    type = "Blog",
    title = "Scripting versus {Point}-and-{Click}, a {Slack} {Debate}",
    url = "https://medium.com/@urban\_institute/scripting-versus-point-and-click-a-slack-debate-6947923f1b9e",
    language = "English",
    urldate = "2019-05-10",
    journal = "Medium: Data@Urban",
    month = "April",
    year = "2019"
}
```
Eric Raymond. Understanding Version-Control Systems (DRAFT). 2019. URL: http://www.catb.org/esr/writings/version-control/version-control.html#why_vcs.
[abstract▼] [BibTeX▼]

Note: This is a draft under intensive development. Some claims made in it may be incorrect. Others may be correct but insufficiently sourced. Corrections and feedback are welcomed, A guide to the history and taxonomy of version-control systems available on Unix-family operating systems. This document is meant to help readers make sense of the version-control landcape and the conflicting claims flying around it, and to help the reader make informed choices. VCS designs analyzed include SCCS, RCS, DSEE/ClearCase, CVS, Subversion, Arch, ArX, monotone.
```
@misc{noauthor_understanding_nodate,
    author = "Raymond, Eric",
    type = "blog",
    title = "Understanding {Version}-{Control} {Systems} ({DRAFT})",
    url = "http://www.catb.org/esr/writings/version-control/version-control.html\#why\_vcs",
    year = "2019",
    language = "English",
    journal = "esr"
}
```
Daniel S. Falster, Richard G. Fitz, Matthew W. Pennell, and William K. Cornwell. Datastorr: a workflow and package for delivering successive versions of 'evolving data' directly into R. GigaScience, May 2019. URL: https://academic.oup.com/gigascience/article/8/5/giz035/5482388, doi:https://doi.org/10.1093/gigascience/giz035.
[abstract▼] [BibTeX▼]

The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow easy publication of datasets. So far, however, platforms for data sharing offer limited functions for distributing and interacting with evolving datasets— those that continue to grow with time as more records are added, errors fixed, and new data structures are created. In this article, we describe a workflow for maintaining and distributing successive versions of an evolving dataset, allowing users to retrieve and load different versions directly into the R platform. Our workflow utilizes tools and platforms used for development and distribution of successive versions of an open source software program, including version control, GitHub, and semantic versioning, and applies these to the analogous process of developing successive versions of an open source dataset. Moreover, we argue that this model allows for individual research groups to achieve a dynamic and versioned model of data delivery at no cost.
```
@article{falster_datastorr:_2019,
    author = "Falster, Daniel S. and Fitz, Richard G. and Pennell, Matthew W. and Cornwell, William K.",
    title = "Datastorr: a workflow and package for delivering successive versions of 'evolving data' directly into {R}",
    volume = "8",
    url = "https://academic.oup.com/gigascience/article/8/5/giz035/5482388",
    doi = "https://doi.org/10.1093/gigascience/giz035",
    language = "English",
    number = "5",
    journal = "GigaScience",
    month = "May",
    year = "2019"
}
```
Joseph Holler. Teaching critical open GIS. Canadian Association of Geographers / l'Association canadienne des géographes, May 2019. URL: https://onlinelibrary.wiley.com/doi/pdf/10.1111/cag.12521, doi:https://doi.org/10.1111/cag.12521.
[abstract▼] [BibTeX▼]

Higher‐education geographic information system (GIS) curricula largely marginalize and separate instruction of critical GIS and open GIS, paralleling a divide between GIS and non‐GIS in geography. GIS is typically represented as a singular, infallibly objective, and universally applicable technology. GIS generally dismisses the critiques from human geography, while critical human geography dismisses GIS for its association with positivism and unethical applications. Teaching critical open GIS may bridge this divide, creating a transformative pedagogical space for human geography to affectively and effectively engage with open GIS technology at the level of code. Critical open GIS students practice and critique GIS as conflicted insiders, bridging the divide between GIS and non‐GIS in their geography education. Reviews of GIS curricula find support for teaching critical and open GIS, but reviews of texts and syllabi confirm their marginalization and separation. A new critical open GIS course is introduced, using GIS in development and political ecology as integrative frameworks.
```
@article{holler_teaching_2019,
    author = "Holler, Joseph",
    title = "Teaching critical open {GIS}",
    url = "https://onlinelibrary.wiley.com/doi/pdf/10.1111/cag.12521",
    doi = "https://doi.org/10.1111/cag.12521",
    language = "English",
    journal = "Canadian Association of Geographers / l'Association canadienne des géographes",
    month = "May",
    year = "2019"
}
```
Lillian Rigling. North Carolina State University Spotlight: Part 3, The Power of Open: Tools and Practices for Opening Up Student Work. In Scholarship in the Sandbox: Academic Libraries as Laboratories, Forums, and Archives for Student Work, pages 253–258. ACRL, April 2019. URL: https://osf.io/preprints/lissa/v6rjy/ (visited on 2019-05-07).
[abstract▼] [BibTeX▼]

North Carolina State University’s (NCSU) mission to “Think and Do” has empowered the NCSU Libraries to be a leader in connecting theory to prac- tice, coursework to careers, and personal passions to global engagement. Ad- ditional information about how this mission informs the work of the NCSU Libraries is provided in the chapter “Preparing Students to ‘Think and Do’: Promoting the Value of Student Work,” which appears in the Articulating the Value of Student Work section of the book.
```
@incollection{rigling_north_2019,
    author = "Rigling, Lillian",
    title = "North {Carolina} {State} {University} {Spotlight}: {Part} 3, {The} {Power} of {Open}: {Tools} and {Practices} for {Opening} {Up} {Student} {Work}",
    url = "https://osf.io/preprints/lissa/v6rjy/",
    language = "English",
    urldate = "2019-05-07",
    booktitle = "Scholarship in the {Sandbox}: {Academic} {Libraries} as {Laboratories}, {Forums}, and {Archives} for {Student} {Work}",
    publisher = "ACRL",
    month = "April",
    year = "2019",
    pages = "253--258"
}
```

2018

Memento Tracer. Memento Tracer Demo - GitHub. 2018. URL: http://tracer.mementoweb.org/demos/github/ (visited on 2019-06-27).
[BibTeX▼]

@misc{memento_tracer_memento_2018,
    author = "{Memento Tracer}",
    title = "Memento {Tracer} {Demo} - {GitHub}",
    url = "http://tracer.mementoweb.org/demos/github/",
    urldate = "2019-06-27",
    year = "2018"
}

Jillian Lohndorf. Archive-It Crawling Technology. 2018. URL: http://support.archive-it.org/hc/en-us/articles/115001081186-Archive-It-Crawling-Technology (visited on 2019-06-25).
[abstract▼] [BibTeX▼]

Crawlers identify materials on the live web that belong in your collections, based upon your choice of seeds and scope. A crawl can also reference the archived content associa...
```
@misc{lohndorf_archive-it_2018,
    author = "Lohndorf, Jillian",
    title = "Archive-{It} {Crawling} {Technology}",
    url = "http://support.archive-it.org/hc/en-us/articles/115001081186-Archive-It-Crawling-Technology",
    language = "en-US",
    urldate = "2019-06-25",
    journal = "Archive-It Help Center",
    year = "2018"
}
```
Martin Fenner, Daniel S. Katz, Lars Holm Nielsen, and Smith Arfon. DOI Registrations for Software. 2018. URL: https://blog.datacite.org/doi-registrations-software/ (visited on 2019-07-08).
[abstract▼] [BibTeX▼]

We know that software is important in research, and some of us in the scholarly communications community, for example, in FORCE11, have been pushing the concept of software citation as a method to allow software developers and maintainers to get academic...
```
@misc{fenner_doi_2018,
    author = "Fenner, Martin and Katz, Daniel S. and Nielsen, Lars Holm and Arfon, Smith",
    type = "website",
    title = "{DOI} {Registrations} for {Software}",
    copyright = "CC-BY",
    url = "https://blog.datacite.org/doi-registrations-software/",
    language = "en",
    urldate = "2019-07-08",
    journal = "DataCite Blog",
    year = "2018"
}
```
Kenning Arlitsch and Carl Grant. Why So Many Repositories? Examining the Limitations and Possibilities of the Institutional Repositories Landscape. Journal of Library Administration, 58(3):264–281, 2018. URL: https://doi.org/10.1080/01930826.2018.1436778 (visited on 2019-07-08), doi:10.1080/01930826.2018.1436778.
[abstract▼] [BibTeX▼]

Academic libraries fail to take advantage of the network effect because they manage too many digital repositories locally. While this argument applies to all manner of digital repositories, this article examines the fragmented environment of institutional repositories (IR), in which effort and costs are duplicated, numerous software platforms and versions are managed simultaneously, metadata are applied inconsistently, users are served poorly, and libraries are unable to take advantage of collective data about content and users. In the meantime, commercial IR vendors and academic social networks have shown much greater success with cloud-based models. Collectively, the library profession has enough funding to create a national-level IR, but it lacks the willingness to abandon local control.
```
@article{arlitsch_why_2018,
    author = "Arlitsch, Kenning and Grant, Carl",
    title = "Why {So} {Many} {Repositories}? {Examining} the {Limitations} and {Possibilities} of the {Institutional} {Repositories} {Landscape}",
    volume = "58",
    issn = "0193-0826",
    url = "https://doi.org/10.1080/01930826.2018.1436778",
    doi = "10.1080/01930826.2018.1436778",
    number = "3",
    urldate = "2019-07-08",
    journal = "Journal of Library Administration",
    year = "2018",
    pages = "264--281"
}
```
John Novak and Annette Day. The IR Has Two Faces: Positioning Institutional Repositories for Success. New Review of Academic Librarianship, 24(2):157–174, 2018. URL: https://www.tandfonline.com/doi/full/10.1080/13614533.2018.1425887 (visited on 2019-07-08), doi:10.1080/13614533.2018.1425887.
[abstract▼] [BibTeX▼]

This article will describe ongoing efforts at University of Nevada, Las Vegas (UNLV) Libraries to evolve the role of the institutional repository (IR) and to effectively position it within the context of the Libraries’ collections, research support, and scholarly communication services. A major component of this process is re-examining the fundamental aims of the IR and aligning it to the Libraries and the campus strategic goals. The authors situate UNLV Libraries’ experience within the context of the current literature to provide background and reasoning for our decision to pursue two, at times conflicting, aims for the IR: one for scholarly communication and another for research administration.
```
@article{novak_ir_2018,
    author = "Novak, John and Day, Annette",
    title = "The {IR} {Has} {Two} {Faces}: {Positioning} {Institutional} {Repositories} for {Success}",
    volume = "24",
    issn = "1361-4533, 1740-7834",
    url = "https://www.tandfonline.com/doi/full/10.1080/13614533.2018.1425887",
    doi = "10.1080/13614533.2018.1425887",
    language = "en",
    number = "2",
    urldate = "2019-07-08",
    journal = "New Review of Academic Librarianship",
    year = "2018",
    pages = "157--174"
}
```

Micah Zeller. Research Guides: How to make your scholarly work open access: Self-archiving. August 2018. URL: https://libguides.wustl.edu/c.php?g=47489&p=304111 (visited on 2019-07-08).
[abstract▼] [BibTeX▼]

@misc{zeller_research_2018,
    author = "Zeller, Micah",
    title = "Research {Guides}: {How} to make your scholarly work open access: {Self}-archiving",
    copyright = "Copyright Washington University in St. Louis 2019",
    url = "https://libguides.wustl.edu/c.php?g=47489\&p=304111",
    language = "en",
    urldate = "2019-07-08",
    month = "August",
    year = "2018"
}

O. Saini. The Emergence of Institutional Repositories: A Conceptual Understanding of Key Issues through Review of Literature. Library Philosophy & Practice, pages 1–19, 2018. URL: http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=lls&AN=133862841&site=eds-live (visited on 2019-07-03).
[abstract▼] [BibTeX▼]

It is the responsibility of the libraries to keep update its users by incorporating different technologies or tricks among the services offered to users. The libraries are managing diversified collection in both electronic and physical formats including the theses and dissertations awarded by their respective parent institutes in physical form. The academic libraries are directed by the Indian government through a mandate to protect and preserve the theses and dissertation in electronic form and provide access to the public domain. Institutional Repositories (IRs) have the prospective to store any amount of information electronically. Therefore, many of the academic libraries are forced to develop their IRs. The present paper is an attempt to find out the answers to some of the burning questions related to creation and management of IRs by the libraries. The library managers are sometimes confused when they asked to install the IRs Software, design the IR policy, motivate faculty, prepare budget estimates for IRs, etc. The current study covered various theoretic aspects related to the creation and maintenance of an IR in an academic institution. The study is based on the review of available literature and analysis focused various aspects of motivations, cost factors and software requirement and its global perspectives for the creation of Institutional Repositories. The paper also discusses the role of IRs in Scholarly Communication. Finally, it highlights the barriers for IRs in an academic environment appeared in the repository literature.
```
@article{saini_emergence_2018,
    author = "Saini, O.",
    title = "The {Emergence} of {Institutional} {Repositories}: {A} {Conceptual} {Understanding} of {Key} {Issues} through {Review} of {Literature}",
    issn = "15220222",
    url = "http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true\&db=lls\&AN=133862841\&site=eds-live",
    urldate = "2019-07-03",
    journal = "Library Philosophy \\& Practice",
    year = "2018",
    pages = "1--19"
}
```

Titus Brown. Where to put your code and data for publication — angus 6.0 documentation. 2018. URL: https://angus.readthedocs.io/en/2019/where_to_put_data.html (visited on 2019-07-08).
[BibTeX▼]

@misc{brown_where_2018,
    author = "Brown, Titus",
    title = "Where to put your code and data for publication — angus 6.0 documentation",
    url = "https://angus.readthedocs.io/en/2019/where\_to\_put\_data.html",
    urldate = "2019-07-08",
    year = "2018"
}

Vicky Steeves. UUtah 2018 Reproducibility Immersive Course. June 2018. URL: https://vickysteeves.gitlab.io/2018-uutah-repro/the-open-science-framework.html (visited on 2019-07-16).
[abstract▼] [BibTeX▼]

@misc{steeves_uutah_2018,
    author = "Steeves, Vicky",
    title = "{UUtah} 2018 {Reproducibility} {Immersive} {Course}",
    url = "https://vickysteeves.gitlab.io/2018-uutah-repro/the-open-science-framework.html",
    urldate = "2019-07-16",
    month = "June",
    year = "2018"
}

The Software Sustainability Institute. Checklist for a Software Management Plan. Technical Report, Zenodo, December 2018. URL: https://zenodo.org/record/2159713#.XStwByYpB7g (visited on 2019-07-14), doi:10.5281/zenodo.2159713.
[abstract▼] [BibTeX▼]

When developing research software, it is easy to focus only on goals and activities such as collaborating with other researchers, writing papers, attending conferences and applying for funding. Together, the demands of daily research practice can all conspire to prevent proper planning for the development of research software. A Software Management Plan (SMP) can help you to define a set of structures and goals to understand your research software including what you are going to develop; who the software is for (even if it is just for yourself); how you will deliver your software to its intended users; how it will help them; and how you will assess whether it has helped them, and contributed to research, in the ways that you intended. An SMP also helps you to understand how you can support those who wish to, or do, use your research software; how your software relates to other artefacts in your research ecosystem; and how you will ensure that your software remains available beyond the lifetime of your current project. This checklist will help you to write an SMP. It consists of sections that cover the key elements that an SMP should include.
```
@techreport{the_software_sustainability_institute_checklist_2018,
    author = "Institute, The Software Sustainability",
    title = "Checklist for a {Software} {Management} {Plan}",
    url = "https://zenodo.org/record/2159713\#.XStwByYpB7g",
    language = "eng",
    urldate = "2019-07-14",
    institution = "Zenodo",
    month = "December",
    year = "2018",
    doi = "10.5281/zenodo.2159713"
}
```
Michael Jackson. Software Deposit: Guidance for Researchers. Technical Report, Zenodo, August 2018. URL: https://zenodo.org/record/1327310#.XStviCYpB7g (visited on 2019-07-14), doi:10.5281/zenodo.1327310.
[abstract▼] [BibTeX▼]

Research software is an integral part of the modern research ecosystem. Taken together, research software, alongside data, facilities, equipment and an overarching research question can be viewed as a research activity or experiment, worthy to be published. Conversely, a publication can be considered as a narrative that describes how the research objects are used together to reply to the research question. Depositing research software into a digital repository can offer significant benefits. By depositing not just papers, but software, and data sets, as well, researchers can store a more complete record of this ecosystem for future use to both the researchers who undertook the research and also the wider research community. Making research software available allows other researchers to inspect, replicate, reproduce and reuse the research, as manifested in the software, in the short term and to inspect, for the historical record, in the long term. It allows research software to remain available beyond the lifetime of any current project, or a researcher's current employment at a specific institution. Digital repositories can also provide unique persistent digital identifiers for software which can be cited and help researchers to get attribution and credit for their research software when it is used by others. The Software Sustainability Institute, funded by Jisc have developed a set of complementary guides covering the main aspects of depositing software into digital repositories. These guides are intended for researchers, principal investigators and research leaders and research data and digital repository managers. This document provides an overview of the content covered by the guides.
```
@techreport{michael_jackson_software_2018,
    author = "Jackson, Michael",
    title = "Software {Deposit}: {Guidance} for {Researchers}",
    url = "https://zenodo.org/record/1327310\#.XStviCYpB7g",
    language = "eng",
    urldate = "2019-07-14",
    institution = "Zenodo",
    month = "August",
    year = "2018",
    doi = "10.5281/zenodo.1327310"
}
```

Generation R. An Interview with Sarven Capadisli, Dokieli-Developer, on Autonomous Linked Research. October 2018. URL: https://genr.eu/wp/an-interview-with-sarven-capadisli-on-autonomous-linked-research/ (visited on 2019-07-12).
[abstract▼] [BibTeX▼]

@misc{r_interview_2018,
    author = "R, Generation",
    type = "Text",
    title = "An {Interview} with {Sarven} {Capadisli}, {Dokieli}-{Developer}, on {Autonomous} {Linked} {Research}",
    url = "https://genr.eu/wp/an-interview-with-sarven-capadisli-on-autonomous-linked-research/",
    language = "en-US",
    urldate = "2019-07-12",
    journal = "https://genr.eu/wp/",
    month = "October",
    year = "2018"
}

Arfon M. Smith, Kyle E. Niemeyer, Daniel S. Katz, Lorena A. Barba, George Githinji, Melissa Gymrek, Kathryn D. Huff, Christopher R. Madan, Abigail Cabunoc Mayes, Kevin M. Moerman, Pjotr Prins, Karthik Ram, Ariel Rokem, Tracy K. Teal, Roman Valls Guimera, and Jacob T. Vanderplas. Journal of Open Source Software (JOSS): design and first-year review. PeerJ Computer Science, 4:e147, February 2018. URL: https://peerj.com/articles/cs-147 (visited on 2019-07-09), doi:10.7717/peerj-cs.147.
[abstract▼] [BibTeX▼]

This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. The article is the entry point of a JOSS submission, which encompasses the full set of software artifacts. Submission and review proceed in the open, on GitHub. Editors, reviewers, and authors work collaboratively and openly. Unlike other journals, JOSS does not reject articles requiring major revision; while not yet accepted, articles remain visible and under review until the authors make adequate changes (or withdraw, if unable to meet requirements). Once an article is accepted, JOSS gives it a digital object identifier (DOI), deposits its metadata in Crossref, and the article can begin collecting citations on indexers like Google Scholar and other services. Authors retain copyright of their JOSS article, releasing it under a Creative Commons Attribution 4.0 International License. In its first year, starting in May 2016, JOSS published 111 articles, with more than 40 additional articles under review. JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative (OSI).
```
@article{smith_journal_2018,
    author = "Smith, Arfon M. and Niemeyer, Kyle E. and Katz, Daniel S. and Barba, Lorena A. and Githinji, George and Gymrek, Melissa and Huff, Kathryn D. and Madan, Christopher R. and Mayes, Abigail Cabunoc and Moerman, Kevin M. and Prins, Pjotr and Ram, Karthik and Rokem, Ariel and Teal, Tracy K. and Guimera, Roman Valls and Vanderplas, Jacob T.",
    title = "Journal of {Open} {Source} {Software} ({JOSS}): design and first-year review",
    volume = "4",
    issn = "2376-5992",
    url = "https://peerj.com/articles/cs-147",
    doi = "10.7717/peerj-cs.147",
    language = "en",
    urldate = "2019-07-09",
    journal = "PeerJ Computer Science",
    month = "February",
    year = "2018",
    pages = "e147"
}
```
Emily Maemura, Nicholas Worby, Ian Milligan, and Christoph Becker. If these crawls could talk: Studying and documenting web archives provenance. Journal of the Association for Information Science and Technology, 69(10):1223–1233, 2018. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/asi.24048 (visited on 2019-05-05), doi:10.1002/asi.24048.
[abstract▼] [BibTeX▼]

The increasing use and prominence of web archives raises the urgency of establishing mechanisms for transparency in the making of web archives to facilitate the process of evaluating a web archive's provenance, scoping, and absences. Some choices and process events are captured automatically, but their interactions are not currently well understood or documented. This study examined the decision space of web archives and its role in shaping what is and what is not captured in the web archiving process. By comparing how three different web archives collections were created and documented, we investigate how curatorial decisions interact with technical and external factors and we compare commonalities and differences. The findings reveal the need to understand both the social and technical context that shapes those decisions and the ways in which these individual decisions interact. Based on the study, we propose a framework for documenting key dimensions of a collection that addresses the situated nature of the organizational context, technical specificities, and unique characteristics of web materials that are the focus of a collection. The framework enables future researchers to undertake empirical work studying the process of creating web archives collections in different contexts.
```
@article{maemura_if_2018,
    author = "Maemura, Emily and Worby, Nicholas and Milligan, Ian and Becker, Christoph",
    title = "If these crawls could talk: {Studying} and documenting web archives provenance",
    volume = "69",
    copyright = "© 2018 ASIS\\&T",
    issn = "2330-1643",
    url = "https://onlinelibrary.wiley.com/doi/abs/10.1002/asi.24048",
    doi = "10.1002/asi.24048",
    language = "en",
    number = "10",
    urldate = "2019-05-05",
    journal = "Journal of the Association for Information Science and Technology",
    year = "2018",
    pages = "1223--1233"
}
```
Emily Maemura. What's cached is prologue: Reviewing recent web archives research towards supporting scholarly use. Proceedings of the Association for Information Science and Technology, 55(1):327–336, 2018. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/pra2.2018.14505501036 (visited on 2019-05-05), doi:10.1002/pra2.2018.14505501036.
[abstract▼] [BibTeX▼]

Web archives are essential to support historical scholarship in the online age. Research on web archives spans many disciplines, often requiring domain-specific expertise. The wide-ranging nature of the literature makes it difficult to obtain a current overview of the field, but this view is needed to identify which core challenges define the field, and assess the different approaches taken to address them. This paper provides such a review of the current landscape of web archives research, focusing on addressing the common challenges faced to support scholarly use of archived web materials. The analysis describes three challenges and identifies key concepts and current approaches for each: (1) how to organize and select from web archives collections; (2) how to critically examine these sources; and (3) how to approach ethics and consent for using archived web materials. The discussion addresses open questions and tensions, highlighting the sociotechnical nature of these challenges and revealing opportunities to apply existing work from the body of knowledge of information studies. It concludes with several recommendations for future research directions to support scholarly use of web archives.
```
@article{maemura_whats_2018,
    author = "Maemura, Emily",
    title = "What's cached is prologue: {Reviewing} recent web archives research towards supporting scholarly use",
    volume = "55",
    copyright = "Copyright © 2018 by Association for Information Science and Technology",
    issn = "2373-9231",
    url = "https://onlinelibrary.wiley.com/doi/abs/10.1002/pra2.2018.14505501036",
    doi = "10.1002/pra2.2018.14505501036",
    language = "en",
    number = "1",
    urldate = "2019-05-05",
    journal = "Proceedings of the Association for Information Science and Technology",
    year = "2018",
    pages = "327--336"
}
```

Bess Pitmann. Why Archive the Web? Online Searcher, Nov/Dec:53–56, 2018.
[BibTeX▼]

@article{pitmann_why_2018,
    author = "Pitmann, Bess",
    title = "Why {Archive} the {Web}?",
    volume = "Nov/Dec",
    journal = "Online Searcher",
    year = "2018",
    pages = "53--56"
}

Jackie M Dooley, Kate Bowers, OCLC, Research Library Partnership, Web Archiving Metadata Working Group, and OCLC Research. Descriptive metadata for web archiving: recommendations of the OCLC Research Library Partnership Web Archiving Metadata Working Group. OCLC, 2018. ISBN 978-1-55653-016-6 978-1-55653-017-3. OCLC: 1021307921. URL: https://www.oclc.org/content/dam/research/publications/2018/oclcresearch-wam-recommendations.pdf (visited on 2019-05-05).
[abstract▼] [BibTeX▼]

Under the auspices of the OCLC Research Library Partnership Web Archiving Metadata Working Group, recommendations for descriptive metadata best practices for archived web content that would meet end-user needs, enhance discovery and improve metadata consistency. These recommended practices can be used by any institution or person with a need to describe web content.
```
@book{dooley_descriptive_2018,
    author = "Dooley, Jackie M and Bowers, Kate and {OCLC} and {Research Library Partnership} and {Web Archiving Metadata Working Group} and {OCLC Research}",
    title = "Descriptive metadata for web archiving: recommendations of the {OCLC} {Research} {Library} {Partnership} {Web} {Archiving} {Metadata} {Working} {Group}",
    isbn = "978-1-55653-016-6 978-1-55653-017-3",
    url = "https://www.oclc.org/content/dam/research/publications/2018/oclcresearch-wam-recommendations.pdf",
    language = "en",
    urldate = "2019-05-05",
    publisher = "OCLC",
    year = "2018",
    note = "OCLC: 1021307921"
}
```
Software Heritage. Browsing the Software Heritage archive: a guided tour. 2018. URL: https://www.softwareheritage.org/2018/09/22/browsing-the-software-heritage-archive-a-guided-tour/ (visited on 2019-04-21).
[abstract▼] [BibTeX▼]

The Software Heritage mission is to collect, preserve, and share the source code from all publicly available software. An important milestone for the project was enabling access and browsing of the Software Heritage archive, and a year ago we made a first step forward by enabling programmatic access via a RESTful API. On June 7th […]
```
@misc{software_heritage_browsing_2018,
    author = "{Software Heritage}",
    title = "Browsing the {Software} {Heritage} archive: a guided tour",
    url = "https://www.softwareheritage.org/2018/09/22/browsing-the-software-heritage-archive-a-guided-tour/",
    language = "en-US",
    urldate = "2019-04-21",
    year = "2018"
}
```
Niels Brügger. The archived web: doing history in the digital age. MIT Press, 2018. ISBN 978-0-262-35011-2. OCLC: 1062395353. URL: http://search.ebscohost.com/login.aspx?direct=true&scope=site&db=nlebk&db=nlabk&AN=1933809 (visited on 2019-06-16).
[abstract▼] [BibTeX▼]

"How will the history of the present be written? As life continues to move online, the web becomes ever more important for an understanding of the past. This book offers an original theoretical framework for approaching the web of the past, both as a source and as an object of study in its own right"--
```
@book{brugger_archived_2018,
    author = "Brügger, Niels",
    title = "The archived web: doing history in the digital age",
    isbn = "978-0-262-35011-2",
    url = "http://search.ebscohost.com/login.aspx?direct=true\&scope=site\&db=nlebk\&db=nlabk\&AN=1933809",
    language = "English",
    publisher = "MIT Press",
    urldate = "2019-06-16",
    year = "2018",
    note = "OCLC: 1062395353"
}
```
Niels Brügger. The Archived Web. 2018. URL: https://mitpress.mit.edu/books/archived-web (visited on 2019-06-16).
[abstract▼] [BibTeX▼]

An original methodological framework for approaching the archived web, both as a source and as an object of study in its own right. As life continues to move online, the web becomes increasingly important as a source for understanding the past. But historians have yet to formulate a methodology for approaching the archived web as a source of study. How should the history of the present be written? In this book, Niels Brügger offers an original methodological framework for approaching the web of the past, both as a source and as an object of study in its own right. While many studies of the web focus solely on its use and users, Brügger approaches the archived web as a semiotic, textual system in order to offer the first book-length treatment of its scholarly use. While the various forms of the archived web can challenge researchers' interactions with it, they also present a range of possibilities for interpretation. The Archived Web identifies characteristics of the online web that are significant now for scholars, investigates how the online web became the archived web, and explores how the particular digitality of the archived web can affect a historian's research process. Brügger offers suggestions for how to translate traditional historiographic methods for the study of the archived web, focusing on provenance, creating an overview of the archived material, evaluating versions, and citing the material. The Archived Web lays the foundations for doing web history in the digital age, offering important and timely guidance for today's media scholars and tomorrow's historians.
```
@misc{press_archived_nodate,
    author = "{Niels Brügger}",
    title = "The {Archived} {Web}",
    url = "https://mitpress.mit.edu/books/archived-web",
    language = "en",
    urldate = "2019-06-16",
    year = "2018",
    journal = "The MIT Press"
}
```

Roberto Di Cosmo, Morane Gruenpeter, and Stefano Zacchiroli. Identifiers for digital objects: The case of software source code preservation. In iPres 2018. Boston, MA, 2018. URL: https://osf.io/kde56/ (visited on 2019-03-19), doi:10.17605/OSF.IO/KDE56.
[BibTeX▼]

@inproceedings{cosmo_identifiers_2018,
    author = "Cosmo, Roberto Di and Gruenpeter, Morane and Zacchiroli, Stefano",
    address = "Boston, MA",
    title = "Identifiers for digital objects: {The} case of software source code preservation",
    url = "https://osf.io/kde56/",
    doi = "10.17605/OSF.IO/KDE56",
    language = "en",
    urldate = "2019-03-19",
    booktitle = "iPres 2018",
    year = "2018"
}

Jean-François Abramatic, Roberto Di Cosmo, and Stefano Zacchiroli. Building the Universal Archive of Source Code. Communications of the ACM, 61(10):29–31, 2018. URL: http://dl.acm.org/citation.cfm?doid=3281635.3183558 (visited on 2019-03-19), doi:10.1145/3183558.
[BibTeX▼]

@article{abramatic_building_2018,
    author = "Abramatic, Jean-François and Di Cosmo, Roberto and Zacchiroli, Stefano",
    title = "Building the {Universal} {Archive} of {Source} {Code}",
    volume = "61",
    issn = "00010782",
    url = "http://dl.acm.org/citation.cfm?doid=3281635.3183558",
    doi = "10.1145/3183558",
    language = "English",
    number = "10",
    urldate = "2019-03-19",
    journal = "Communications of the ACM",
    year = "2018",
    pages = "29--31"
}

E. Leigh Bonds. First Things First: Conducting an Environmental Scan. January 2018. URL: https://acrl.ala.org/dh/2018/01/31/first-things-first-conducting-an-environmental-scan/ (visited on 2019-04-04).
[abstract▼] [BibTeX▼]

As a digital humanities librarian, E. Leigh Bonds (The Ohio State University) undertook an institutional environmental scan as the basis for assessment, identifying gaps, and developing recommendations. In this post, Bonds details her approach and framework, which prompted conversations and coordination across campus.
```
@misc{bonds_first_2018,
    author = "Bonds, E. Leigh",
    type = "Text",
    title = "First {Things} {First}: {Conducting} an {Environmental} {Scan}",
    copyright = "http://acrl.ala.org/dh/rights-permissions/",
    url = "https://acrl.ala.org/dh/2018/01/31/first-things-first-conducting-an-environmental-scan/",
    language = "en",
    urldate = "2019-04-04",
    journal = "dh+lib",
    month = "January",
    year = "2018"
}
```

Clelia O. Rodriguez. The #shitholes Syllabus: Undoing His(story). Radical Teacher: a socialist, feminist, and anti-racist journal on the theory and practice of teaching, 2018. URL: http://radicalteacher.library.pitt.edu (visited on 2019-06-09), doi:10.5195/rt.2018.456.
[BibTeX▼]

@article{rodriguez_shitholes_2018,
    author = "Rodriguez, Clelia O.",
    title = "The \\#shitholes {Syllabus}: {Undoing} {His}(story)",
    volume = "111",
    issn = "1942-0832",
    url = "http://radicalteacher.library.pitt.edu",
    doi = "10.5195/rt.2018.456",
    language = "English",
    urldate = "2019-06-09",
    journal = "Radical Teacher: a socialist, feminist, and anti-racist journal on the theory and practice of teaching",
    year = "2018"
}

Glenda M. Yenni, Erica M. Christensen, Ellen K. Bledsoe, Sarah R. Supp, Renata M. Diaz, Ethan P. White, and S.K. Morgan Ernest. Developing a modern data workflow for evolving data. bioRxiv, 2018. URL: https://www.biorxiv.org/content/early/2018/07/24/344804, arXiv:https://www.biorxiv.org/content/early/2018/07/24/344804.full.pdf, doi:10.1101/344804.
[abstract▼] [BibTeX▼]

Data management and publication are core components of the research process. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. \textquotedblleftEvolving data\textquotedblright present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a evolving data workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to: 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow uses two tools from software development, version control and continuous integration, to create a modern data management system that automates the pipeline.
```
@article{Yenni344804,
    author = "Yenni, Glenda M. and Christensen, Erica M. and Bledsoe, Ellen K. and Supp, Sarah R. and Diaz, Renata M. and White, Ethan P. and Ernest, S.K. Morgan",
    title = "Developing a modern data workflow for evolving data",
    elocation-id = "344804",
    year = "2018",
    doi = "10.1101/344804",
    publisher = "Cold Spring Harbor Laboratory",
    URL = "https://www.biorxiv.org/content/early/2018/07/24/344804",
    eprint = "https://www.biorxiv.org/content/early/2018/07/24/344804.full.pdf",
    journal = "bioRxiv"
}
```
Matthew Farrell, Edward McCain, Maria Praetzellis, Grace Thomas, and Paige Walker. Web Archiving in the United States: A 2017 Survey. Report, National Digital Stewardship Alliance, 2018. URL: https://osf.io/3QH6N/ (visited on 2019-05-05).
[abstract▼] [BibTeX▼]

From October 2 to November 20, 2017, a working group of individuals representing multiple NDSA member institutions and interest groups conducted a survey of organizations in the United States actively involved in, or planning to start, programs to archive content from the Web. This effort builds upon and extends a broader effort begun in three earlier surveys, which the NDSA Web Archiving Survey working group has conducted since 2011. The goal of these surveys is to better understand the landscape of Web archiving activities in the United States by investigating the organizations involved; the history and scope of their Web archiving programs; the types of Web content being preserved; the tools and services being used; access and discovery services being offered; and overall policies related to Web archiving programs. The responses from this survey document the current state of U.S. Web archiving initiatives and the comparison with the results of the 2011, 2013, and 2016 surveys enables an analysis of emerging trends. This report describes the current state of the field, tracks the evolution of the field over the last few years, and points to future opportunities and developments.
```
@techreport{farrell_web_2018,
    author = "Farrell, Matthew and McCain, Edward and Praetzellis, Maria and Thomas, Grace and Walker, Paige",
    type = "Report",
    title = "Web {Archiving} in the {United} {States}: {A} 2017 {Survey}",
    url = "https://osf.io/3QH6N/",
    language = "en",
    urldate = "2019-05-05",
    year = "2018",
    institution = "National Digital Stewardship Alliance"
}
```
Harriet Alexander, Lisa K Johnson, and Titus Brown. Keeping it light: (re)analyzing community-wide datasets without major infrastructure. GigaScience, December 2018. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350038/ (visited on 2019-05-12), doi:10.1093/gigascience/giy159.
[abstract▼] [BibTeX▼]

DNA sequencing technology has revolutionized the field of biology, shifting biology from a data-limited to data-rich state. Central to the interpretation of sequencing data are the computational tools and approaches that convert raw data into biologically meaningful information. Both the tools and the generation of data are actively evolving, yet the practice of re-analysis of previously generated data with new tools is not commonplace. Re-analysis of existing data provides an affordable means of generating new information and will likely become more routine within biology, yet necessitates a new set of considerations for best practices and resource development. Here, we discuss several practices that we believe to be broadly applicable when re-analyzing data, especially when done by small research groups.
```
@article{alexander_keeping_2018,
    author = "Alexander, Harriet and Johnson, Lisa K and Brown, Titus",
    title = "Keeping it light: (re)analyzing community-wide datasets without major infrastructure",
    volume = "8",
    url = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350038/",
    doi = "10.1093/gigascience/giy159",
    language = "English",
    number = "2",
    urldate = "2019-05-12",
    journal = "GigaScience",
    month = "December",
    year = "2018"
}
```
Morgan G. I. Langille, Jacques Ravel, and W. Florian Fricke. “Available upon request”: not good enough for microbiome data! Microbiome Journal, January 2018. URL: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0394-z (visited on 2019-05-11), doi:https://doi.org/10.1186/s40168-017-0394-z.
[abstract▼] [BibTeX▼]

Open data that is free and publicly available without restrictions is critical for progress in any scientific discipline and has been the cornerstone of sound and reproducible genomics research. Microbiome research is still a relatively young, thriving, active research field, with great biomedical potential. As a large data-driven research field, microbiome projects can include hundreds or even thousands of participants, samples, and associated background (“metadata”) parameters. Processing this data, identifying meaningful associations, and determining significance depends on complex, often non-standardized bioinformatics and biostatistics protocols. Reproducibility, transparency, and expandability of these protocols to review, evaluate, and build upon this work is crucial to fulfill on the promise of microbiome research and maintain credibility. At the absolute minimum, unrestricted access to the raw sequencing data and associated metadata is needed and has been recognized and implemented by the scientific community, some journals, and funding agencies. In practice, access to open protocols for data processing and analysis is also important to promote reproducibility and advances in the field but rarely provided. Unfortunately, there appears to be an increasing number of studies that are failing to satisfy even basic, community-accepted standards.
```
@article{langille_available_2018,
    author = "Langille, Morgan G. I. and Ravel, Jacques and Fricke, W. Florian",
    title = "“{Available} upon request”: not good enough for microbiome data!",
    volume = "6",
    issn = "2049-2618",
    url = "https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0394-z",
    doi = "https://doi.org/10.1186/s40168-017-0394-z",
    language = "English",
    number = "8",
    urldate = "2019-05-11",
    journal = "Microbiome Journal",
    month = "January",
    year = "2018"
}
```

2017

Phoebe Ayers. LibGuides: Citing & publishing software: Publishing research software. 2017. URL: https://libguides.mit.edu/c.php?g=551454&p=3786120 (visited on 2019-07-08).
[abstract▼] [BibTeX▼]

@misc{ayers_libguides:_2017,
    author = "Ayers, Phoebe",
    title = "{LibGuides}: {Citing} \\& publishing software: {Publishing} research software",
    copyright = "Copyright MIT Libraries 2019",
    url = "https://libguides.mit.edu/c.php?g=551454\&p=3786120",
    language = "en",
    urldate = "2019-07-08",
    year = "2017"
}

Paolo Mangiafico. Rethinking Repositories: Time to (re-)focus on the researchers? 2017. URL: https://figshare.com/articles/Rethinking_Repositories_Time_to_re-_focus_on_the_researchers_/4836293 (visited on 2019-07-08), doi:10.6084/m9.figshare.4836293.v1.
[abstract▼] [BibTeX▼]

Slides from a presentation at the Coalition for Networked Information spring meeting in Albuquerque, NM, in April 2017.Abstract from the session:At many institutions, repository initiatives provide access, preservation and services for multiple programs - at-risk digital special collections, digitized materials, and the outputs of research, including publications and data. No single software stack, platform, service portfolio, or even library program can support all of these areas. Given this diffusion of stakeholders, needs, and processes, is there a unifying aspect for the institutional repository? I not, then what do we mean by "institutional repository?" In a time where both the needs of researchers and repository technologies are rapidly evolving, what strategies should libraries employ for developin technology, staffing, services, and policies to provide access and preservation for a wide range of institutional assets? In this panel discussion, repository leaders from the University of North Carolina a d Duke University will start a conversation by describing their approaches, what they have learned, and how they think these services should evolve. They will pose some provocative questions for discussion w th all attendees, and hope to stimulate a better understanding of cohesive approaches for repository programs. Panel convened at the CNI Spring 2017 Membership Meeting with Jason Casden (Head, Software Devel pment at UNC University Libraries), Paolo Mangiafico (Coordinator, Scholarly Communications Technology at Duke University Libraries), and Julie Rudder (Repository Program Librarian at UNC University Libraries).
```
@misc{mangiafico_rethinking_2017,
    author = "Mangiafico, Paolo",
    title = "Rethinking {Repositories}: {Time} to (re-)focus on the researchers?",
    url = "https://figshare.com/articles/Rethinking\_Repositories\_Time\_to\_re-\_focus\_on\_the\_researchers\_/4836293",
    urldate = "2019-07-08",
    year = "2017",
    doi = "10.6084/m9.figshare.4836293.v1"
}
```
Paolo Manghi, Michele Artini, Claudio Atzori, Miriam Baglioni, Alessia Bardi, Sandro1 La Bruzzo, Michele1 De Bonis, Harry2 Dimitropoulos, Ioannis2 Foufoulas, Katerina2 Iatropoulou, Natalia2 Manola, Stefania2 Martziou, and Pedro3 Principe. OpenAIRE: Advancing Open Science. Conference Papers: International Conference on Grey Literature, 19:107–112, 2017. URL: http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=lls&AN=129378527&site=eds-live (visited on 2019-07-03).
[abstract▼] [BibTeX▼]

OpenAIRE, the point of reference for Open Access in Europe, is now addressing the problem of enabling the Open Science paradigm. To this aim it will provide services to: (i) overcome the limits of today's scientific communication landscape, by allowing research communities and the relative e-infrastructures to fully publish, interlink, package and reuse their research artefacts (e.g. literature, data, and software) and their funding grants within the European and global ecosystem as supported/promoted by OpenAIRE, (ii) enable end-users (e.g. researchers, funder officers) to search and consult a rich and up-to-date knowledge graph of research results and (iii) enable scientific and educational information repositories and publishers to subscribe and be notified of changes in the OpenAIRE knowledge graph. These combined actions will bring longterm and immediate benefits to research communities, research organisations, repository managers, and funders by affecting the way research results are disseminated and reused. On the one hand, publishing the interlinked and packaged research literature, data and software via OpenAIRE drives research communities to an Open Science transition in a consistent and interoperable fashion. On the other hand, the resulting infrastructure concretely enables the construction of Open Science oriented services, supporting practices such as machine-assisted research reproducibility and evaluation.
```
@article{manghi_openaire:_2017,
    author = "Manghi, Paolo and Artini, Michele and Atzori, Claudio and Baglioni, Miriam and Bardi, Alessia and La Bruzzo, Sandro1 and De Bonis, Michele1 and Dimitropoulos, Harry2 and Foufoulas, Ioannis2 and Iatropoulou, Katerina2 and Manola, Natalia2 and Martziou, Stefania2 and Principe, Pedro3",
    title = "{OpenAIRE}: {Advancing} {Open} {Science}",
    volume = "19",
    issn = "13862316",
    url = "http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true\&db=lls\&AN=129378527\&site=eds-live",
    urldate = "2019-07-03",
    journal = "Conference Papers: International Conference on Grey Literature",
    year = "2017",
    pages = "107--112"
}
```

Clifford Lynch. Updating the Agenda for Academic Libraries and Scholarly Communications. College & Research Libraries, 78(2):126–130, 2017. URL: https://crl.acrl.org/index.php/crl/article/view/16577 (visited on 2019-07-08), doi:10.5860/crl.78.2.126.
[BibTeX▼]

@article{lynch_updating_2017,
    author = "Lynch, Clifford",
    title = "Updating the {Agenda} for {Academic} {Libraries} and {Scholarly} {Communications}",
    volume = "78",
    issn = "0010-0870, 2150-6701",
    url = "https://crl.acrl.org/index.php/crl/article/view/16577",
    doi = "10.5860/crl.78.2.126",
    language = "en",
    number = "2",
    urldate = "2019-07-08",
    journal = "College \\& Research Libraries",
    year = "2017",
    pages = "126--130"
}

Chris Awre and Richard Green. From Hydra to Samvera: an open source community journey. Insights: the UKSG journal, 30(3):82–88, 2017. URL: http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=lls&AN=130788897&site=eds-live (visited on 2019-07-08), doi:10.1629/uksg.383.
[abstract▼] [BibTeX▼]

The Hydra Project started in 2008 through a partnership between the University of Hull, the University of Virginia, Stanford University and Fedora Commons (now DuraSpace) to create tools that support use of the Fedora digital repository. Hull adopted the software outputs from this collaboration for its institutional repository in 2011 and remains an active Partner in the community, serving on the Steering Group and fostering development of the community and software in the UK and mainland Europe: the community now has 35 formal Partners and over 70 known adopters internationally. In June 2017 Hydra changed its name to Samvera, Icelandic for 'being together', to recognize the value gained from multiple institutions working together to create the underlying common basis upon which multiple different repository solutions have been implemented. Samvera can be adopted through a set of tools to develop your own repository (using a package called Hyrax as the starting point) and is also available as a complete repository solution, hosted or local, through the use of Hyku. The community has been at the heart of making Samvera a success, and will continue to underpin its future direction.
```
@article{awre_hydra_2017,
    author = "Awre, Chris and Green, Richard",
    title = "From {Hydra} to {Samvera}: an open source community journey",
    volume = "30",
    issn = "20487754",
    url = "http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true\&db=lls\&AN=130788897\&site=eds-live",
    doi = "10.1629/uksg.383",
    number = "3",
    urldate = "2019-07-08",
    journal = "Insights: the UKSG journal",
    year = "2017",
    pages = "82--88"
}
```
David Wilcox. Supporting Digital Preservation and Access with Fedora. IFLA WLIC, pages 5, 2017. URL: http://library.ifla.org/1758/1/150-wilcox-en.pdf.
[abstract▼] [BibTeX▼]

Digital preservation is complex, and the vocabulary is not well-defined. A long-term digital preservation and access strategy incorporates many components, and there are levels of preservation to match the risk tolerance and available resources of an institution - there is no "one size fits all" approach. Digital preservation systems with modular components provide the greatest flexibility for organizations to choose an approach that can scale up or down as needed over time. Fedora is an open source, durable repository for digital objects, that is part of a long-term digital preservation and access solution. Fedora is used in a wide variety of institutions including libraries, museums, archives, and government organizations. It is a community-based solution that leverages existing, widely used standards whenever possible to ensure long-term sustainability. Fedora stakeholders from around the world have come together to clearly define how Fedora supports digital preservation, and how it fits into a larger digital preservation solution. This paper will provide an overview of the considerations and complexities of a digital preservation strategy, and describe how Fedora can serve as a key component of a digital preservation and access solution.
```
@article{wilcox_supporting_2017,
    author = "Wilcox, David",
    title = "Supporting {Digital} {Preservation} and {Access} with {Fedora}",
    language = "en",
    journal = "IFLA WLIC",
    year = "2017",
    url = "http://library.ifla.org/1758/1/150-wilcox-en.pdf",
    pages = "5"
}
```

David Wilcox. Fedora, Islandora, & Samvera: Requirements and Gaps. September 2017. URL: https://www.rd-alliance.org/sites/default/files/attachment/2017-09%20RDA-Fedora%20and%20Samvera%20Requirements%20and%20GapsWilcox_0.pdf.
[BibTeX▼]

@misc{wilcox_fedora_2017,
    author = "Wilcox, David",
    title = "Fedora, {Islandora}, \\& {Samvera}: {Requirements} and {Gaps}",
    url = "https://www.rd-alliance.org/sites/default/files/attachment/2017-09\%20RDA-Fedora\%20and\%20Samvera\%20Requirements\%20and\%20GapsWilcox\_0.pdf",
    language = "en",
    month = "September",
    year = "2017"
}

Erin D. Foster and Ariel Deardorff. Open Science Framework (OSF). Journal of the Medical Library Association : JMLA, 105(2):203–206, April 2017. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370619/ (visited on 2019-07-16), doi:10.5195/jmla.2017.88.
[abstract▼] [BibTeX▼]

The Open Science Framework (OSF) is a tool that promotes open, centralized workflows by enabling capture of different aspects and products of the research lifecycle, including developing a research idea, designing a study, storing and analyzing collected data, and writing and publishing reports or papers. It is developed and maintained by the Center for Open Science (COS), a nonprofit organization founded in 2013 that conducts research into scientific practice, builds and supports scientific research communities, and develops research tools and infrastructure to enable managing and archiving research [1]. As an organization, the COS encourages openness, integrity, and reproducibility in research across scientific disciplines [2]. The OSF supports a variety of tools and services to assist in the research process. This review focuses primarily on the core functionality of the OSF, with brief descriptions of some of the other existing tools and services.
```
@article{foster_open_2017,
    author = "Foster, Erin D. and Deardorff, Ariel",
    title = "Open {Science} {Framework} ({OSF})",
    volume = "105",
    issn = "1536-5050",
    url = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370619/",
    doi = "10.5195/jmla.2017.88",
    number = "2",
    urldate = "2019-07-16",
    journal = "Journal of the Medical Library Association : JMLA",
    month = "April",
    year = "2017",
    pmid = "null",
    pmcid = "PMC5370619",
    pages = "203--206"
}
```
Sarah Bond. Dear Scholars, Delete Your Account At Academia.Edu. January 2017. URL: https://www.forbes.com/sites/drsarahbond/2017/01/23/dear-scholars-delete-your-account-at-academia-edu/ (visited on 2019-07-16).
[abstract▼] [BibTeX▼]

As for-profit platforms like Academia.edu look to monetize the dissemination of scholarly writing even further, academics across the globe must now consider alternatives to proprietary companies which profit from our writing. Here are a few suggestions.
```
@misc{bond_dear_2017,
    author = "Bond, Sarah",
    title = "Dear {Scholars}, {Delete} {Your} {Account} {At} {Academia}.{Edu}",
    url = "https://www.forbes.com/sites/drsarahbond/2017/01/23/dear-scholars-delete-your-account-at-academia-edu/",
    language = "en",
    urldate = "2019-07-16",
    journal = "Forbes",
    month = "January",
    year = "2017"
}
```

European Commission. Open Science Monitoring - Impact Case Study Zenodo. Technical Report, European Commission, 2017. URL: https://ec.europa.eu/research/openscience/pdf/monitor/zenodo_case_study.pdf (visited on 2019-07-11).
[BibTeX▼]

@techreport{european_commission_open_2017,
    author = "{European Commission}",
    title = "Open {Science} {Monitoring} - {Impact} {Case} {Study} {Zenodo}",
    url = "https://ec.europa.eu/research/openscience/pdf/monitor/zenodo\_case\_study.pdf",
    institution = "{European Commission}",
    urldate = "2019-07-11",
    year = "2017"
}

Herbert Van de Sompel. Scholarly Communication: Deconstruct & Decentralize? December 2017. URL: https://www.youtube.com/watch?v=o4nUe-6Ln-8 (visited on 2019-07-09).
[BibTeX▼]

@misc{herbert_van_de_sompel_scholarly_2017,
    author = "{Herbert Van de Sompel}",
    address = "Washington, D. C.",
    title = "Scholarly {Communication}: {Deconstruct} \\& {Decentralize}?",
    url = "https://www.youtube.com/watch?v=o4nUe-6Ln-8",
    urldate = "2019-07-09",
    month = "December",
    year = "2017"
}

Ethan Gruber. Open Access, Academia.edu, and why I’m all-in on Zenodo.org \textbar Pocket Change. January 2017. URL: http://numismatics.org/pocketchange/open-access-academia-edu-and-why-im-all-in-on-zenodo-org/ (visited on 2019-07-11).
[BibTeX▼]

@misc{gruber_open_2017,
    author = "Gruber, Ethan",
    title = "Open {Access}, {Academia}.edu, and why {I}’m all-in on {Zenodo}.org {\textbar} {Pocket} {Change}",
    url = "http://numismatics.org/pocketchange/open-access-academia-edu-and-why-im-all-in-on-zenodo-org/",
    language = "en-US",
    urldate = "2019-07-11",
    journal = "Pocket Change",
    month = "January",
    year = "2017"
}

Kevin Smith. Join the Movement: The 2.5% Commitment – IO: In The Open. 2017. URL: http://intheopen.net/2017/09/join-the-movement-the-2-5-commitment/ (visited on 2019-07-10).
[BibTeX▼]

@misc{smith_join_2017,
    author = "Smith, Kevin",
    title = "Join the {Movement}: {The} 2.5\\% {Commitment} – {IO}: {In} {The} {Open}",
    url = "http://intheopen.net/2017/09/join-the-movement-the-2-5-commitment/",
    language = "en-US",
    urldate = "2019-07-10",
    journal = "IO - In the Open",
    year = "2017"
}

Shan Sutton. Accelerating academy-owned publishing. November 2017. URL: http://intheopen.net/2017/11/accelerating-academy-owned-publishing/ (visited on 2019-07-10).
[BibTeX▼]

@misc{sutton_accelerating_2017,
    author = "Sutton, Shan",
    title = "Accelerating academy-owned publishing",
    url = "http://intheopen.net/2017/11/accelerating-academy-owned-publishing/",
    language = "en-US",
    urldate = "2019-07-10",
    journal = "IO - In the Open",
    month = "November",
    year = "2017"
}

Mark D. Wilkinson, Ruben Verborgh, Luiz Olavo Bonino da Silva Santos, Tim Clark, Morris A. Swertz, Fleur D. L. Kelpin, Alasdair J. G. Gray, Erik A. Schultes, Erik M. van Mulligen, Paolo Ciccarese, Arnold Kuzniar, Anand Gavai, Mark Thompson, Rajaram Kaliyaperumal, Jerven T. Bolleman, and Michel Dumontier. Interoperability and FAIRness through a novel combination of Web technologies. PeerJ Computer Science, 3:e110, April 2017. URL: https://peerj.com/articles/cs-110 (visited on 2019-07-11), doi:10.7717/peerj-cs.110.
[abstract▼] [BibTeX▼]

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.
```
@article{wilkinson_interoperability_2017,
    author = "Wilkinson, Mark D. and Verborgh, Ruben and Santos, Luiz Olavo Bonino da Silva and Clark, Tim and Swertz, Morris A. and Kelpin, Fleur D. L. and Gray, Alasdair J. G. and Schultes, Erik A. and Mulligen, Erik M. van and Ciccarese, Paolo and Kuzniar, Arnold and Gavai, Anand and Thompson, Mark and Kaliyaperumal, Rajaram and Bolleman, Jerven T. and Dumontier, Michel",
    title = "Interoperability and {FAIRness} through a novel combination of {Web} technologies",
    volume = "3",
    issn = "2376-5992",
    url = "https://peerj.com/articles/cs-110",
    doi = "10.7717/peerj-cs.110",
    language = "en",
    urldate = "2019-07-11",
    journal = "PeerJ Computer Science",
    month = "April",
    year = "2017",
    pages = "e110"
}
```
Isabella Peters, Peter Kraker, Elisabeth Lex, Christian Gumpenberger, and Juan Ignacio Gorraiz. Zenodo in the Spotlight of Traditional and New Metrics. Frontiers in Research Metrics and Analytics, 2017. URL: https://www.frontiersin.org/articles/10.3389/frma.2017.00013/full (visited on 2019-07-11), doi:10.3389/frma.2017.00013.
[abstract▼] [BibTeX▼]

In this case study, we aim to explore the characteristics and the reception of files uploaded to Zenodo and the role the repository plays itself in generating usage. To this end, we first apply descriptive statistics on Zenodo’s full set of data record metadata with DOIs until and including January 2017 (n=141,777 records). Second, we estimate the coverage of Zenodo datasets in the Data Citation Index (DCI) as well as of Zenodo journal articles in the Science Citation Index (SCI), Social Science Citation Index (SSCI) and Arts and Humanities Citation Index (A\&HCI), Zenodo books and book chapters in the Book Citation Index, and Zenodo conference papers in the Proceedings Citation Index, and analyse their citedness according to the different data record types in Zenodo (e.g., journal article, dataset, book, or conference paper). Third, we provide a bibliometric analysis of Zenodo records by using different metrics for citedness, including citation, usage and altmetrics. Altmetrics data are gathered from two of the most popular tools for altmetric analyses, PlumX and Altmetric.com, and we compare the results. Moreover, we study how open access and DOIs provided by Zenodo influence the impact of Zenodo data records and we find a tendency towards a positive relationship between permissive access rights and altmetrics in certain data records.
```
@article{peters_zenodo_2017,
    author = "Peters, Isabella and Kraker, Peter and Lex, Elisabeth and Gumpenberger, Christian and Gorraiz, Juan Ignacio",
    title = "Zenodo in the {Spotlight} of {Traditional} and {New} {Metrics}",
    volume = "2",
    issn = "2504-0537",
    url = "https://www.frontiersin.org/articles/10.3389/frma.2017.00013/full",
    doi = "10.3389/frma.2017.00013",
    language = "English",
    urldate = "2019-07-11",
    journal = "Frontiers in Research Metrics and Analytics",
    year = "2017"
}
```

Zenodo. Zenodo now supports DOI versioning! 2017. URL: https://blog.zenodo.org/2017/05/30/doi-versioning-launched/ (visited on 2019-07-19).
[BibTeX▼]

@misc{vers_zenodo_2017,
    author = "Zenodo",
    title = "Zenodo now supports {DOI} versioning!",
    url = "https://blog.zenodo.org/2017/05/30/doi-versioning-launched/",
    urldate = "2019-07-19",
    year = "2017"
}

Greg Wilson, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, and Tracy K. Teal. Good enough practices in scientific computing. PLoS Computational Biology, 13(6):20, June 2017. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5480810/ (visited on 2019-04-25), doi:10.1371/journal.pcbi.1005510.
[abstract▼] [BibTeX▼]

Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.
```
@article{wilson_good_2017,
    author = "Wilson, Greg and Bryan, Jennifer and Cranston, Karen and Kitzes, Justin and Nederbragt, Lex and Teal, Tracy K.",
    editor = "Ouellette, Francis",
    title = "Good enough practices in scientific computing",
    volume = "13",
    url = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5480810/",
    doi = "10.1371/journal.pcbi.1005510",
    language = "English",
    number = "6",
    urldate = "2019-04-25",
    journal = "PLoS Computational Biology",
    month = "June",
    year = "2017",
    pages = "20"
}
```
Megan Squire. The Lives and Deaths of Open Source Code Forges. In Proceedings of the 13th International Symposium on Open Collaboration - OpenSym '17, 1–8. Galway, Ireland, 2017. ACM Press. URL: http://dl.acm.org/citation.cfm?doid=3125433.3125468 (visited on 2019-04-05), doi:10.1145/3125433.3125468.
[abstract▼] [BibTeX▼]

Code forges are third party software repositories that also provide various tools and facilities for distributed software development teams to use, including source code control systems, mailing lists and communication forums, bug tracking systems, web hosting space, and so on. The main contributions of this paper are to present some new data sets relating to the technology adoption lifecycles of a group of six free, libre, and open source software (FLOSS) code forges, and to compare the lifecycles of the forges to each other and to the model presented by classical Diffusion of Innovation (DoI) theory. We find that the observed adoption patterns of code forges rarely follow the DoI model, especially as larger code forges are beset by spam and abuse. The only forge exhibiting a DoI-like lifecycle was a smaller, community-managed, special-purpose forge whose demise was planned in advance. The results of this study will be useful in explaining adoption trajectories, both to practitioners building collaborative FLOSS ecosystems and to researchers who study the evolution and adoption of socio-technical systems.
```
@inproceedings{squire_lives_2017,
    author = "Squire, Megan",
    address = "Galway, Ireland",
    title = "The {Lives} and {Deaths} of {Open} {Source} {Code} {Forges}",
    isbn = "978-1-4503-5187-4",
    url = "http://dl.acm.org/citation.cfm?doid=3125433.3125468",
    doi = "10.1145/3125433.3125468",
    language = "en",
    urldate = "2019-04-05",
    booktitle = "Proceedings of the 13th {International} {Symposium} on {Open} {Collaboration} - {OpenSym} '17",
    publisher = "ACM Press",
    year = "2017",
    pages = "1--8"
}
```

Fernando Rios, Bridget Almas, Nicole Contaxis, Paula Jabloner, and Heidi Kelly. Exploring Curation-ready Software: Use Cases. 2017. URL: https://osf.io/8rz9e/ (visited on 2019-03-29), doi:10.17605/OSF.IO/8RZ9E.
[BibTeX▼]

@misc{rios_exploring_2017,
    author = "Rios, Fernando and Almas, Bridget and Contaxis, Nicole and Jabloner, Paula and Kelly, Heidi",
    title = "Exploring {Curation}-ready {Software}: {Use} {Cases}",
    url = "https://osf.io/8rz9e/",
    urldate = "2019-03-29",
    publisher = "Open Science Framework",
    year = "2017",
    doi = "10.17605/OSF.IO/8RZ9E"
}

Jessica Meyerson, Zac Vowell, Wendy Hagenmaier, Aliza Leventhal, Elizabeth Russey Roke, Fernando Rios, and Tim Walsh. The Software Preservation Network (SPN): A Community Effort to Ensure Long Term Access to Digital Cultural Heritage. D-Lib Magazine, May 2017. URL: http://www.dlib.org/dlib/may17/meyerson/05meyerson.html (visited on 2019-03-29), doi:10.1045/may2017-meyerson.
[BibTeX▼]

@article{meyerson_software_2017,
    author = "Meyerson, Jessica and Vowell, Zac and Hagenmaier, Wendy and Leventhal, Aliza and Roke, Elizabeth Russey and Rios, Fernando and Walsh, Tim",
    title = "The {Software} {Preservation} {Network} ({SPN}): {A} {Community} {Effort} to {Ensure} {Long} {Term} {Access} to {Digital} {Cultural} {Heritage}",
    volume = "23",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/may17/meyerson/05meyerson.html",
    doi = "10.1045/may2017-meyerson",
    language = "en",
    number = "5/6",
    urldate = "2019-03-29",
    journal = "D-Lib Magazine",
    month = "May",
    year = "2017"
}

Kim Dulin and Adam Ziegler. Scaling Up Perma.cc: Ensuring the Integrity of the Digital Scholarly Record. D-Lib Magazine, May 2017. URL: http://www.dlib.org/dlib/may17/dulin/05dulin.html (visited on 2019-03-29), doi:10.1045/may2017-dulin.
[BibTeX▼]

@article{dulin_scaling_2017,
    author = "Dulin, Kim and Ziegler, Adam",
    title = "Scaling {Up} {Perma}.cc: {Ensuring} the {Integrity} of the {Digital} {Scholarly} {Record}",
    volume = "23",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/may17/dulin/05dulin.html",
    doi = "10.1045/may2017-dulin",
    language = "en",
    number = "5/6",
    urldate = "2019-03-29",
    journal = "D-Lib Magazine",
    month = "May",
    year = "2017"
}

Trevor Owens. The Theory and Craft of Digital Preservation. The LIS Scholarship Archive, July 2017. URL: https://osf.io/preprints/lissa/5cpjt/ (visited on 2019-03-29), doi:10.31229/osf.io/5cpjt.
[abstract▼] [BibTeX▼]

The historical record is increasingly digital. Over the last half century, under headings of “electronic records management” and “digital preservation,” librarians, archivists, and curators have established practices to ensure that our digital scientific, social and cultural record will be available to scholars and researchers into the future. This book is intended as a point of entry into that theory and practice. The book serves as both a basic introduction to the issues and practices of digital preservation and a theoretical framework for deliberately and intentionally approaching digital preservation as a field with multiple lineages. The intended audience is current and emerging library, archive, and museum professionals as well as the scholars and researchers who interface with these fields.
```
@article{owens_theory_2017,
    author = "Owens, Trevor",
    title = "The {Theory} and {Craft} of {Digital} {Preservation}",
    url = "https://osf.io/preprints/lissa/5cpjt/",
    doi = "10.31229/osf.io/5cpjt",
    journal = "The LIS Scholarship Archive",
    urldate = "2019-03-29",
    month = "July",
    year = "2017"
}
```

Roberto Di Cosmo and Stefano Zacchiroli. Software Heritage: Why and How to Preserve Software Source Code. In iPRES 2017 - 14th International Conference on Digital Preservation, 1–10. Kyoto, Japan, September 2017. URL: https://hal.archives-ouvertes.fr/hal-01590958 (visited on 2019-03-26).
[BibTeX▼]

@inproceedings{di_cosmo_software_2017,
    author = "Di Cosmo, Roberto and Zacchiroli, Stefano",
    address = "Kyoto, Japan",
    title = "Software {Heritage}: {Why} and {How} to {Preserve} {Software} {Source} {Code}",
    url = "https://hal.archives-ouvertes.fr/hal-01590958",
    urldate = "2019-03-26",
    booktitle = "{iPRES} 2017 - 14th {International} {Conference} on {Digital} {Preservation}",
    month = "September",
    year = "2017",
    pages = "1--10"
}

Miguel Costa, Daniel Gomes, and Mário J. Silva. The evolution of web archiving. International Journal on Digital Libraries, 18(3):191–205, 2017. URL: http://link.springer.com/10.1007/s00799-016-0171-9 (visited on 2019-05-05), doi:10.1007/s00799-016-0171-9.
[abstract▼] [BibTeX▼]

Web archives preserve information published on the web or digitized from printed publications. Much of this information is unique and historically valuable. However, the lack of knowledge about the global status of web archiving initiatives hamper their improvement and collaboration. To overcome this problem, we conducted two surveys, in 2010 and 2014, which provide a comprehensive characterization on web archiving initiatives and their evolution. We identiﬁed several patterns and trends that highlight challenges and opportunities. We discuss these patterns and trends that enable to deﬁne strategies, estimate resources and provide guidelines for research and development of better technology. Our results show that during the last years there was a signiﬁcant growth in initiatives and countries hosting these initiatives, volume of data and number of contents preserved. While this indicates that the web archiving community is dedicating a growing effort on preserving digital information, other results presented throughout the paper raise concerns such as the small amount of archived data in comparison with the amount of data that is being published online.
```
@article{costa_evolution_2017,
    author = "Costa, Miguel and Gomes, Daniel and Silva, Mário J.",
    title = "The evolution of web archiving",
    volume = "18",
    issn = "1432-5012, 1432-1300",
    url = "http://link.springer.com/10.1007/s00799-016-0171-9",
    doi = "10.1007/s00799-016-0171-9",
    language = "en",
    number = "3",
    urldate = "2019-05-05",
    journal = "International Journal on Digital Libraries",
    year = "2017",
    pages = "191--205"
}
```

Vicky Steeves. Reproducibility Librarianship. Collaborative Librarianship, July 2017. URL: https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4.
[BibTeX▼]

@article{steeves_reproducibility_2017,
    author = "Steeves, Vicky",
    title = "Reproducibility {Librarianship}",
    volume = "9",
    issn = "1943-7528",
    url = "https://digitalcommons.du.edu/collaborativelibrarianship/vol9/iss2/4",
    language = "en",
    number = "2",
    journal = "Collaborative Librarianship",
    month = "July",
    year = "2017"
}

ACRL. Environmental Scan 2017. Technical Report, Association of College and Research Libraries, March 2017. URL: http://www.ala.org/acrl/sites/ala.org.acrl/files/content/publications/whitepapers/EnvironmentalScan2017.pdf.
[BibTeX▼]

@techreport{acrl_environmental_2017,
    author = "{ACRL}",
    title = "Environmental {Scan} 2017",
    url = "http://www.ala.org/acrl/sites/ala.org.acrl/files/content/publications/whitepapers/EnvironmentalScan2017.pdf",
    language = "en",
    institution = "{Association of College and Research Libraries}",
    month = "March",
    year = "2017",
    pages = "54"
}

Vicky Steeves. How GitLab can help in research reproducibility. August 2017. URL: https://about.gitlab.com/2017/08/25/gitlab-and-reproducibility/ (visited on 2019-05-06).
[abstract▼] [BibTeX▼]

NYU reproducibility librarian Vicky Steeves shares why GitLab is her choice for ongoing collaborative research, and how it can help overcome challenges with sharing code in academia.
```
@misc{steeves_how_2017,
    author = "Steeves, Vicky",
    type = "Blog",
    title = "How {GitLab} can help in research reproducibility",
    url = "https://about.gitlab.com/2017/08/25/gitlab-and-reproducibility/",
    language = "English",
    urldate = "2019-05-06",
    month = "August",
    year = "2017"
}
```

2016

101 Innovations. GitHub and more: sharing data & code. October 2016. URL: https://101innovations.wordpress.com/2016/10/09/github-and-more-sharing-data-code/ (visited on 2019-07-08).
[abstract▼] [BibTeX▼]

A recent Nature News article ‘Democratic databases: Science on GitHub’ discussed GitHub and other programs used for sharing code and data. Our survey results can provide another measure…
```
@misc{innovations_github_2016,
    author = "Innovations, 101",
    title = "{GitHub} and more: sharing data \\& code",
    url = "https://101innovations.wordpress.com/2016/10/09/github-and-more-sharing-data-code/",
    language = "en",
    urldate = "2019-07-08",
    journal = "Innovations in Scholarly Communication",
    month = "October",
    year = "2016"
}
```

Richard Poynder. Open and Shut?: Q&A with CNI’s Clifford Lynch: Time to re-think the institutional repository? September 2016. URL: https://poynder.blogspot.com/2016/09/q-with-cnis-clifford-lynch-time-to-re_22.html (visited on 2019-07-08).
[BibTeX▼]

@misc{poynder_open_2016,
    author = "Poynder, Richard",
    title = "Open and {Shut}?: {Q}\\&{A} with {CNI}’s {Clifford} {Lynch}: {Time} to re-think the institutional repository?",
    url = "https://poynder.blogspot.com/2016/09/q-with-cnis-clifford-lynch-time-to-re\_22.html",
    urldate = "2019-07-08",
    journal = "Open and Shut?",
    month = "September",
    year = "2016"
}

Jake Vanderplas. Driving Reproducibility at UW. April 2016.
[BibTeX▼]

@misc{vanderplas_driving_2016,
    author = "Vanderplas, Jake",
    address = "Brooklyn, NY",
    type = "Presentation",
    title = "Driving {Reproducibility} at {UW}",
    language = "English",
    month = "April",
    year = "2016"
}

Jeffrey Perkel. Democratic databases: science on GitHub. Nature News, 538(7623):127, October 2016. URL: http://www.nature.com/news/democratic-databases-science-on-github-1.20719 (visited on 2019-07-17), doi:10.1038/538127a.
[abstract▼] [BibTeX▼]

@article{perkel_democratic_2016,
    author = "Perkel, Jeffrey",
    title = "Democratic databases: science on {GitHub}",
    volume = "538",
    url = "http://www.nature.com/news/democratic-databases-science-on-github-1.20719",
    doi = "10.1038/538127a",
    language = "en",
    number = "7623",
    urldate = "2019-07-17",
    journal = "Nature News",
    month = "October",
    year = "2016",
    pages = "127"
}

Alan Hyndman. Figshare launches revamped GitHub integration. 2016. URL: https://figshare.com/blog/figshare_launches_revamped_GitHub_integration/243 (visited on 2019-07-14).
[BibTeX▼]

@misc{hyndman_figshare_2016,
    author = "Hyndman, Alan",
    title = "figshare launches revamped {GitHub} integration",
    url = "https://figshare.com/blog/figshare\_launches\_revamped\_GitHub\_integration/243",
    urldate = "2019-07-14",
    year = "2016"
}

Arfon M. Smith, Daniel S. Katz, and Kyle E. Niemeyer. Software citation principles. PeerJ Computer Science, 2:e86, September 2016. URL: https://peerj.com/articles/cs-86 (visited on 2019-07-15), doi:10.7717/peerj-cs.86.
[abstract▼] [BibTeX▼]

Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.
```
@article{smith_software_2016,
    author = "Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E.",
    title = "Software citation principles",
    volume = "2",
    issn = "2376-5992",
    url = "https://peerj.com/articles/cs-86",
    doi = "10.7717/peerj-cs.86",
    language = "en",
    urldate = "2019-07-15",
    journal = "PeerJ Computer Science",
    month = "September",
    year = "2016",
    pages = "e86"
}
```

Uknown. SciTechSociety: Let IR RIP. July 2016. URL: http://scitechsociety.blogspot.com/2016/07/let-ir-rip.html (visited on 2019-07-09).
[BibTeX▼]

@misc{uknown_scitechsociety:_2016,
    author = "{Uknown}",
    title = "{SciTechSociety}: {Let} {IR} {RIP}",
    url = "http://scitechsociety.blogspot.com/2016/07/let-ir-rip.html",
    urldate = "2019-07-09",
    journal = "SciTechSociety",
    month = "July",
    year = "2016"
}

GitHub. Making Your Code Citable · GitHub Guides. 2016. URL: https://guides.github.com/activities/citable-code/ (visited on 2019-07-11).
[BibTeX▼]

@misc{github_making_2016,
    author = "{GitHub}",
    title = "Making {Your} {Code} {Citable} · {GitHub} {Guides}",
    url = "https://guides.github.com/activities/citable-code/",
    urldate = "2019-07-11",
    year = "2016"
}

Janne Nielsen. Using web archives in research: an introduction. NetLab, 2016. ISBN 978-87-93533-00-4. OCLC: 960018046. URL: http://www.netlab.dk/wp-content/uploads/2016/10/Nielsen_Using_Web_Archives_in_Research.pdf.
[BibTeX▼]

@book{nielsen_using_2016,
    author = "Nielsen, Janne",
    title = "Using web archives in research: an introduction",
    isbn = "978-87-93533-00-4",
    url = "http://www.netlab.dk/wp-content/uploads/2016/10/Nielsen\_Using\_Web\_Archives\_in\_Research.pdf",
    language = "en",
    publisher = "NetLab",
    year = "2016",
    note = "OCLC: 960018046"
}

Helge Holzmann, Wolfram Sperber, and Mila Runnwerth. Archiving Software Surrogates on the Web for Future Reference. arXiv, 9819:215–226, 2016. URL: http://arxiv.org/abs/1702.01163 (visited on 2019-05-05), doi:10.1007/978-3-319-43997-6_17.
[abstract▼] [BibTeX▼]

Software has long been established as an essential aspect of the scientific process in mathematics and other disciplines. However, reliably referencing software in scientific publications is still challenging for various reasons. A crucial factor is that software dynamics with temporal versions or states are difficult to capture over time. We propose to archive and reference surrogates instead, which can be found on the Web and reflect the actual software to a remarkable extent. Our study shows that about a half of the webpages of software are already archived with almost all of them including some kind of documentation.
```
@article{holzmann_archiving_2016,
    author = "Holzmann, Helge and Sperber, Wolfram and Runnwerth, Mila",
    title = "Archiving {Software} {Surrogates} on the {Web} for {Future} {Reference}",
    volume = "9819",
    url = "http://arxiv.org/abs/1702.01163",
    doi = "10.1007/978-3-319-43997-6\_17",
    urldate = "2019-05-05",
    journal = "arXiv",
    year = "2016",
    pages = "215--226"
}
```
Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Robert M. Flight, Kai Blin, and Juan Antonio Vizcaíno. Ten Simple Rules for Taking Advantage of Git and GitHub. PLoS Computational Biology, July 2016. URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004947 (visited on 2019-05-02), doi:https://doi.org/10.1371/journal.pcbi.1004947.
[abstract▼] [BibTeX▼]

Bioinformatics is a broad discipline in which one common denominator is the need to produce and/or use software that can be applied to biological data in different contexts. To enable and ensure the replicability and traceability of scientific claims, it is essential that the scientific publication, the corresponding datasets, and the data analysis are made publicly available [1,2]. All software used for the analysis should be either carefully documented (e.g., for commercial software) or, better yet, openly shared and directly accessible to others [3,4]. The rise of openly available software and source code alongside concomitant collaborative development is facilitated by the existence of several code repository services such as SourceForge, Bitbucket, GitLab, and GitHub, among others. These resources are also essential for collaborative software projects because they enable the organization and sharing of programming tasks between different remote contributors. Here, we introduce the main features of GitHub, a popular web-based platform that offers a free and integrated environment for hosting the source code, documentation, and project-related web content for open-source projects. GitHub also offers paid plans for private repositories (see Box 1) for individuals and businesses as well as free plans including private repositories for research and educational use.
```
@article{perez-riverol_ten_2016,
    author = "Perez-Riverol, Yasset and Gatto, Laurent and Wang, Rui and Sachsenberg, Timo and Uszkoreit, Julian and da Veiga Leprevost, Felipe and Fufezan, Christian and Ternent, Tobias and Eglen, Stephen J. and Katz, Daniel S. and Pollard, Tom J. and M. Flight, Robert and Blin, Kai and Vizcaíno, Juan Antonio",
    title = "Ten {Simple} {Rules} for {Taking} {Advantage} of {Git} and {GitHub}",
    volume = "12",
    url = "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004947",
    doi = "https://doi.org/10.1371/journal.pcbi.1004947",
    language = "English",
    number = "7",
    urldate = "2019-05-02",
    journal = "PLoS Computational Biology",
    month = "July",
    year = "2016"
}
```

Arjun Raj. From reproducibility to over-reproducibility. February 2016. URL: http://rajlaboratory.blogspot.com/2016/02/from-reproducibility-to-over.html (visited on 2019-04-25).
[BibTeX▼]

@misc{raj_reproducibility_2016,
    author = "Raj, Arjun",
    type = "Blog",
    title = "From reproducibility to over-reproducibility",
    url = "http://rajlaboratory.blogspot.com/2016/02/from-reproducibility-to-over.html",
    language = "English",
    urldate = "2019-04-25",
    journal = "RajLab",
    month = "February",
    year = "2016"
}

Arjun Raj. From over-reproducibility to a reproducibility wish-list. March 2016. URL: http://rajlaboratory.blogspot.com/2016/03/from-over-reproducibility-to.html (visited on 2019-04-25).
[BibTeX▼]

@misc{raj_over-reproducibility_2016,
    author = "Raj, Arjun",
    type = "Blog",
    title = "From over-reproducibility to a reproducibility wish-list",
    url = "http://rajlaboratory.blogspot.com/2016/03/from-over-reproducibility-to.html",
    language = "English",
    urldate = "2019-04-25",
    journal = "RajLab",
    month = "March",
    year = "2016"
}

Justin F. Brunelle, Mat Kelly, Michele C. Weigle, and Michael L. Nelson. The impact of JavaScript on archivability. International Journal on Digital Libraries, 17(2):95–117, 2016. URL: http://link.springer.com/10.1007/s00799-015-0140-8 (visited on 2019-05-05), doi:10.1007/s00799-015-0140-8.
[BibTeX▼]

@article{brunelle_impact_2016,
    author = "Brunelle, Justin F. and Kelly, Mat and Weigle, Michele C. and Nelson, Michael L.",
    title = "The impact of {JavaScript} on archivability",
    volume = "17",
    issn = "1432-5012, 1432-1300",
    url = "http://link.springer.com/10.1007/s00799-015-0140-8",
    doi = "10.1007/s00799-015-0140-8",
    language = "en",
    number = "2",
    urldate = "2019-05-05",
    journal = "International Journal on Digital Libraries",
    year = "2016",
    pages = "95--117"
}

Shawn M. Jones, Herbert Van de Sompel, Harihar Shankar, Martin Klein, Richard Tobin, and Claire Grover. Scholarly Context Adrift: Three out of Four URI References Lead to Changed Content. PLOS ONE, 11(12):e0167475, December 2016. URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167475 (visited on 2019-05-30), doi:10.1371/journal.pone.0167475.
[abstract▼] [BibTeX▼]

Increasingly, scholarly articles contain URI references to “web at large” resources including project web sites, scholarly wikis, ontologies, online debates, presentations, blogs, and videos. Authors reference such resources to provide essential context for the research they report on. A reader who visits a web at large resource by following a URI reference in an article, some time after its publication, is led to believe that the resource’s content is representative of what the author originally referenced. However, due to the dynamic nature of the web, that may very well not be the case. We reuse a dataset from a previous study in which several authors of this paper were involved, and investigate to what extent the textual content of web at large resources referenced in a vast collection of Science, Technology, and Medicine (STM) articles published between 1997 and 2012 has remained stable since the publication of the referencing article. We do so in a two-step approach that relies on various well-established similarity measures to compare textual content. In a first step, we use 19 web archives to find snapshots of referenced web at large resources that have textual content that is representative of the state of the resource around the time of publication of the referencing paper. We find that representative snapshots exist for about 30\% of all URI references. In a second step, we compare the textual content of representative snapshots with that of their live web counterparts. We find that for over 75\% of references the content has drifted away from what it was when referenced. These results raise significant concerns regarding the long term integrity of the web-based scholarly record and call for the deployment of techniques to combat these problems.
```
@article{jones_scholarly_2016,
    author = "Jones, Shawn M. and Sompel, Herbert Van de and Shankar, Harihar and Klein, Martin and Tobin, Richard and Grover, Claire",
    title = "Scholarly {Context} {Adrift}: {Three} out of {Four} {URI} {References} {Lead} to {Changed} {Content}",
    volume = "11",
    issn = "1932-6203",
    url = "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167475",
    doi = "10.1371/journal.pone.0167475",
    language = "en",
    number = "12",
    urldate = "2019-05-30",
    journal = "PLOS ONE",
    month = "December",
    year = "2016",
    pages = "e0167475"
}
```

Gail Truman. Web Archiving Environmental Scan. Harvard Library Report, 2016. URL: https://dash.harvard.edu/handle/1/25658314 (visited on 2019-05-28).
[BibTeX▼]

@article{truman_web_2016,
    author = "Truman, Gail",
    title = "Web {Archiving} {Environmental} {Scan}",
    copyright = "Gail Truman",
    url = "https://dash.harvard.edu/handle/1/25658314",
    language = "en\\_US",
    urldate = "2019-05-28",
    journal = "Harvard Library Report",
    year = "2016"
}

2015

Megan Potter and Tim Smith. Making code citable with Zenodo and GitHub \textbar Software Sustainability Institute. 2015. URL: https://www.software.ac.uk/blog/2016-09-26-making-code-citable-zenodo-and-github (visited on 2019-07-08).
[BibTeX▼]

@misc{potter_making_2015,
    author = "Potter, Megan and Smith, Tim",
    title = "Making code citable with {Zenodo} and {GitHub} {\textbar} {Software} {Sustainability} {Institute}",
    url = "https://www.software.ac.uk/blog/2016-09-26-making-code-citable-zenodo-and-github",
    urldate = "2019-07-08",
    year = "2015"
}

Jill Lepore. The cobweb: Can the Internet be archived? The New Yorker, January 2015. URL: https://www.newyorker.com/magazine/2015/01/26/cobweb (visited on 2019-04-16).
[abstract▼] [BibTeX▼]

@article{lepore_cobweb:_2015,
    author = "Lepore, Jill",
    title = "The cobweb: {Can} the {Internet} be archived?",
    issn = "0028-792X",
    url = "https://www.newyorker.com/magazine/2015/01/26/cobweb",
    language = "en",
    urldate = "2019-04-16",
    journal = "The New Yorker",
    month = "January",
    year = "2015"
}

Carol Goble. Results Vary: The Pragmatics of Reproducibility and Research Object Frameworks. March 2015. URL: https://www.slideshare.net/carolegoble/i-conference2015-goblefinalupload (visited on 2019-04-29).
[BibTeX▼]

@misc{goble_results_2015,
    author = "Goble, Carol",
    address = "Newport Beach, Los Angeles",
    type = "Keynote presentation",
    title = "Results {Vary}: {The} {Pragmatics} of {Reproducibility} and {Research} {Object} {Frameworks}",
    url = "https://www.slideshare.net/carolegoble/i-conference2015-goblefinalupload",
    language = "English",
    urldate = "2019-04-29",
    month = "March",
    year = "2015"
}

Arjun Raj. Will reproducibility reduce the need for supplementary figures? December 2015. URL: http://rajlaboratory.blogspot.com/2015/12/will-reproducibility-reduce-need-for.html (visited on 2019-04-25).
[BibTeX▼]

@misc{raj_will_2015,
    author = "Raj, Arjun",
    type = "Blog",
    title = "Will reproducibility reduce the need for supplementary figures?",
    url = "http://rajlaboratory.blogspot.com/2015/12/will-reproducibility-reduce-need-for.html",
    language = "English",
    urldate = "2019-04-25",
    journal = "RajLab",
    month = "December",
    year = "2015"
}

Robin Camille Davis. Git and GitHub for Librarians. Behavioral & Social Sciences Librarian, 34(3):159–164, August 2015. URL: https://academicworks.cuny.edu/jj_pubs/34/ (visited on 2019-04-25), doi:https://doi.org/10.1080/01639269.2015.1062586.
[abstract▼] [BibTeX▼]

One of the fastest-growing professional social networks is GitHub, an online space to share code. GitHub is based on free and open-source software called Git, a version control system used in many digital projects, from library websites to government data portals to scientific research. For projects that involve developing code and collaborating with others, Git is an invaluable tool; it also creates a backup system and structured documentation. In this article, we examine version control, the particulars of Git, the burgeoning social network of GitHub, and how Git can be an archival tool.
```
@article{davis_git_2015,
    author = "Davis, Robin Camille",
    title = "Git and {GitHub} for {Librarians}",
    volume = "34",
    url = "https://academicworks.cuny.edu/jj\_pubs/34/",
    doi = "https://doi.org/10.1080/01639269.2015.1062586",
    language = "English",
    number = "3",
    urldate = "2019-04-25",
    journal = "Behavioral \\& Social Sciences Librarian",
    month = "August",
    year = "2015",
    pages = "159--164"
}
```

Justin F. Brunelle, Mat Kelly, Hany SalahEldeen, Michele C. Weigle, and Michael L. Nelson. Not all mementos are created equal: measuring the impact of missing resources. International Journal on Digital Libraries, 16(3-4):283–301, 2015. URL: http://link.springer.com/10.1007/s00799-015-0150-6 (visited on 2019-05-05), doi:10.1007/s00799-015-0150-6.
[BibTeX▼]

@article{brunelle_not_2015,
    author = "Brunelle, Justin F. and Kelly, Mat and SalahEldeen, Hany and Weigle, Michele C. and Nelson, Michael L.",
    title = "Not all mementos are created equal: measuring the impact of missing resources",
    volume = "16",
    issn = "1432-5012, 1432-1300",
    url = "http://link.springer.com/10.1007/s00799-015-0150-6",
    doi = "10.1007/s00799-015-0150-6",
    language = "en",
    number = "3-4",
    urldate = "2019-05-05",
    journal = "International Journal on Digital Libraries",
    year = "2015",
    pages = "283--301"
}

Francesco Musumeci, Camilla Bellanzon, Nicola Carapellese, and Massimo Tornatore. Optimal BBU placement for 5g C-RAN deployment over WDM aggregation networks. Journal of Lightwave Technology, 34(8):1963–1970, December 2015. URL: https://www.researchgate.net/profile/Teemu_Leppaenen/publication/332801714_Open-source_RANs_in_practice_an_over-the-air_deployment_for_5G_MEC/links/5ccab11392851c8d221410aa/Open-source-RANs-in-practice-an-over-the-air-deployment-for-5G-MEC.pdf (visited on 2019-05-10), doi:10.1109/JLT.2015.2513101.
[abstract▼] [BibTeX▼]

5G mobile access targets unprecedented performance, not only in terms of higher data rates per user and lower latency, but also in terms of network intelligence and capillarity. To achieve this, 5G networks will resort to solutions as small cell deployment, multipoint coordination (CoMP, ICIC) and centralized radio access network (C-RAN) with baseband units (BBUs) hotelling. As adopting such techniques requires a high-capacity low-latency access/aggregation network to support backhaul, radio coordination and fronthaul (i.e., digitized baseband signal) traffic, optical access/aggregation networks based on wavelength division multiplexing (WDM) are considered as an outstanding candidate for 5G-transport. By physically separating BBUs from the corresponding cell sites, BBU hotelling promises substantial savings in terms of cost and power consumption. However, this requires to insert additional high bit-rate traffic, i.e., the fronthaul, which also has very strict latency requirements. Therefore, a tradeoff between the number of BBU-hotels (BBU consolidation), the fronthaul latency and network-capacity utilization arises. We introduce the novel BBU-placement optimization problem for C-RAN deployment over a WDM aggregation network and formalize it by integer linear programming. Thus, we evaluate the impact of 1) jointly supporting converged fixed and mobile traffic, 2) different fronthaul-transport options (namely, OTN and Overlay) and 3) joint optimization of BBU and electronic switches placement, on the amount of BBU consolidation achievable on the aggregation network.
```
@article{musumeci_optimal_2015,
    author = "Musumeci, Francesco and Bellanzon, Camilla and Carapellese, Nicola and Tornatore, Massimo",
    title = "Optimal {BBU} placement for 5G {C}-{RAN} deployment over {WDM} aggregation networks",
    volume = "34",
    issn = "0733-8724",
    url = "https://www.researchgate.net/profile/Teemu\_Leppaenen/publication/332801714\_Open-source\_RANs\_in\_practice\_an\_over-the-air\_deployment\_for\_5G\_MEC/links/5ccab11392851c8d221410aa/Open-source-RANs-in-practice-an-over-the-air-deployment-for-5G-MEC.pdf",
    doi = "10.1109/JLT.2015.2513101",
    number = "8",
    urldate = "2019-05-10",
    journal = "Journal of Lightwave Technology",
    month = "December",
    year = "2015",
    pages = "1963--1970"
}
```

2014

Martin Klein, Herbert Van de Sompel, Robert Sanderson, Harihar Shankar, Lyudmila Balakireva, Ke Zhou, and Richard Tobin. Scholarly Context Not Found: One in Five Articles Suffers from Reference Rot. PLOS ONE, December 2014. URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115253 (visited on 2019-06-27), doi:10.1371/journal.pone.0115253.
[abstract▼] [BibTeX▼]

The emergence of the web has fundamentally affected most aspects of information communication, including scholarly communication. The immediacy that characterizes publishing information to the web, as well as accessing it, allows for a dramatic increase in the speed of dissemination of scholarly knowledge. But, the transition from a paper-based to a web-based scholarly communication system also poses challenges. In this paper, we focus on reference rot, the combination of link rot and content drift to which references to web resources included in Science, Technology, and Medicine (STM) articles are subject. We investigate the extent to which reference rot impacts the ability to revisit the web context that surrounds STM articles some time after their publication. We do so on the basis of a vast collection of articles from three corpora that span publication years 1997 to 2012. For over one million references to web resources extracted from over 3.5 million articles, we determine whether the HTTP URI is still responsive on the live web and whether web archives contain an archived snapshot representative of the state the referenced resource had at the time it was referenced. We observe that the fraction of articles containing references to web resources is growing steadily over time. We find one out of five STM articles suffering from reference rot, meaning it is impossible to revisit the web context that surrounds them some time after their publication. When only considering STM articles that contain references to web resources, this fraction increases to seven out of ten. We suggest that, in order to safeguard the long-term integrity of the web-based scholarly record, robust solutions to combat the reference rot problem are required. In conclusion, we provide a brief insight into the directions that are explored with this regard in the context of the Hiberlink project.
```
@article{klein_scholarly_2014,
    author = "Klein, Martin and Sompel, Herbert Van de and Sanderson, Robert and Shankar, Harihar and Balakireva, Lyudmila and Zhou, Ke and Tobin, Richard",
    title = "Scholarly {Context} {Not} {Found}: {One} in {Five} {Articles} {Suffers} from {Reference} {Rot}",
    volume = "9",
    issn = "1932-6203",
    url = "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115253",
    doi = "10.1371/journal.pone.0115253",
    language = "en",
    number = "12",
    urldate = "2019-06-27",
    journal = "PLOS ONE",
    month = "December",
    year = "2014"
}
```

Jonathan Zittrain, Kendra Albert, and Lawrence Lessig. Perma: Scoping and Addressing the Problem of Link and Reference Rot in Legal Citations. 2014. URL: https://harvardlawreview.org/2014/03/perma-scoping-and-addressing-the-problem-of-link-and-reference-rot-in-legal-citations/ (visited on 2019-06-21).
[abstract▼] [BibTeX▼]

@misc{jonathan_zittrain_perma:_2014,
    author = "{Jonathan Zittrain} and {Kendra Albert} and {Lawrence Lessig}",
    title = "Perma: {Scoping} and {Addressing} the {Problem} of {Link} and {Reference} {Rot} in {Legal} {Citations}",
    url = "https://harvardlawreview.org/2014/03/perma-scoping-and-addressing-the-problem-of-link-and-reference-rot-in-legal-citations/",
    urldate = "2019-06-21",
    year = "2014"
}

Nick Summers. Mozilla Science Lab, GitHub and Figshare Fix Code Citation in Academia. March 2014. URL: https://thenextweb.com/dd/2014/03/17/mozilla-science-lab-github-figshare-team-fix-citation-code-academia/ (visited on 2019-07-14).
[abstract▼] [BibTeX▼]

Academia has a problem. Research is becoming increasingly computational and data-driven, but the traditional paper and scientific journal has barely changed to accommodate this growing form of analysis. The current referencing structure makes it difficult for anyone to reproduce the results in a paper, either to check findings or build upon their results. In addition, scientists …
```
@misc{summers_mozilla_2014,
    author = "Summers, Nick",
    title = "Mozilla {Science} {Lab}, {GitHub} and {Figshare} {Fix} {Code} {Citation} in {Academia}",
    url = "https://thenextweb.com/dd/2014/03/17/mozilla-science-lab-github-figshare-team-fix-citation-code-academia/",
    language = "en-us",
    urldate = "2019-07-14",
    journal = "The Next Web",
    month = "March",
    year = "2014"
}
```
Alexis Antracoli, Steven Duckworth, Judith Silva, and Kristen Yarmey. Capture All the URLs: First Steps in Web Archiving. Pennsylvania Libraries: Research & Practice, 2(2):155–170, November 2014. URL: https://palrap.pitt.edu/ojs/index.php/palrap/article/view/67 (visited on 2019-04-16), doi:10.5195/palrap.2014.67.
[abstract▼] [BibTeX▼]

As higher education embraces new technologies, university activities—including teaching, learning, and research—increasingly take place on university websites, on university-related social media pages, and elsewhere on the open Web. Despite perceptions that “once it’s on the Web, it’s there forever,” this dynamic digital content is highly vulnerable to degradation and loss. In order to preserve and provide enduring access to this complex body of university records, archivists and librarians must rise to the challenge of Web archiving. As digital archivists at our respective institutions, the authors introduce the concept of Web archiving and articulate its importance in higher education. We provide our institutions’ rationale for selecting subscription service Archive-It as a preservation tool, outline the progress of our institutional Web archiving initiatives, and share lessons learned, from unexpected stumbling blocks to strategies for raising funds and support from campus stakeholders.
```
@article{antracoli_capture_2014,
    author = "Antracoli, Alexis and Duckworth, Steven and Silva, Judith and Yarmey, Kristen",
    title = "Capture {All} the {URLs}: {First} {Steps} in {Web} {Archiving}",
    volume = "2",
    copyright = "Copyright (c) 2014 Alexis Antracoli, Steven Duckworth, Judith Silva, Kristen Yarmey",
    issn = "2324-7878",
    url = "https://palrap.pitt.edu/ojs/index.php/palrap/article/view/67",
    doi = "10.5195/palrap.2014.67",
    language = "en",
    number = "2",
    urldate = "2019-04-16",
    journal = "Pennsylvania Libraries: Research \\& Practice",
    month = "November",
    year = "2014",
    pages = "155--170"
}
```

2013

Nikos Koutras and Maria Bottis. Institutional Repositories of Open Access: A Paradigm of Innovation and Changing in Educational Politics. Procedia - Social and Behavioral Sciences, 106:1499–1504, 2013. URL: http://www.sciencedirect.com/science/article/pii/S1877042813047927 (visited on 2019-07-02), doi:10.1016/j.sbspro.2013.12.169.
[abstract▼] [BibTeX▼]

In the Lisbon Summit (2000), the European Commission adopted the triangle of knowledge (education, research, innovation). These three concepts are fundamental "ingredients" of the European educational policy. In today's societies, education is the tool leading to research and then, to innovation. Thus, institutional repositories play a key role here. They represent a major and an alternative gate of knowledge. In conclusion, this paper will examine relevant and current initiatives (open access initiatives) and policies among European countries.
```
@article{koutras_institutional_2013,
    author = "Koutras, Nikos and Bottis, Maria",
    series = "4th {International} {Conference} on {New} {Horizons} in {Education}",
    title = "Institutional {Repositories} of {Open} {Access}: {A} {Paradigm} of {Innovation} and {Changing} in {Educational} {Politics}",
    volume = "106",
    issn = "1877-0428",
    url = "http://www.sciencedirect.com/science/article/pii/S1877042813047927",
    doi = "10.1016/j.sbspro.2013.12.169",
    urldate = "2019-07-02",
    journal = "Procedia - Social and Behavioral Sciences",
    year = "2013",
    pages = "1499--1504"
}
```

Ellen Finnie Duranceau and Sue Kriegsman. Implementing Open Access Policies Using Institutional Repositories. In Pamela Bluh and Cindy Hepfer, editors, The institutional repository: Benefits and challenges, pages 75–97. American Library Association, Chicago, 2013. URL: http://www.ala.org/alcts/sites/ala.org.alcts/files/content/resources/papers/ir_ch05_.pdf.
[BibTeX▼]

@incollection{duranceau_implementing_2013,
    author = "Duranceau, Ellen Finnie and Kriegsman, Sue",
    editor = "Bluh, Pamela and Hepfer, Cindy",
    address = "Chicago",
    title = "Implementing {Open} {Access} {Policies} {Using} {Institutional} {Repositories}",
    url = "http://www.ala.org/alcts/sites/ala.org.alcts/files/content/resources/papers/ir\_ch05\_.pdf",
    language = "en",
    booktitle = "The institutional repository: {Benefits} and challenges",
    publisher = "American Library Association",
    year = "2013",
    pages = "75--97"
}

Timothy H. Vines, Arianne Y.K. Albert, Rose L. Andrew, Florence Débarre, Dan G. Bock, Michelle T. Franklin, Kimberly J. Gilbert, Jean-Sébastien Moore, Sébastien Renaut, and Diana J. Rennison. The Availability of Research Data Declines Rapidly with Article Age. Current Biology, 24(1):94–97, December 2013. URL: https://doi.org/10.1016/j.cub.2013.11.014 (visited on 2019-07-03), doi:10.1016/j.cub.2013.11.014.
[abstract▼] [BibTeX▼]

Policies ensuring that research data are available on public archives are increasingly being implemented at the government [1], funding agency [2?4], and journal [5, 6] level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term [7], and indeed many studies have found that authors are often unable or unwilling to share their data [8?11]. However, there are no systematic estimates of how the availability of research data changes with time since publication. We therefore requested data sets from a relatively homogenous set of 516 articles published between 2 and 22 years ago, and found that availability of the data was strongly affected by article age. For papers where the authors gave the status of their data, the odds of a data set being extant fell by 17\% per year. In addition, the odds that we could find a working e-mail address for the first, last, or corresponding author fell by 7\% per year. Our results reinforce the notion that, in the long term, research data cannot be reliably preserved by individual researchers, and further demonstrate the urgent need for policies mandating data sharing via public archives.
```
@article{vines_availability_2013,
    author = "Vines, Timothy H. and Albert, Arianne Y.K. and Andrew, Rose L. and Débarre, Florence and Bock, Dan G. and Franklin, Michelle T. and Gilbert, Kimberly J. and Moore, Jean-Sébastien and Renaut, Sébastien and Rennison, Diana J.",
    title = "The {Availability} of {Research} {Data} {Declines} {Rapidly} with {Article} {Age}",
    volume = "24",
    issn = "0960-9822",
    url = "https://doi.org/10.1016/j.cub.2013.11.014",
    doi = "10.1016/j.cub.2013.11.014",
    language = "English",
    number = "1",
    urldate = "2019-07-03",
    journal = "Current Biology",
    month = "December",
    year = "2013",
    pages = "94--97"
}
```
Daphne Kyriaki-Manessi, Alexandros Koulouris, Georgios Giannakopoulos, and Spiros Zervos. Exploratory Research Regarding Faculty Attitudes towards the Institutional Repository and Self Archiving. Procedia - Social and Behavioral Sciences, 73:777–784, 2013. URL: http://www.sciencedirect.com/science/article/pii/S1877042813004114 (visited on 2019-07-02), doi:10.1016/j.sbspro.2013.02.118.
[abstract▼] [BibTeX▼]

Over the past year the Library of the TEI of Athens has launched an Institutional Repository containing Faculty's published and unpublished work, students’ theses and a major collection called "Institutional Archives". The latter was also used as a vehicle for promoting the Repository and had attracted a lot of interest from all faculty members and the Institute's administration. While in the making, special effort was made to secure faculty's understanding of the undertaking and faculty's participation. Information was communicated through e- letters from the Library, the Deans and the Institute's President as well. A web site was developed and a feedback mechanism was set in place. A system of approaching individually each faculty member and create customized lists of publications to be incorporated in the IR had given surprisingly good results. The assessment of these measures in relation to faculty's willingness to participate in the IR is examined. Furthermore, faculty's attitude towards self-archiving is also examined. A bibliographic review was carried out regarding faculty attitudes and factors that shape it. A questionnaire was distributed to all faculty members in order to assess the effectiveness of the communication system and the degree of their willingness to practice self archiving. This explored faculty reactions and determined the effectiveness of the IR.Major findings include the faculty's positive reception of the IR due to the fact that the information was communicated properly through the aforementioned mechanism and their enthusiasm and overcoming of hesitations after understanding the capabilities of the IR.
```
@article{kyriaki-manessi_exploratory_2013,
    author = "Kyriaki-Manessi, Daphne and Koulouris, Alexandros and Giannakopoulos, Georgios and Zervos, Spiros",
    series = "Proceedings of the 2nd {International} {Conference} on {Integrated} {Information} ({IC}-{ININFO} 2012), {Budapest}, {Hungary}, {August} 30 – {September} 3, 2012",
    title = "Exploratory {Research} {Regarding} {Faculty} {Attitudes} towards the {Institutional} {Repository} and {Self} {Archiving}",
    volume = "73",
    issn = "1877-0428",
    url = "http://www.sciencedirect.com/science/article/pii/S1877042813004114",
    doi = "10.1016/j.sbspro.2013.02.118",
    urldate = "2019-07-02",
    journal = "Procedia - Social and Behavioral Sciences",
    year = "2013",
    pages = "777--784"
}
```
Andrew Purcell. CERN and OpenAIREplus launch new European research repository. May 2013. URL: https://sciencenode.org/feature/cern-and-openaireplus-launch-new-european-research-repository.php (visited on 2019-07-13).
[abstract▼] [BibTeX▼]

Zenodo is an online repository, developed and hosted at CERN, which allows researchers to share publications and supporting data, facilitating open collaboration. The repository is launched today (8 May, 2013) and is designed specifically to help 'the long tail' of researchers based at smaller institutions to share results in a wide variety of formats across all fields of science.
```
@misc{andrew_purcell_cern_2013,
    author = "{Andrew Purcell}",
    title = "{CERN} and {OpenAIREplus} launch new {European} research repository",
    url = "https://sciencenode.org/feature/cern-and-openaireplus-launch-new-european-research-repository.php",
    urldate = "2019-07-13",
    journal = "Science Node",
    month = "May",
    year = "2013"
}
```
Victoria Stodden and Sheila Miguez. Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research. SSRN, pages 9, September 2013. URL: https://ssrn.com/abstract=2322276, doi:http://dx.doi.org/10.2139/ssrn.2322276.
[abstract▼] [BibTeX▼]

Scholarly dissemination and communication standards are changing to reflect the increasingly computational nature of scholarly research, primarily to include the sharing of the data and code associated with published results. This paper presents a formalized set of best practice recommendations for computational scientists wishing to disseminate reproducible research, facilitate innovation by enabling data and code re-use, and enable broader communication of the output of digital scientific research. We distinguish two forms of collaboration to motivate choices of software environment for computational scientific research. We also present these Best Practices as a living, evolving, and changing document on wiki.
```
@article{stodden_best_2013,
    author = "Stodden, Victoria and Miguez, Sheila",
    title = "Best {Practices} for {Computational} {Science}: {Software} {Infrastructure} and {Environments} for {Reproducible} and {Extensible} {Research}",
    url = "https://ssrn.com/abstract=2322276",
    doi = "http://dx.doi.org/10.2139/ssrn.2322276",
    language = "English",
    journal = "SSRN",
    month = "September",
    year = "2013",
    pages = "9"
}
```

Maureen Pennock. Web-Archiving. Technical Report, Digital Preservation Coalition, March 2013. URL: http://www.dpconline.org/component/docman/doc_download/865-dpctw13-01pdf (visited on 2019-05-05), doi:10.7207/twr13-01.
[BibTeX▼]

@techreport{pennock_web-archiving_2013,
    author = "Pennock, Maureen",
    title = "Web-{Archiving}",
    url = "http://www.dpconline.org/component/docman/doc\_download/865-dpctw13-01pdf",
    language = "en",
    urldate = "2019-05-05",
    institution = "Digital Preservation Coalition",
    month = "March",
    year = "2013",
    doi = "10.7207/twr13-01"
}

Deborah Kempe. It is Time to Embrace the Present: Guest Post by Deborah Kempe. December 2013. URL: https://webarchivingrt.wordpress.com/2013/12/06/it-is-time-to-embrace-the-present-guest-post-by-deborah-kempe/ (visited on 2019-04-16).
[abstract▼] [BibTeX▼]

“Water, water, everywhere, And all the boards did shrink; Water, water, everywhere, Nor any drop to drink.” ― Samuel Taylor Coleridge, The Rime of the Ancient Mariner Colleagues, do you not share t…
```
@misc{kempe_it_2013,
    author = "Kempe, Deborah",
    title = "It is {Time} to {Embrace} the {Present}: {Guest} {Post} by {Deborah} {Kempe}",
    url = "https://webarchivingrt.wordpress.com/2013/12/06/it-is-time-to-embrace-the-present-guest-post-by-deborah-kempe/",
    language = "en",
    urldate = "2019-04-16",
    journal = "Web Archiving Section, Society of American Archivist",
    month = "December",
    year = "2013"
}
```

Molly Bragg and Kristine Hanna. The Web Archiving Life Cycle Model. 2013. URL: http://ait.blog.archive.org/files/2014/04/archiveit_life_cycle_model.pdf (visited on 2019-04-16).
[BibTeX▼]

@misc{bragg_web_2013,
    author = "Bragg, Molly and Hanna, Kristine",
    title = "The {Web} {Archiving} {Life} {Cycle} {Model}",
    url = "http://ait.blog.archive.org/files/2014/04/archiveit\_life\_cycle\_model.pdf",
    language = "en",
    urldate = "2019-04-16",
    year = "2013"
}

Iain Hrynaszkiewicz. Version control for scientific research. February 2013. URL: http://blogs.biomedcentral.com/bmcblog/2013/02/28/version-control-for-scientific-research/ (visited on 2019-04-28).
[abstract▼] [BibTeX▼]

Guest blog post from Dr Karthik Ram (KR) and Dr C. Titus Brown (CTB) who have been working with BioMed Central on our recently announced collaboration with the social coding repository, GitHub. We live in an increasingly collaborative era, where the Internet enables distance collaboration almost trivially – not just with e-mail and videoconferencing, but with collaborative realtime document editing and networked transmission of data and analyses. These tools allow us to collectively leverage many resources to rapidly solve problems and ultimately accelerate scientific discovery. While these tools and technologies are fundamentally changing how we collaborate on science, there is still considerable room for improvement in how we are using them.
```
@misc{hrynaszkiewicz_version_2013,
    author = "Hrynaszkiewicz, Iain",
    type = "Journal {Blog}",
    title = "Version control for scientific research",
    url = "http://blogs.biomedcentral.com/bmcblog/2013/02/28/version-control-for-scientific-research/",
    language = "English",
    urldate = "2019-04-28",
    journal = "Research in progress blog",
    month = "February",
    year = "2013"
}
```
Karthik Ram. Git can facilitate greater reproducibility and increased transparency in science. Source Code for Biology and Medicine, 8(7):8, February 2013. URL: https://scfbm.biomedcentral.com/articles/10.1186/1751-0473-8-7 (visited on 2019-04-25), doi:https://doi.org/10.1186/1751-0473-8-7.
[abstract▼] [BibTeX▼]

Background: Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but also for facilitating the development of new ideas. Sharing data and computer code associated with publications is becoming increasingly common, motivated partly in response to data deposition requirements from journals and mandates from funders. Despite this increase in transparency, it is still difficult to reproduce or build upon the findings of most scientific publications without access to a more complete workflow. Findings: Version control systems (VCS), which have long been used to maintain code repositories in the software industry, are now finding new applications in science. One such open source VCS, Git, provides a lightweight yet robust framework that is ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts. For individual researchers, Git provides a powerful way to track and compare versions, retrace errors, explore new approaches in a structured manner, while maintaining a full audit trail. For larger collaborative efforts, Git and Git hosting services make it possible for everyone to work asynchronously and merge their contributions at any time, all the while maintaining a complete authorship trail. In this paper I provide an overview of Git along with use-cases that highlight how this tool can be leveraged to make science more reproducible and transparent, foster new collaborations, and support novel uses.
```
@article{ram_git_2013,
    author = "Ram, Karthik",
    title = "Git can facilitate greater reproducibility and increased transparency in science",
    volume = "8",
    issn = "1751-0473",
    url = "https://scfbm.biomedcentral.com/articles/10.1186/1751-0473-8-7",
    doi = "https://doi.org/10.1186/1751-0473-8-7",
    language = "English",
    number = "7",
    urldate = "2019-04-25",
    journal = "Source Code for Biology and Medicine",
    month = "February",
    year = "2013",
    pages = "8"
}
```

Konrad Lawson. Getting Started With a GitHub Repository. March 2013. URL: https://www.chronicle.com/blogs/profhacker/getting-started-with-a-github-repository/47393 (visited on 2019-04-25).
[BibTeX▼]

@misc{lawson_getting_2013,
    author = "Lawson, Konrad",
    type = "News",
    title = "Getting {Started} {With} a {GitHub} {Repository}",
    url = "https://www.chronicle.com/blogs/profhacker/getting-started-with-a-github-repository/47393",
    language = "English",
    urldate = "2019-04-25",
    journal = "ProfHacker: Teaching, tech, and productivity.",
    month = "March",
    year = "2013"
}

Konrad Lawson. The Limitations of GitHub for Writers. April 2013. URL: https://www.chronicle.com/blogs/profhacker/the-limitations-of-github-for-writers/48299 (visited on 2019-04-25).
[abstract▼] [BibTeX▼]

This posting is the last in a series introducing the text hosting and version control service GitHub (See parts 1, 2, 3, 4, and 5). Up until this posting I have talked about some of the great features of working with repositories of text in GitHub and the ways in which it facilitates collaboration even without direct collaboration. It is, in its own motto, a "social coding" environment that allows anyone to "fork" code, issue "pull requests" to propose improvements on someone else’s work, as well as keep a history of changes and improvements on work over time. I have argued that these innovations have much to teach us in our own worlds of scholarship.
```
@misc{lawson_limitations_2013,
    author = "Lawson, Konrad",
    type = "News",
    title = "The {Limitations} of {GitHub} for {Writers}",
    url = "https://www.chronicle.com/blogs/profhacker/the-limitations-of-github-for-writers/48299",
    language = "English",
    urldate = "2019-04-25",
    journal = "ProfHacker: Teaching, tech, and productivity.",
    month = "April",
    year = "2013"
}
```
Kris Shaffer. GitHub for Academics: the open-source way to host, create and curate knowledge. June 2013. URL: https://blogs.lse.ac.uk/impactofsocialsciences/2013/06/04/github-for-academics/ (visited on 2019-04-25).
[abstract▼] [BibTeX▼]

Though originally developed as a way to share and merge software code, any types of files can be part of a GitHub repository, making it a great collaborative tool for academics, finds Kris Shaffer. Since any open-licensed project can be hosted on GitHub for free, it can function as a publishing platform, a peer-review system, a learning management tool, and a locus for intra- and inter-institutional collaboration.
```
@misc{shaffer_github_2013,
    author = "Shaffer, Kris",
    type = "Blog",
    title = "{GitHub} for {Academics}: the open-source way to host, create and curate knowledge",
    url = "https://blogs.lse.ac.uk/impactofsocialsciences/2013/06/04/github-for-academics/",
    language = "English",
    urldate = "2019-04-25",
    journal = "LSE Impact Blog",
    month = "June",
    year = "2013"
}
```
National Digital Information Infrastructure and Preservation Program of the Library of Congress. Preserving.exe: Toward a National Strategy for Software Preservation. Technical Report, National Digital Information Infrastructure and Preservation Program of the Library of Congress, October 2013. URL: http://www.digitalpreservation.gov/multimedia/documents/PreservingEXE_report_final101813.pdf (visited on 2019-04-01).
[abstract▼] [BibTeX▼]

A report from the National Digital Information Infrastructure and Preservation Program of the Library of Congress, focused on identifying valuable and at-risk software. Topics covered include executable software preservation, game preservation, electronic literature and ideas for approaches to ensure long-term access.
```
@techreport{national_digital_information_infrastructure_and_preservation_program_of_the_library_of_congress_preserving.exe:_2013,
    author = "{National Digital Information Infrastructure and Preservation Program of the Library of Congress}",
    title = "Preserving.exe: {Toward} a {National} {Strategy} for {Software} {Preservation}",
    url = "http://www.digitalpreservation.gov/multimedia/documents/PreservingEXE\_report\_final101813.pdf",
    language = "English",
    urldate = "2019-04-01",
    institution = "National Digital Information Infrastructure and Preservation Program of the Library of Congress",
    month = "October",
    year = "2013",
    pages = "1--41"
}
```
Michel Castagné. Consider the Source: The Value of Source Code to Digital Preservation Strategies. Student Research Journal, 2(2):1–11, 2013. URL: https://scholarworks.sjsu.edu/slissrj/vol2/iss2/5 (visited on 2019-03-26).
[abstract▼] [BibTeX▼]

One of the major challenges in the digital preservation field is the difficulty of ensuring long-term access to digital objects, especially in cases when the software that was used to create an object is no longer current. Software source code has a human-readable, documentary structure that makes it an overlooked aspect of digital preservation strategies, in addition to a valuable component for the records of modern computing history. The author surveys several approaches to software preservation and finds that, by supporting open source initiatives, digital libraries can improve their ability to preserve access to their collections for future generations.
```
@article{castagne_consider_2013,
    author = "Castagné, Michel",
    title = "Consider the {Source}: {The} {Value} of {Source} {Code} to {Digital} {Preservation} {Strategies}",
    volume = "2",
    issn = "2575-2499",
    url = "https://scholarworks.sjsu.edu/slissrj/vol2/iss2/5",
    language = "eng",
    number = "2",
    urldate = "2019-03-26",
    journal = "Student Research Journal",
    year = "2013",
    pages = "1--11"
}
```

C. Sean Burns, Amy Lana, and John M. Budd. Institutional Repositories: Exploration of Costs and Value. D-Lib Magazine, 2013. URL: http://www.dlib.org/dlib/january13/burns/01burns.html (visited on 2019-06-13), doi:10.1045/january2013-burns.
[BibTeX▼]

@article{burns_institutional_2013,
    author = "Burns, C. Sean and Lana, Amy and Budd, John M.",
    title = "Institutional {Repositories}: {Exploration} of {Costs} and {Value}",
    volume = "19",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/january13/burns/01burns.html",
    doi = "10.1045/january2013-burns",
    language = "en",
    number = "1/2",
    urldate = "2019-06-13",
    journal = "D-Lib Magazine",
    year = "2013"
}

Alexandra Simons, Irene Ke, and Loretta Wallace. From the Outside In: Using Environmental Scanning for Evidence-based Planning. In 2013 ACRL Conference Proceedings, 230–239. Indianapolis, IN, 2013. URL: http://www.ala.org/acrl/sites/ala.org.acrl/files/content/conferences/confsandpreconfs/2013/papers/SimonsKeWallace_FromOutside.pdf (visited on 2019-04-04).
[BibTeX▼]

@inproceedings{simons_outside_2013,
    author = "Simons, Alexandra and Ke, Irene and Wallace, Loretta",
    address = "Indianapolis, IN",
    title = "From the {Outside} {In}: {Using} {Environmental} {Scanning} for {Evidence}-based {Planning}",
    url = "http://www.ala.org/acrl/sites/ala.org.acrl/files/content/conferences/confsandpreconfs/2013/papers/SimonsKeWallace\_FromOutside.pdf",
    language = "en",
    urldate = "2019-04-04",
    booktitle = "2013 {ACRL} {Conference} {Proceedings}",
    year = "2013",
    pages = "230--239"
}

Iain Hrynaszkiewicz. Social coding and scholarly communication – open for collaboration. February 2013. URL: http://blogs.biomedcentral.com/bmcblog/2013/02/28/github-and-biomed-central/.
[abstract▼] [BibTeX▼]

Innovation in how social online tools and their features develop is frequently defined and driven by the network’s users. A collaboration between BioMed Central, some of our authors and editors, and the team behind a powerful social software development platform aims to stimulate innovation in scholarly communication.
```
@misc{hrynaszkiewicz_social_2013,
    author = "Hrynaszkiewicz, Iain",
    type = "Blog",
    title = "Social coding and scholarly communication – open for collaboration",
    url = "http://blogs.biomedcentral.com/bmcblog/2013/02/28/github-and-biomed-central/",
    language = "English",
    journal = "Research in progress blog",
    month = "February",
    year = "2013"
}
```

2012

Alma Swan. Institutional repositories. March 2012. URL: https://hstalks-com.proxy.library.nyu.edu/t/2293/institutional-repositories/ (visited on 2019-07-03).
[abstract▼] [BibTeX▼]

Click to launch \& play an online audio visual presentation by Dr. Alma Swan on Institutional repositories, part of a collection of online lectures.
```
@misc{swan_institutional_2012,
    author = "Swan, Alma",
    title = "Institutional repositories",
    url = "https://hstalks-com.proxy.library.nyu.edu/t/2293/institutional-repositories/",
    language = "en",
    urldate = "2019-07-03",
    month = "March",
    year = "2012"
}
```
Richard Ball and Norm Medeiros. Teaching Integrity in Empirical Research: A Protocol for Documenting Data Management and Analysis. The Journal of Economic Education, 43(2):182–189, April 2012. URL: https://doi.org/10.1080/00220485.2012.659647 (visited on 2019-06-30), doi:10.1080/00220485.2012.659647.
[abstract▼] [BibTeX▼]

This article describes a protocol the authors developed for teaching undergraduates to document their statistical analyses for empirical research projects so that their results are completely reproducible and verifiable. The protocol is guided by the principle that the documentation prepared to accompany an empirical research project should be sufficient to allow an independent researcher to replicate easily and exactly every step of the data management and analysis that generated the results reported in a study. The authors hope that requiring students to follow this protocol will not only teach them how to document their research appropriately, but also instill in them the belief that such documentation is an important professional responsibility.
```
@article{ball_teaching_2012,
    author = "Ball, Richard and Medeiros, Norm",
    title = "Teaching {Integrity} in {Empirical} {Research}: {A} {Protocol} for {Documenting} {Data} {Management} and {Analysis}",
    volume = "43",
    issn = "0022-0485",
    url = "https://doi.org/10.1080/00220485.2012.659647",
    doi = "10.1080/00220485.2012.659647",
    language = "English",
    number = "2",
    urldate = "2019-06-30",
    journal = "The Journal of Economic Education",
    month = "April",
    year = "2012",
    pages = "182--189"
}
```

Jinfang Niu. Functionalities of Web Archives. D-Lib Magazine, 2012. URL: http://www.dlib.org/dlib/march12/niu/03niu2.html (visited on 2019-04-15), doi:10.1045/march2012-niu2.
[BibTeX▼]

@article{niu_functionalities_2012,
    author = "Niu, Jinfang",
    title = "Functionalities of {Web} {Archives}",
    volume = "18",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/march12/niu/03niu2.html",
    doi = "10.1045/march2012-niu2",
    language = "en",
    number = "3/4",
    urldate = "2019-04-15",
    journal = "D-Lib Magazine",
    year = "2012"
}

Jinfang Niu. An Overview of Web Archiving. D-Lib Magazine, 2012. URL: http://www.dlib.org/dlib/march12/niu/03niu1.html (visited on 2019-04-15), doi:10.1045/march2012-niu1.
[BibTeX▼]

@article{niu_overview_2012,
    author = "Niu, Jinfang",
    title = "An {Overview} of {Web} {Archiving}",
    volume = "18",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/march12/niu/03niu1.html",
    doi = "10.1045/march2012-niu1",
    language = "en",
    number = "3/4",
    urldate = "2019-04-15",
    journal = "D-Lib Magazine",
    year = "2012"
}

Robert McMillan. Lord of the Files: How GitHub Tamed Free Software (And More). February 2012. Published article at https://www.wired.com/2012/02/github-2/. URL: https://github.com/WiredEnterprise/Lord-of-the-Files (visited on 2019-04-29).
[abstract▼] [BibTeX▼]

@misc{mcmillan_lord_2012,
    author = "McMillan, Robert",
    type = "News",
    title = "Lord of the {Files}: {How} {GitHub} {Tamed} {Free} {Software} ({And} {More})",
    url = "https://github.com/WiredEnterprise/Lord-of-the-Files",
    language = "English",
    urldate = "2019-04-29",
    journal = "Wired.com",
    month = "February",
    year = "2012",
    note = "Published article at https://www.wired.com/2012/02/github-2/"
}

Brian Croxall. Forking Your Syllabus. March 2012. URL: https://www.chronicle.com/blogs/profhacker/forking-your-syllabus/39137 (visited on 2019-04-25).
[BibTeX▼]

@misc{croxall_forking_2012,
    author = "Croxall, Brian",
    type = "News",
    title = "Forking {Your} {Syllabus}",
    url = "https://www.chronicle.com/blogs/profhacker/forking-your-syllabus/39137",
    language = "English",
    urldate = "2019-04-25",
    journal = "ProfHacker: Teaching, tech, and productivity.",
    month = "March",
    year = "2012"
}

Mark Sample. Git a Fork in My Syllabus, It’s Done. June 2012. URL: https://www.chronicle.com/blogs/profhacker/git-a-fork-in-my-syllabus-its-done/40331 (visited on 2019-04-25).
[BibTeX▼]

@misc{sample_git_2012,
    author = "Sample, Mark",
    type = "News",
    title = "Git a {Fork} in {My} {Syllabus}, {It}’s {Done}",
    url = "https://www.chronicle.com/blogs/profhacker/git-a-fork-in-my-syllabus-its-done/40331",
    language = "English",
    urldate = "2019-04-25",
    journal = "ProfHacker: Teaching, tech, and productivity.",
    month = "June",
    year = "2012"
}

Trevor Owens. Preserving.exe: A Short List of Readings on Software Preservation \textbar The Signal. November 2012. URL: //blogs.loc.gov/thesignal/2012/11/preserving-exe-a-short-list-of-readings-on-software-preservation/ (visited on 2019-04-04).
[abstract▼] [BibTeX▼]

@misc{owens_preserving.exe:_2012,
    author = "Owens, Trevor",
    type = "webpage",
    title = "Preserving.exe: {A} {Short} {List} of {Readings} on {Software} {Preservation} {\textbar} {The} {Signal}",
    url = "//blogs.loc.gov/thesignal/2012/11/preserving-exe-a-short-list-of-readings-on-software-preservation/",
    language = "eng",
    urldate = "2019-04-04",
    journal = "The Signal",
    month = "November",
    year = "2012"
}

Kenning Arlitsch and Patrick S. O'Brien. Invisible institutional repositories: Addressing the low indexing ratios of IRs in Google Scholar. Library Hi Tech, 30(1):60–81, 2012. URL: https://www.emeraldinsight.com/doi/10.1108/07378831211213210 (visited on 2019-06-13), doi:10.1108/07378831211213210.
[BibTeX▼]

@article{arlitsch_invisible_2012,
    author = "Arlitsch, Kenning and O'Brien, Patrick S.",
    title = "Invisible institutional repositories: {Addressing} the low indexing ratios of {IRs} in {Google} {Scholar}",
    volume = "30",
    issn = "0737-8831",
    url = "https://www.emeraldinsight.com/doi/10.1108/07378831211213210",
    doi = "10.1108/07378831211213210",
    language = "en",
    number = "1",
    urldate = "2019-06-13",
    journal = "Library Hi Tech",
    year = "2012",
    pages = "60--81"
}

Xue Zhang, Shaheen Majid, and Schubert Foo. Environmental Scanning-An Emerging Discipline for LIS Education. In A Spinks and D Singh, editors, Library and Information Science Trends and Research: Asia-Oceania, Emerald LIS Book Series UK, pages 124–147. Emerald Group Publishing Limited, Bingley, United Kingdom, 2012.
[BibTeX▼]

@incollection{zhang_environmental_2012,
    author = "Zhang, Xue and Majid, Shaheen and Foo, Schubert",
    editor = "Spinks, A and Singh, D",
    address = "Bingley, United Kingdom",
    series = "Emerald {LIS} {Book} {Series} {UK}",
    title = "Environmental {Scanning}-{An} {Emerging} {Discipline} for {LIS} {Education}",
    language = "en",
    booktitle = "Library and {Information} {Science} {Trends} and {Research}: {Asia}-{Oceania}",
    publisher = "Emerald Group Publishing Limited",
    year = "2012",
    pages = "124--147"
}

Martha A. Rubenstein. Dear Colleague Letter - Issuance of a new NSF Proposal & Award Policies and Procedures Guide. October 2012. URL: https://www.nsf.gov/pubs/2013/nsf13004/nsf13004.jsp?WT.mc_id=USNSF_109 (visited on 2019-06-10).
[abstract▼] [BibTeX▼]

A new version of the NSF Proposal \& Award Policies \& Procedures Guide (PAPPG), (NSF 13-1), has been issued. The PAPPG is comprised of documents relating to the Foundation's proposal and award process and consists of the:
```
@misc{rubenstein_dear_2012,
    author = "Rubenstein, Martha A.",
    type = "Letter",
    title = "Dear {Colleague} {Letter} - {Issuance} of a new {NSF} {Proposal} \\& {Award} {Policies} and {Procedures} {Guide}",
    url = "https://www.nsf.gov/pubs/2013/nsf13004/nsf13004.jsp?WT.mc\_id=USNSF\_109",
    language = "English",
    urldate = "2019-06-10",
    month = "October",
    year = "2012"
}
```
Jennifer Loertscher. Using a scholarly approach to improve teaching and learning in biochemistry higher education. Biochemistry and Molecular Biology Education, 40(6):388–389, October 2012. URL: https://www.ncbi.nlm.nih.gov/pubmed/23166027 (visited on 2019-05-12), doi:https://doi-org.offcampus.lib.washington.edu/10.1002/bmb.20648.
[abstract▼] [BibTeX▼]

and philosophical statements are a common part of the landscape. Recently, I noticed a sticker plastered to a street sign that asked, “What would happen if we collaborated instead of avoiding?” I found this question especially thought‐provoking given my recent rereading of Huber and Hutching's The Advancement of Learning: Building the Teaching Commons [1]. Although the biochemistry education community is far from avoiding conversations about improving teaching and learning, reexamining our individual and community teaching practices through the lens of the scholarship of teaching and learning (SoTL) is critical for continued growth and improvement. The contemporary vision of SoTL, which has been promoted tirelessly by the Carnegie Foundation for the Advancement of Teaching [2], is generally thought to have its origin in Ernest Boyer's Scholarship Reconsidered: Priorities of the Professorate [3]. Boyer proposed an expanded definition of professorial scholarship, which includes the scholarship of teaching. Soon after, Lee Shulman asserted that the way to legitimize the scholarly work of teaching is to make it “community property” [4]. Shulman suggested that contrary to our public work as disciplinary scholars, teaching has historically taken place in isolation. In order to make teaching a more valued part of the academy, he argued that our work in the classroom must be made visible, be connected to our disciplines, and be subject to peer‐review.
```
@article{loertscher_using_2012,
    author = "Loertscher, Jennifer",
    title = "Using a scholarly approach to improve teaching and learning in biochemistry higher education",
    volume = "40",
    url = "https://www.ncbi.nlm.nih.gov/pubmed/23166027",
    doi = "https://doi-org.offcampus.lib.washington.edu/10.1002/bmb.20648",
    language = "English",
    number = "6",
    urldate = "2019-05-12",
    journal = "Biochemistry and Molecular Biology Education",
    month = "October",
    year = "2012",
    pages = "388--389"
}
```

2011

Gale Moore. Survey of University of Toronto Faculty Awareness, Attitudes, and Practices Regarding Scholarly Communication: A Preliminary Report. TSpace, 2011. URL: https://tspace.library.utoronto.ca/handle/1807/26446.
[abstract▼] [BibTeX▼]

This report presents the results from a 2010 online survey of the University of Toronto faculty on their awareness, attitudes and practices regarding scholarly communication. The objectives were to collect evidence regarding the current practices of faculty with regard to scholarly communication – primarily scholarly publishing and dissemination; to obtain evidence of their awareness and attitudes toward the changes in practices and forms that are occurring in publishing and dissemination with the turn to the digital, and to stimulate conversation on these topics among faculty within departments, faculties and academic units across the university, as well as with other members of the scholarly communication ecosystem. The survey has five sections that ask about i) current practices ii) scholarly publishing, including copyright and peer review iii) newer practices relating to open access, subject or institutional repositories, policies and mandates iv) costs associated with scholarly communication and iv) local services. Detailed findings, including faculty comments, and a summary of findings organized around a number of broad themes that emerged out of the detailed findings are included. The summary includes comparisons with the results from a 2006 survey of faculty at the University of California.
```
@article{moore_survey_2011,
    author = "Moore, Gale",
    title = "Survey of {University} of {Toronto} {Faculty} {Awareness}, {Attitudes}, and {Practices} {Regarding} {Scholarly} {Communication}: {A} {Preliminary} {Report}",
    url = "https://tspace.library.utoronto.ca/handle/1807/26446",
    language = "en",
    journal = "TSpace",
    year = "2011"
}
```
Megan Wacha and Meredith Wisner. Measuring Value in Open Access Repositories. The Serials Librarian, 61(3-4):377–388, 2011. URL: https://doi.org/10.1080/0361526X.2011.580423 (visited on 2019-07-02), doi:10.1080/0361526X.2011.580423.
[abstract▼] [BibTeX▼]

Open access institutional repositories were created to promote access to information, encourage scholarly communication, and demonstrate institutional prestige. While these repositories have been widely adopted, the quality of their contents often fails to represent their institution's scholarly output. Moreover, current research uses measurements of quantity, not quality, to assess their value. In response, this article opens new areas of scholarly inquiry by assessing the quality of contents. This is accomplished through a cross-sectional study of repositories at American colleges and universities across the academic spectrum, using citation indexing to identify an institution's articles and authors of highest impact.
```
@article{wacha_measuring_2011,
    author = "Wacha, Megan and Wisner, Meredith",
    title = "Measuring {Value} in {Open} {Access} {Repositories}",
    volume = "61",
    issn = "0361-526X",
    url = "https://doi.org/10.1080/0361526X.2011.580423",
    doi = "10.1080/0361526X.2011.580423",
    number = "3-4",
    urldate = "2019-07-02",
    journal = "The Serials Librarian",
    year = "2011",
    pages = "377--388"
}
```
Neil Chue Hong. Publish or be damned? An alternative impact manifesto for research software \textbar Software Sustainability Institute. May 2011. URL: https://www.software.ac.uk/blog/2016-10-06-publish-or-be-damned-alternative-impact-manifesto-research-software (visited on 2019-07-16).
[abstract▼] [BibTeX▼]

In the research world, we're often told that the the only way for our work to have a measurable impact is through the citation of publications based on our work. The mechanisms for this are in place, the stakeholders understand the framework, and everyone is happy... or so we're led to believe. However, the status quo neglects the many research outputs, including software, that may be generated by a research activity and certainly doesn't encourage their sharing and reuse, let alone give proper credit for their production.
```
@misc{neil_chue_hong_publish_2011,
    author = "{Neil Chue Hong}",
    title = "Publish or be damned? {An} alternative impact manifesto for research software {\textbar} {Software} {Sustainability} {Institute}",
    url = "https://www.software.ac.uk/blog/2016-10-06-publish-or-be-damned-alternative-impact-manifesto-research-software",
    urldate = "2019-07-16",
    month = "May",
    year = "2011"
}
```
Bing Liu and Filippo Menczer. Web Crawling. In Bing Liu, editor, Web Data Mining: Exploring Hyperlinks, Contents, and Usage Data, Data-Centric Systems and Applications, pages 311–362. Springer Berlin Heidelberg, Berlin, Heidelberg, 2011. URL: https://doi.org/10.1007/978-3-642-19460-3_8 (visited on 2019-05-05), doi:10.1007/978-3-642-19460-3_8.
[abstract▼] [BibTeX▼]

Web crawlers, also known as spiders or robots, are programs that automatically download Web pages. Since information on the Web is scattered among billions of pages served by millions of servers around the globe, users who browse the Web can follow hyperlinks to access information, virtually moving from one page to the next. A crawler can visit many sites to collect information that can be analyzed and mined in a central location, either online (as it is downloaded) or off-line (after it is stored).
```
@incollection{liu_web_2011,
    author = "Liu, Bing and Menczer, Filippo",
    editor = "Liu, Bing",
    address = "Berlin, Heidelberg",
    series = "Data-{Centric} {Systems} and {Applications}",
    title = "Web {Crawling}",
    isbn = "978-3-642-19460-3",
    url = "https://doi.org/10.1007/978-3-642-19460-3\_8",
    language = "en",
    urldate = "2019-05-05",
    booktitle = "Web {Data} {Mining}: {Exploring} {Hyperlinks}, {Contents}, and {Usage} {Data}",
    publisher = "Springer Berlin Heidelberg",
    year = "2011",
    doi = "10.1007/978-3-642-19460-3\_8",
    keywords = "Anchor Text, Cosine Similarity, Domain Name System, Priority Queue, Search Engine",
    pages = "311--362"
}
```

The National Archives. Web Archive Guidance. Technical Report, NARA, 2011. URL: http://www.nationalarchives.gov.uk/documents/information-management/web-archiving-guidance.pdf (visited on 2019-04-15).
[BibTeX▼]

@techreport{the_national_archives_web_2011,
    author = "Archives, The National",
    title = "Web {Archive} {Guidance}",
    url = "http://www.nationalarchives.gov.uk/documents/information-management/web-archiving-guidance.pdf",
    language = "en",
    institution = "NARA",
    urldate = "2019-04-15",
    year = "2011",
    pages = "1--15"
}

Sebastian J. Schultheiss, Marc-Christian Münch, Gergana D. Andreeva, and Gunnar Rätsch. Persistence and Availability of Web Services in Computational Biology. PLoS ONE, September 2011. URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024914, doi:https://doi.org/10.1371/journal.pone.0024914.
[abstract▼] [BibTeX▼]

We have conducted a study on the long-term availability of bioinformatics Web services: an observation of 927 Web services published in the annual Nucleic Acids Research Web Server Issues between 2003 and 2009. We found that 72\% of Web sites are still available at the published addresses, only 9\% of services are completely unavailable. Older addresses often redirect to new pages. We checked the functionality of all available services: for 33\%, we could not test functionality because there was no example data or a related problem; 13\% were truly no longer working as expected; we could positively confirm functionality only for 45\% of all services. Additionally, we conducted a survey among 872 Web Server Issue corresponding authors; 274 replied. 78\% of all respondents indicate their services have been developed solely by students and researchers without a permanent position. Consequently, these services are in danger of falling into disrepair after the original developers move to another institution, and indeed, for 24\% of services, there is no plan for maintenance, according to the respondents. We introduce a Web service quality scoring system that correlates with the number of citations: services with a high score are cited 1.8 times more often than low-scoring services. We have identified key characteristics that are predictive of a service's survival, providing reviewers, editors, and Web service developers with the means to assess or improve Web services. A Web service conforming to these criteria receives more citations and provides more reliable service for its users. The most effective way of ensuring continued access to a service is a persistent Web address, offered either by the publishing journal, or created on the authors' own initiative, for example at http://bioweb.me. The community would benefit the most from a policy requiring any source code needed to reproduce results to be deposited in a public repository.
```
@article{schultheiss_persistence_2011,
    author = "Schultheiss, Sebastian J. and Münch, Marc-Christian and Andreeva, Gergana D. and Rätsch, Gunnar",
    title = "Persistence and {Availability} of {Web} {Services} in {Computational} {Biology}",
    volume = "6",
    url = "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024914",
    doi = "https://doi.org/10.1371/journal.pone.0024914",
    language = "English",
    number = "9",
    journal = "PLoS ONE",
    month = "September",
    year = "2011"
}
```
Daniel Gomes, João Miranda, and Miguel Costa. A Survey on Web Archiving Initiatives. In Stefan Gradmann, Francesca Borri, Carlo Meghini, and Heiko Schuldt, editors, Research and Advanced Technology for Digital Libraries, volume 6966, pages 408–420. Springer Berlin Heidelberg, Berlin, Heidelberg, 2011. URL: http://link.springer.com/10.1007/978-3-642-24469-8_41 (visited on 2019-04-25), doi:10.1007/978-3-642-24469-8_41.
[abstract▼] [BibTeX▼]

Web archiving has been gaining interest and recognized importance for modern societies around the world. However, for web archivists it is frequently difﬁcult to demonstrate this fact, for instance, to funders. This study provides an updated and global overview of web archiving. The obtained results showed that the number of web archiving initiatives signiﬁcantly grew after 2003 and they are concentrated on developed countries. We statistically analyzed metrics, such as, the volume of archived data, archive ﬁle formats or number of people engaged. Web archives all together must process more data than any web search engine. Considering the complexity and large amounts of data involved in web archiving, the results showed that the assigned resources are scarce. A Wikipedia page was created to complement the presented work and be collaboratively kept up-to-date by the community.
```
@incollection{gradmann_survey_2011,
    author = "Gomes, Daniel and Miranda, João and Costa, Miguel",
    editor = "Gradmann, Stefan and Borri, Francesca and Meghini, Carlo and Schuldt, Heiko",
    address = "Berlin, Heidelberg",
    title = "A {Survey} on {Web} {Archiving} {Initiatives}",
    volume = "6966",
    isbn = "978-3-642-24468-1 978-3-642-24469-8",
    url = "http://link.springer.com/10.1007/978-3-642-24469-8\_41",
    language = "en",
    urldate = "2019-04-25",
    booktitle = "Research and {Advanced} {Technology} for {Digital} {Libraries}",
    publisher = "Springer Berlin Heidelberg",
    year = "2011",
    doi = "10.1007/978-3-642-24469-8\_41",
    pages = "408--420",
    file = "Gomes et al. - 2011 - A Survey on Web Archiving Initiatives.pdf:/home/vicky/Zotero/storage/FCF226T7/Gomes et al. - 2011 - A Survey on Web Archiving Initiatives.pdf:application/pdf"
}
```
Abbie Grotke. Web Archiving at the Library of Congress. EventDV, 24(10):15–19, 2011.
[abstract▼] [BibTeX▼]

The article discusses the latest Web archiving activities being implemented by the U.S. Library of Congress (LC) as of December 2011. It cites the National Digital Information Infrastructure and Preservation Program (NDIIPP) that was established in 2000 to create a national approach to collect, preserve and offer a massive digital content for the present and future generations.
```
@article{grotke_web_2011,
    author = "Grotke, Abbie",
    title = "Web {Archiving} at the {Library} of {Congress}",
    volume = "24",
    issn = "15542009",
    number = "10",
    urldate = "2019-04-15",
    journal = "EventDV",
    year = "2011",
    pages = "15--19"
}
```

American Library Association. The Institutional Repository: Benefits and Challenges. November 2011. URL: http://www.ala.org/alcts/resources/papers/irs (visited on 2019-06-13).
[BibTeX▼]

@misc{noauthor_institutional_2011,
    author = "Association, American Library",
    type = "Text",
    title = "The {Institutional} {Repository}: {Benefits} and {Challenges}",
    url = "http://www.ala.org/alcts/resources/papers/irs",
    language = "en",
    urldate = "2019-06-13",
    journal = "Association for Library Collections \\& Technical Services (ALCTS)",
    month = "November",
    year = "2011"
}

Jihyun Kim. Motivations of Faculty Self-archiving in Institutional Repositories. The Journal of Academic Librarianship, 37(3):246–254, 2011. URL: https://linkinghub.elsevier.com/retrieve/pii/S0099133311000310 (visited on 2019-06-13), doi:10.1016/j.acalib.2011.02.017.
[BibTeX▼]

@article{kim_motivations_2011,
    author = "Kim, Jihyun",
    title = "Motivations of {Faculty} {Self}-archiving in {Institutional} {Repositories}",
    volume = "37",
    issn = "00991333",
    url = "https://linkinghub.elsevier.com/retrieve/pii/S0099133311000310",
    doi = "10.1016/j.acalib.2011.02.017",
    language = "en",
    number = "3",
    urldate = "2019-06-13",
    journal = "The Journal of Academic Librarianship",
    year = "2011",
    pages = "246--254"
}

Joan Giesecke. Institutional Repositories: Keys to Success. Journal of Library Administration, 51(5-6):529–542, 2011. URL: http://www.tandfonline.com/doi/abs/10.1080/01930826.2011.589340 (visited on 2019-06-13), doi:10.1080/01930826.2011.589340.
[BibTeX▼]

@article{giesecke_institutional_2011,
    author = "Giesecke, Joan",
    title = "Institutional {Repositories}: {Keys} to {Success}",
    volume = "51",
    issn = "0193-0826, 1540-3564",
    url = "http://www.tandfonline.com/doi/abs/10.1080/01930826.2011.589340",
    doi = "10.1080/01930826.2011.589340",
    language = "en",
    number = "5-6",
    urldate = "2019-06-13",
    journal = "Journal of Library Administration",
    year = "2011",
    pages = "529--542"
}

Yuan Li and Meghan Banach. Institutional Repositories and Digital Preservation: Assessing Current Practices at Research Libraries. D-Lib Magazine, 2011. URL: http://www.dlib.org/dlib/may11/yuanli/05yuanli.html (visited on 2019-06-13), doi:10.1045/may2011-yuanli.
[BibTeX▼]

@article{li_institutional_2011,
    author = "Li, Yuan and Banach, Meghan",
    title = "Institutional {Repositories} and {Digital} {Preservation}: {Assessing} {Current} {Practices} at {Research} {Libraries}",
    volume = "17",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/may11/yuanli/05yuanli.html",
    doi = "10.1045/may2011-yuanli",
    language = "en",
    number = "5/6",
    urldate = "2019-06-13",
    journal = "D-Lib Magazine",
    year = "2011"
}

Sebastian J. Schultheiss. Ten Simple Rules for Providing a Scientific Web Resource. PLOS Computational Biology, May 2011. URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001126, doi:https://doi.org/10.1371/journal.pcbi.1001126.
[abstract▼] [BibTeX▼]

Many projects in computational biology lead to the creation of a small application program or collection of scripts that can be of use to other scientists. A natural progression is to make this tool available via a Web site or by creating a service for it, from now on collectively called "Web resource." We conducted a survey among providers and users of scientific Web resources, as well as a study on availability. The following rules reflect the experiences and opinions of over 250 scientists who have answered our questions and who use Web resources regularly, as well as our own experience. The study of availability allows us to draw objective conclusions about the characteristics of those Web resources that are still available and correlate the features that distinguish them from disappeared or nonfunctional ones. These ten simple rules aid you in designing and maintaining a scientific Web resource that is available to anyone interested in using it.
```
@article{schultheiss_ten_2011,
    author = "Schultheiss, Sebastian J.",
    title = "Ten {Simple} {Rules} for {Providing} a {Scientific} {Web} {Resource}",
    volume = "7",
    issn = "1553-7358",
    url = "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001126",
    doi = "https://doi.org/10.1371/journal.pcbi.1001126",
    language = "English",
    number = "5",
    journal = "PLOS Computational Biology",
    month = "May",
    year = "2011"
}
```

2010

Chad Hutchens. An Interview with Suzanne Bell, Administrator of the University of Rochester's New Open Source Institutional Repository, UR Research. Serials Review, 36(1):37–39, 2010. URL: http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=edselp&AN=S009879130900166X&site=eds-live (visited on 2019-07-03), doi:10.1016/j.serrev.2009.11.006.
[BibTeX▼]

@article{hutchens_interview_2010,
    author = "Hutchens, Chad",
    title = "An {Interview} with {Suzanne} {Bell}, {Administrator} of the {University} of {Rochester}'s {New} {Open} {Source} {Institutional} {Repository}, {UR} {Research}",
    volume = "36",
    issn = "0098-7913",
    url = "http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true\&db=edselp\&AN=S009879130900166X\&site=eds-live",
    doi = "10.1016/j.serrev.2009.11.006",
    number = "1",
    urldate = "2019-07-03",
    journal = "Serials Review",
    year = "2010",
    pages = "37--39"
}

Brian Matthews, Arif Shaon, Juan Bicarregui, and Catherine Jones. A Framework for Software Preservation \textbar International Journal of Digital Curation. International Journal of Digital Curation, June 2010. URL: http://www.ijdc.net/article/view/148 (visited on 2019-06-30), doi:10.2218/ijdc.v5i1.145.
[abstract▼] [BibTeX▼]

Software preservation has not had detailed consideration as a research topic or in practical application. In this paper, we present a conceptual framework to capture and organise the main notions of software preservation, which are required for a coherent and comprehensive approach. This framework has three main aspects. Firstly a discussion of what it means to preserve software via a performance model which considers how a software artefact can be rebuilt from preserved components and can then be seen to be representative of the original software product. Secondly the development of a model of software artefacts, describing the basic components of all software, loosely based on the FRBR model for representing digital artefacts and their history within a library context. Finally, the definition and categorisation of the properties of software artefacts which are required to ensure that the software product has been adequately preserved. These are broken down into a number of categories and related to the concepts defined in the OAIS standard. We also discuss our experience of recording these preservation properties for a number of BADC software products, which arose from a series of case studies conducted to evaluate the software preservation framework, and also briefly describe the SPEQS toolkit, a tool to capture software preservation properties within a software development.
```
@article{brian_matthews_framework_2010,
    author = "{Brian Matthews} and {Arif Shaon} and {Juan Bicarregui} and {Catherine Jones}",
    title = "A {Framework} for {Software} {Preservation} {\textbar} {International} {Journal} of {Digital} {Curation}",
    volume = "5",
    url = "http://www.ijdc.net/article/view/148",
    doi = "10.2218/ijdc.v5i1.145",
    language = "en-US",
    number = "1",
    urldate = "2019-06-30",
    journal = "International Journal of Digital Curation",
    month = "June",
    year = "2010"
}
```

Kevin Ashley and Susan Farrell. A guide to web preservation: practical advice for web and records managers based on best practices from the JISC-funded PoWR project. Lulu.com, U.K.?, 2010. ISBN 978-0-9516856-7-9.
[BibTeX▼]

@book{ashley_guide_2010,
    author = "Ashley, Kevin and Farrell, Susan",
    address = "U.K.?",
    title = "A guide to web preservation: practical advice for web and records managers based on best practices from the {JISC}-funded {PoWR} project",
    isbn = "978-0-9516856-7-9",
    language = "en",
    publisher = "Lulu.com",
    collaborator = "UK Office for Library Networking and University of London and Joint Information Systems Committee",
    year = "2010",
    keywords = "Digital preservation, Web archiving"
}

B. Mathews, A. Shaon, J. Bicarregui, and C. Jones. A Framework for Software Preservation. In International Journal of Digital Curation, volume 5, 91–105. 2010. URL: http://www.ijdc.net/article/view/148 (visited on 2019-05-13).
[abstract▼] [BibTeX▼]

Software preservation has not had detailed consideration as a research topic or in practical application. In this paper, we present a conceptual framework to capture and organise the main notions of software preservation, which are required for a coherent and comprehensive approach. This framework has three main aspects. Firstly a discussion of what it means to preserve software via a performance model which considers how a software artefact can be rebuilt from preserved components and can then be seen to be representative of the original software product. Secondly the development of a model of software artefacts, describing the basic components of all software, loosely based on the FRBR model for representing digital artefacts and their history within a library context. Finally, the definition and categorisation of the properties of software artefacts which are required to ensure that the software product has been adequately preserved. These are broken down into a number of categories and related to the concepts defined in the OAIS standard. We also discuss our experience of recording these preservation properties for a number of BADC software products, which arose from a series of case studies conducted to evaluate the software preservation framework, and also briefly describe the SPEQS toolkit, a tool to capture software preservation properties within a software development.
```
@inproceedings{mathews_framework_2010,
    author = "Mathews, B. and Shaon, A. and Bicarregui, J. and Jones, C.",
    title = "A {Framework} for {Software} {Preservation}",
    volume = "5",
    url = "http://www.ijdc.net/article/view/148",
    language = "en",
    urldate = "2019-05-13",
    booktitle = "International {Journal} of {Digital} {Curation}",
    year = "2010",
    pages = "91--105"
}
```

2009

Susan Douglas Franzosa. Encyclopedia of the Social and Cultural Foundations of Education. Sage Publications, Thousand Oaks, CA, 2009. ISBN 978-1-4129-0678-4. URL: https://digitalcommons.fairfield.edu/education-books/4/.
[BibTeX▼]

@book{franzosa_encyclopedia_2009,
    author = "Franzosa, Susan Douglas",
    address = "Thousand Oaks, CA",
    title = "Encyclopedia of the {Social} and {Cultural} {Foundations} of {Education}",
    isbn = "978-1-4129-0678-4",
    url = "https://digitalcommons.fairfield.edu/education-books/4/",
    publisher = "Sage Publications",
    year = "2009",
    keywords = "scholarship"
}

R. M. Darby, C. M. Jones, L. D. Gilbert, and S. C. Lambert. Increasing the Productivity of Interactions Between Subject and Institutional Repositories. New Review of Information Networking, 14(2):117–135, 2009. URL: http://www.tandfonline.com/doi/abs/10.1080/13614570903359381 (visited on 2019-06-13), doi:10.1080/13614570903359381.
[BibTeX▼]

@article{darby_increasing_2009,
    author = "Darby, R. M. and Jones, C. M. and Gilbert, L. D. and Lambert, S. C.",
    title = "Increasing the {Productivity} of {Interactions} {Between} {Subject} and {Institutional} {Repositories}",
    volume = "14",
    issn = "1361-4576, 1740-7869",
    url = "http://www.tandfonline.com/doi/abs/10.1080/13614570903359381",
    doi = "10.1080/13614570903359381",
    language = "en",
    number = "2",
    urldate = "2019-06-13",
    journal = "New Review of Information Networking",
    year = "2009",
    pages = "117--135"
}

2008

Dorothea Salo. Innkeeper at the Roach Motel. Library Trends, 57(2):98–123, 2008. URL: http://muse.jhu.edu/article/262026, doi:10.1353/lib.0.0031.
[abstract▼] [BibTeX▼]

Library-run institutional repositories face a crossroads: adapt or die. The "build it and they will come" proposition has been decisively proven wrong. Citation advantages and preservation have not attracted faculty participants, though current-generation software and services offer faculty little else. Academic librarianship has not supported repositories or their managers. Most libraries consistently under-resource and understaff repositories, further worsening the participation gap. Software and services have been wildly out of touch with faculty needs and the realities of repository management. These problems are not insoluble, especially in light of Harvard University arts and science faculty’s recent permissions mandate, but they demand serious reconsideration of repository missions, goals, and means if we are to be ready for Harvard imitators, and especially to be ready should those imitators not surface.
```
@article{salo_innkeeper_2008,
    author = "Salo, Dorothea",
    title = "Innkeeper at the {Roach} {Motel}",
    volume = "57",
    issn = "1559-0682",
    url = "http://muse.jhu.edu/article/262026",
    doi = "10.1353/lib.0.0031",
    language = "en",
    number = "2",
    journal = "Library Trends",
    year = "2008",
    pages = "98--123"
}
```

Stella Veretnik, J. Lynn Fink, and Philip E. Bourne. Computational Biology Resources Lack Persistence and Usability. PLoS Computational Biology, July 2008. URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000136, doi:doi.org/10.1371/journal.pcbi.1000136.
[BibTeX▼]

@article{veretnik_computational_2008,
    author = "Veretnik, Stella and Fink, J. Lynn and Bourne, Philip E.",
    series = "Perspective",
    title = "Computational {Biology} {Resources} {Lack} {Persistence} and {Usability}",
    volume = "4",
    url = "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000136",
    doi = "doi.org/10.1371/journal.pcbi.1000136",
    number = "7",
    journal = "PLoS Computational Biology",
    month = "July",
    year = "2008"
}

Michael Norris, Charles Oppenheim, and Fytton Rowland. Finding open access articles using Google, Google Scholar, OAIster and OpenDOAR. Online Information Review, 32(6):709–715, 2008. URL: http://www.emeraldinsight.com/doi/10.1108/14684520810923881 (visited on 2019-06-13), doi:10.1108/14684520810923881.
[BibTeX▼]

@article{norris_finding_2008,
    author = "Norris, Michael and Oppenheim, Charles and Rowland, Fytton",
    title = "Finding open access articles using {Google}, {Google} {Scholar}, {OAIster} and {OpenDOAR}",
    volume = "32",
    issn = "1468-4527",
    url = "http://www.emeraldinsight.com/doi/10.1108/14684520810923881",
    doi = "10.1108/14684520810923881",
    language = "en",
    number = "6",
    urldate = "2019-06-13",
    journal = "Online Information Review",
    year = "2008",
    pages = "709--715"
}

Mary Piorun and Lisa A. Palmer. Digitizing Dissertations for an Institutional Repository: A Process and Cost Analysis. Journal of the Medical Library Association : JMLA, 96(3):223–229, 2008. URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2479051/ (visited on 2019-06-13), doi:10.3163/1536-5050.96.3.008.
[BibTeX▼]

@article{piorun_digitizing_2008,
    author = "Piorun, Mary and Palmer, Lisa A.",
    title = "Digitizing {Dissertations} for an {Institutional} {Repository}: {A} {Process} and {Cost} {Analysis}",
    volume = "96",
    issn = "1536-5050, 1558-9439",
    url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2479051/",
    doi = "10.3163/1536-5050.96.3.008",
    number = "3",
    urldate = "2019-06-13",
    journal = "Journal of the Medical Library Association : JMLA",
    year = "2008",
    pages = "223--229"
}

Jingfeng Xia. A Comparison of Subject and Institutional Repositories in Self-archiving Practices. The Journal of Academic Librarianship, 34(6):489–495, 2008. URL: https://linkinghub.elsevier.com/retrieve/pii/S0099133308001572 (visited on 2019-06-13), doi:10.1016/j.acalib.2008.09.016.
[BibTeX▼]

@article{xia_comparison_2008,
    author = "Xia, Jingfeng",
    title = "A {Comparison} of {Subject} and {Institutional} {Repositories} in {Self}-archiving {Practices}",
    volume = "34",
    issn = "00991333",
    url = "https://linkinghub.elsevier.com/retrieve/pii/S0099133308001572",
    doi = "10.1016/j.acalib.2008.09.016",
    language = "en",
    number = "6",
    urldate = "2019-06-13",
    journal = "The Journal of Academic Librarianship",
    year = "2008",
    pages = "489--495"
}

A. E. Hassan. The road ahead for Mining Software Repositories. In 2008 Frontiers of Software Maintenance, 48–57. September 2008. doi:10.1109/FOSM.2008.4659248.
[abstract▼] [BibTeX▼]

Source control repositories, bug repositories, archived communications, deployment logs, and code repositories are examples of software repositories that are commonly available for most software projects. The mining software repositories (MSR) field analyzes and cross-links the rich data available in these repositories to uncover interesting and actionable information about software systems. By transforming these repositories from static record-keeping ones into active repositories, we can guide decision processes in modern software projects. For example, data in source control repositories, traditionally used to archive code, could be linked with data in bug repositories to help practitioners propagate complex changes and to warn them about risky code based on prior changes and bugs. In this paper, we present a brief history of the MSR field and discuss several recent achievements and results of using MSR techniques to support software research and practice. We then discuss the various opportunities and challenges that lie in the road ahead for this important and emerging field.
```
@inproceedings{hassan_road_2008,
    author = "Hassan, A. E.",
    title = "The road ahead for {Mining} {Software} {Repositories}",
    doi = "10.1109/FOSM.2008.4659248",
    booktitle = "2008 {Frontiers} of {Software} {Maintenance}",
    month = "September",
    year = "2008",
    pages = "48--57"
}
```

2007

Simon J. Bevan. Developing an institutional repository: Cranfield QUEprints – a case study. OCLC Systems & Services: International digital library perspectives, 23(2):170–182, 2007. URL: http://www.emeraldinsight.com/doi/10.1108/10650750710748478 (visited on 2019-06-13), doi:10.1108/10650750710748478.
[BibTeX▼]

@article{bevan_developing_2007,
    author = "Bevan, Simon J.",
    title = "Developing an institutional repository: {Cranfield} {QUEprints} – a case study",
    volume = "23",
    issn = "1065-075X",
    url = "http://www.emeraldinsight.com/doi/10.1108/10650750710748478",
    doi = "10.1108/10650750710748478",
    language = "en",
    number = "2",
    urldate = "2019-06-13",
    journal = "OCLC Systems \\& Services: International digital library perspectives",
    year = "2007",
    pages = "170--182"
}

Soo Young Rieh, Karen Markey, Beth St. Jean, Elizabeth Yakel, and Jihyun Kim. Census of Institutional Repositories in the U.S.: A Comparison Across Institutions at Different Stages of IR Development. D-Lib Magazine, 2007. URL: http://www.dlib.org/dlib/november07/rieh/11rieh.html (visited on 2019-06-13), doi:10.1045/november2007-rieh.
[BibTeX▼]

@article{rieh_census_2007,
    author = "Rieh, Soo Young and Markey, Karen and St. Jean, Beth and Yakel, Elizabeth and Kim, Jihyun",
    title = "Census of {Institutional} {Repositories} in the {U}.{S}.: {A} {Comparison} {Across} {Institutions} at {Different} {Stages} of {IR} {Development}",
    volume = "13",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/november07/rieh/11rieh.html",
    doi = "10.1045/november2007-rieh",
    language = "en",
    number = "11/12",
    urldate = "2019-06-13",
    journal = "D-Lib Magazine",
    year = "2007"
}

2006

Carl Lagoze, Sandy Payette, Edwin Shin, and Chris Wilper. Fedora: an architecture for complex objects and their relationships. International Journal on Digital Libraries, 6(2):124–138, 2006. URL: http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true&db=aci&AN=20391982&site=eds-live (visited on 2019-07-08), doi:10.1007/s00799-005-0130-3.
[abstract▼] [BibTeX▼]

The Fedora architecture is an extensible framework for the storage, management, and dissemination of complex objects and the relationships among them. Fedora accommodates the aggregation of local and distributed content into digital objects and the association of services with objects. This allows an object to have several accessible representations, some of them dynamically produced. The architecture includes a generic Resource Description Framework (RDF)-based relationship model that represents relationships among objects and their components. Queries against these relationships are supported by an RDF triple store. The architecture is implemented as a web service, with all aspects of the complex object architecture and related management functions exposed through REST and SOAP interfaces. The implementation is available as open-source software, providing the foundation for a variety of end-user applications for digital libraries, archives, institutional repositories, and learning object systems.
```
@article{lagoze_fedora:_2006,
    author = "Lagoze, Carl and Payette, Sandy and Shin, Edwin and Wilper, Chris",
    title = "Fedora: an architecture for complex objects and their relationships",
    volume = "6",
    issn = "14325012",
    url = "http://proxy.library.nyu.edu/login?url=http://search.ebscohost.com/login.aspx?direct=true\&db=aci\&AN=20391982\&site=eds-live",
    doi = "10.1007/s00799-005-0130-3",
    number = "2",
    urldate = "2019-07-08",
    journal = "International Journal on Digital Libraries",
    year = "2006",
    pages = "124--138"
}
```

2005

Clifford A. Lynch and Joan K. Lippincott. Institutional Repository Deployment in the United States as of Early 2005. D-Lib Magazine, 2005. URL: http://www.dlib.org/dlib/september05/lynch/09lynch.html (visited on 2019-06-13), doi:10.1045/september2005-lynch.
[BibTeX▼]

@article{lynch_institutional_2005,
    author = "Lynch, Clifford A. and Lippincott, Joan K.",
    title = "Institutional {Repository} {Deployment} in the {United} {States} as of {Early} 2005",
    volume = "11",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/september05/lynch/09lynch.html",
    doi = "10.1045/september2005-lynch",
    language = "en",
    number = "09",
    urldate = "2019-06-13",
    journal = "D-Lib Magazine",
    year = "2005"
}

Birger Hjørland. Domain Analysis: A Socio‐Cognitive Orientation for Information Science Research. Bulletin of the American Society for Information Science and Technology, 30(3):17–21, January 2005. URL: https://onlinelibrary.wiley.com/doi/full/10.1002/bult.312 (visited on 2019-05-09), doi:https://doi.org/10.1002/bult.312.
[abstract▼] [BibTeX▼]

This article outlines my view on humanizing information technology as well as on the fundamentals of information science (IS) and on the deep connection between these two issues. What is the meaning of "humanizing information technology" — our conference theme? Is it just making information technology (IT) "smart," "efficient," "reliable" and "user friendly"? Or are wider social consequences of computing involved, too? Is it just a question of getting information quickly, or is the quality of the information that the users gain also involved? I will argue in support of a wider conception of "humanizing information technology," especially as a concern that distinguishes IS from computer science. While computer science is the science about IT, we in IS try to optimize people's access to information, knowledge and documents. This optimization is extremely dependent on IT, which explains the close relationship between the two fields. But an important goal for IS involves the quality of information and the social perspective related to information intermediating. That goal is to enable users to make informed choices about how they are informed.
```
@article{hjorland_domain_2005,
    author = "Hjørland, Birger",
    title = "Domain {Analysis}: {A} {Socio}‐{Cognitive} {Orientation} for {Information} {Science} {Research}",
    volume = "30",
    url = "https://onlinelibrary.wiley.com/doi/full/10.1002/bult.312",
    doi = "https://doi.org/10.1002/bult.312",
    language = "English",
    number = "3",
    urldate = "2019-05-09",
    journal = "Bulletin of the American Society for Information Science and Technology",
    month = "January",
    year = "2005",
    pages = "17--21"
}
```

2004

Leslie Chan. Supporting and Enhancing Scholarship in the Digital Age: The Role of Open Access Institutional Repository. Canadian Journal of Communication, 2004. URL: https://www.cjc-online.ca/index.php/journal/article/view/1455 (visited on 2019-07-01), doi:10.22230/cjc.2004v29n3a1455.
[BibTeX▼]

@article{chan_supporting_2004,
    author = "Chan, Leslie",
    title = "Supporting and {Enhancing} {Scholarship} in the {Digital} {Age}: {The} {Role} of {Open} {Access} {Institutional} {Repository}",
    volume = "29",
    copyright = "Copyright (c)",
    issn = "1499-6642",
    url = "https://www.cjc-online.ca/index.php/journal/article/view/1455",
    doi = "10.22230/cjc.2004v29n3a1455",
    language = "en",
    number = "3",
    urldate = "2019-07-01",
    journal = "Canadian Journal of Communication",
    year = "2004"
}

Herbert Van de Sompel, Sandy Payette, John Erickson, Carl Lagoze, and Simeon Warner. Rethinking Scholarly Communication: Building the System that Scholars Deserve. D-Lib Magazine, September 2004. URL: http://www.dlib.org/dlib/september04/vandesompel/09vandesompel.html (visited on 2019-07-16), doi:10.1045/september2004-vandesompel.
[BibTeX▼]

@article{van_de_sompel_rethinking_2004,
    author = "Van de Sompel, Herbert and Payette, Sandy and Erickson, John and Lagoze, Carl and Warner, Simeon",
    title = "Rethinking {Scholarly} {Communication}: {Building} the {System} that {Scholars} {Deserve}",
    volume = "10",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/september04/vandesompel/09vandesompel.html",
    doi = "10.1045/september2004-vandesompel",
    language = "en",
    number = "9",
    urldate = "2019-07-16",
    journal = "D-Lib Magazine",
    month = "September",
    year = "2004"
}

Kendra Albright. Environmental Scanning: Radar for Success. The Information Management Journal, 38(3):38–45, 2004. URL: https://www.researchgate.net/publication/239970846_Environmental_Scanning_Radar_for_Success (visited on 2019-04-04).
[BibTeX▼]

@article{albright_environmental_2004,
    author = "Albright, Kendra",
    title = "Environmental {Scanning}: {Radar} for {Success}",
    volume = "38",
    url = "https://www.researchgate.net/publication/239970846\_Environmental\_Scanning\_Radar\_for\_Success",
    language = "en",
    number = "3",
    urldate = "2019-04-04",
    journal = "The Information Management Journal",
    year = "2004",
    pages = "38--45"
}

2003

Clifford A. Lynch. Institutional Repositories: Essential Infrastructure for Scholarship in the Digital Age. 2003.
[BibTeX▼]

@misc{lynch_institutional_2003,
    author = "Lynch, Clifford A.",
    title = "Institutional {Repositories}: {Essential} {Infrastructure} for {Scholarship} in the {Digital} {Age}",
    language = "en",
    year = "2003",
    pages = "1--3"
}

Thornton Staples, Ross Wayland, and Sandra Payette. The Fedora Project: An Open-source Digital Object Repository Management System. D-Lib Magazine, April 2003. URL: http://www.dlib.org/dlib/april03/staples/04staples.html (visited on 2019-07-16), doi:10.1045/april2003-staples.
[BibTeX▼]

@article{staples_fedora_2003,
    author = "Staples, Thornton and Wayland, Ross and Payette, Sandra",
    title = "The {Fedora} {Project}: {An} {Open}-source {Digital} {Object} {Repository} {Management} {System}",
    volume = "9",
    issn = "1082-9873",
    url = "http://www.dlib.org/dlib/april03/staples/04staples.html",
    doi = "10.1045/april2003-staples",
    language = "en",
    number = "4",
    urldate = "2019-07-16",
    journal = "D-Lib Magazine",
    month = "April",
    year = "2003"
}

James W. Guthrie. Boyer, Ernest (1928–1995). 2003. URL: http://link.galegroup.com.offcampus.lib.washington.edu/apps/doc/CX3403200081/GVRL?u=wash_main&sid=GVRL&xid=fbb1a9d3.
[BibTeX▼]

@misc{guthrie_boyer_2003,
    author = "Guthrie, James W.",
    address = "New York, NY",
    edition = "2",
    title = "Boyer, {Ernest} (1928–1995)",
    volume = "1",
    url = "http://link.galegroup.com.offcampus.lib.washington.edu/apps/doc/CX3403200081/GVRL?u=wash\_main\&sid=GVRL\&xid=fbb1a9d3.",
    language = "English",
    journal = "Encyclopedia of Education",
    publisher = "Macmillan Reference USA",
    year = "2003",
    keywords = "scholarship",
    pages = "199--202"
}

2002

Eileen Abels. Hot Topics: Environmental Scanning. Bulletin of the American Society for Information Science and Technology, 28(3):16–17, 2002. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/bult.236 (visited on 2019-04-04), doi:10.1002/bult.236.
[BibTeX▼]

@article{abels_hot_2002,
    author = "Abels, Eileen",
    title = "Hot {Topics}: {Environmental} {Scanning}",
    volume = "28",
    issn = "1550-8366",
    url = "https://onlinelibrary.wiley.com/doi/abs/10.1002/bult.236",
    doi = "10.1002/bult.236",
    language = "en",
    number = "3",
    urldate = "2019-04-04",
    journal = "Bulletin of the American Society for Information Science and Technology",
    year = "2002",
    pages = "16--17"
}

Arthur L. Norberg Ulf Hashagen, Reinhard Keil-Slawik. History of Computing: Software Issues. Springer Berlin Heidelberg, Berlin, Heidelberg, 2002. ISBN 978-3-642-07653-4 978-3-662-04954-9. URL: http://link.springer.com/10.1007/978-3-662-04954-9 (visited on 2019-03-29), doi:10.1007/978-3-662-04954-9.
[BibTeX▼]

@book{hashagen_history_2002,
    author = "Ulf Hashagen, Reinhard Keil-Slawik, Arthur L. Norberg",
    editor = "Hashagen, Ulf and Keil-Slawik, Reinhard and Norberg, Arthur L.",
    address = "Berlin, Heidelberg",
    title = "History of {Computing}: {Software} {Issues}",
    isbn = "978-3-642-07653-4 978-3-662-04954-9",
    url = "http://link.springer.com/10.1007/978-3-662-04954-9",
    language = "en",
    urldate = "2019-03-29",
    publisher = "Springer Berlin Heidelberg",
    year = "2002",
    doi = "10.1007/978-3-662-04954-9"
}

1998

Charles E. Glassick, Mary Taylor Huber, and Gene I. Maeroff. Scholarship assessed: Evaluation of the professoriate. The Journal of Academic Librarianship, 24(4):336–337, July 1998. URL: https://www.sciencedirect.com/science/article/pii/S0099133398901252, doi:https://doi.org/10.1016/S0099-1333(98)90125-2.
[BibTeX▼]

@article{glassick_scholarship_1998,
    author = "Glassick, Charles E. and Huber, Mary Taylor and Maeroff, Gene I.",
    title = "Scholarship assessed: {Evaluation} of the professoriate",
    volume = "24",
    issn = "0099-1333",
    url = "https://www.sciencedirect.com/science/article/pii/S0099133398901252",
    doi = "https://doi.org/10.1016/S0099-1333(98)90125-2",
    language = "English",
    number = "4",
    journal = "The Journal of Academic Librarianship",
    month = "July",
    year = "1998",
    keywords = "scholarship",
    pages = "336--337"
}

1996

Eleanor J. Sullivan. Expanding the definition of scholarship. Journal of Professional Nursing, 1996. URL: https://www-sciencedirect-com.offcampus.lib.washington.edu/science/article/pii/S8755722396800664?via%3Dihub, doi:https://doi.org/10.1016/S8755-7223(96)80066-4.
[BibTeX▼]

@article{sullivan_expanding_1996,
    author = "Sullivan, Eleanor J.",
    title = "Expanding the definition of scholarship",
    volume = "12",
    url = "https://www-sciencedirect-com.offcampus.lib.washington.edu/science/article/pii/S8755722396800664?via\%3Dihub",
    doi = "https://doi.org/10.1016/S8755-7223(96)80066-4",
    language = "English",
    number = "1",
    journal = "Journal of Professional Nursing",
    year = "1996",
    keywords = "scholarship"
}

1995

Ann Shumelda Okerson and James J. O'Donnell. Scholarly journals at the crossroads: a subversive proposal for electronic publishing. Washington, D.C. :, 1995. URL: http://hdl.handle.net/2027/mdp.39015034923758.
[BibTeX▼]

@book{okerson_scholarly_nodate,
    author = "Okerson, Ann Shumelda and O'Donnell, James J.",
    title = "Scholarly journals at the crossroads: a subversive proposal for electronic publishing",
    url = "http://hdl.handle.net/2027/mdp.39015034923758",
    publisher = "Washington, D.C. :",
    year = "1995"
}

1990

Ernest Boyer, Drew Moser, Todd C Ream, and John M Braxton. Scholarship Reconsidered: Priorities of the Professoriate. Carnegie Foundation for the Advancement of Teaching, 1990. ISBN 0-7879-4069-0.
[BibTeX▼]

@book{boyer_scholarship_1990,
    author = "Boyer, Ernest and Moser, Drew and Ream, Todd C and Braxton, John M",
    title = "Scholarship {Reconsidered}: {Priorities} of the {Professoriate}",
    isbn = "0-7879-4069-0",
    language = "English",
    publisher = "Carnegie Foundation for the Advancement of Teaching",
    year = "1990",
    keywords = "scholarship"
}