GitHub for academic research

[Joyce Ogburn]

DId you all see this article in Slate about a Github for academic research? Joyce

http://www.slate.com/articles/technology/future_tense/2017/04/we_need_a_github_for_academic_research.html

Joyce L. Ogburn

Appalachian State University

218 College Street

Boone NC 28608-2026

Lifelong learning requires lifelong access 

[Anthony Watkinson]

What about Figshare?

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[Mike Taylor]

GitHub *is* GitHub for academic research. See for example
http://blogs.lse.ac.uk/impactofsocialsciences/2013/06/04/github-for-academics/

-- Mike.



On 25 April 2017 at 15:32, Anthony Watkinson

[Keith Webster]

We’ve recently implemented Figshare as our institutional repository for (almost) all products of the research process - data, publications, code, etc.

We ran a competition to name the service, and the winning entry was KiltHub - kilthub.cmu.edu - we haven’t moved into production yet, but have pulled in some stuff from PLoS to make it feel a bit less empty.

[Amy L. Nurnberger]

The Reproducibility Project is supported on the Open Science Framework (a scholarly commons that includes some repository & data publication services), which has integrations with GitHub (a development platform that includes a version management system, *not* a repository). Figshare is a repository. 

Best,

Amy

On Tue, Apr 25, 2017 at 10:32 AM, Anthony Watkinson <anthony....@btinternet.com> wrote:

What about Figshare?

 

From: osi20...@googlegroups.com [mailto:osi2016-25@googlegroups.com] On Behalf Of Joyce Ogburn
Sent: 25 April 2017 14:13
To: The Open Scholarship Initiative
Subject: GitHub for academic research

 

DId you all see this article in Slate about a Github for academic research? Joyce

 

http://www.slate.com/articles/technology/future_tense/2017/04/we_need_a_github_for_academic_research.html

 

Joyce L. Ogburn

Appalachian State University

218 College Street

Boone NC 28608-2026

 

Lifelong learning requires lifelong access 

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[Anthony Watkinson]

Thanks Amy. I was speaking from a definite level of ignorance.

 

From: osi20...@googlegroups.com [mailto:osi20...@googlegroups.com] On Behalf Of Amy L. Nurnberger
Sent: 25 April 2017 15:41
To: The Open Scholarship Initiative
Subject: Re: GitHub for academic research

 

The Reproducibility Project is supported on the Open Science Framework (a scholarly commons that includes some repository & data publication services), which has integrations with GitHub (a development platform that includes a version management system, *not* a repository). Figshare is a repository. 

 

Best,

Amy

On Tue, Apr 25, 2017 at 10:32 AM, Anthony Watkinson <anthony....@btinternet.com> wrote:

What about Figshare?

 

From: osi20...@googlegroups.com [mailto:osi20...@googlegroups.com] On Behalf Of Joyce Ogburn
Sent: 25 April 2017 14:13
To: The Open Scholarship Initiative
Subject: GitHub for academic research

 

DId you all see this article in Slate about a Github for academic research? Joyce

 

http://www.slate.com/articles/technology/future_tense/2017/04/we_need_a_github_for_academic_research.html

 

Joyce L. Ogburn

Appalachian State University

218 College Street

Boone NC 28608-2026

 

Lifelong learning requires lifelong access 

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[Eric L Olson]

Going to ping Matt Spitzer, who works on OSF.  Thoughts, Matt?

Eric

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From: osi20...@googlegroups.com <osi20...@googlegroups.com> on behalf of Amy L. Nurnberger <anurn...@columbia.edu>
Sent: Tuesday, April 25, 2017 10:41:10 AM

To: The Open Scholarship Initiative

Subject: Re: GitHub for academic research

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[Alexander Garcia Castro]

I get lost in this mailing list wrt the meaning of repositories. as a researcher I consider Github as a repository. it has additional advantages like version control; git is a version control repository. Git is not a development platform, Azure, Google app engine, cumlogic those are development platforms. 

I have at least one student who writes his papers using Git because he can manage the versioning, include snippets of code, etc. I have another student using overleaf and has it connected to her git -again versioning control. If I were to consider the paper as an object that I release instead of publishing it, very much following the practices of software development where they have multiple releases, then I have a git for science. One that makes it possible to release instead of just publishing -the dont publish release was put forward long ago at a FORCE11 conference in Amsterdam. Many research objects depend version control, datasets, software, manuscripts, etc. 

Git has been mentioned, Blockchain and the IPFS have also been mentioned (this is an area of research that I am starting now) as candidates to support scholarly communication and managing the assets that come out of research. 

On Tue, Apr 25, 2017 at 4:41 PM, Amy L. Nurnberger <anurn...@columbia.edu> wrote:

The Reproducibility Project is supported on the Open Science Framework (a scholarly commons that includes some repository & data publication services), which has integrations with GitHub (a development platform that includes a version management system, *not* a repository). Figshare is a repository. 

Best,

Amy

--

Alexander Garcia
http://www.alexandergarcia.name/
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac

[Amy L. Nurnberger]

No worries! Everyone has their own areas of knowledge, and we're all about sharing :).

Sorry I missed OSI this year.

Best,

Amy

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[Amy L. Nurnberger]

Hi, Alexander,

When I named GitHub a development platform, I was going off of what their page said (https://github.com) "GitHub is a development platform inspired by the way you work". 

While GitHub calls their collections 'repos', they have integrations with Zenodo, and OSF has integrations with GitHub, to provide actual repository services. 

A nice definition for repository comes from the CASRAI dictionary: http://dictionary.casrai.org/Repository "Repositories preserve, manage, and provide access to many types of digital materials in a variety of formats. Materials in online repositories are curated to enable search, discovery, and reuse. There must be sufficient control for the digital material to be authentic, reliable, accessible and usable on a continuing basis."

All that said, I agree that GitHub is a great space to work in, and to Mike's point, in fact is the "GitHub for research." Your experiences also support this. At the same time, I would recommend basing work in OSF because of the many benefits it provides (Matt, this is for you to fill in...), and then linking the GitHub repo to the OSF project. Often, the intent of making work public is best supported when it is released through a repository that provides those characteristics mentioned in the CASRAI definition.

Best,

Amy

[Glenn Hampson]

One cool factoid here: The author of this Slate piece is OSI’s own Marcus Banks. Nice article Marcus!

 

Glenn Hampson

Executive Director

National Science Communication Institute (nSCI)

Program Director
Open Scholarship Initiative (OSI)

 

 

2320 N 137th Street | Seattle, WA 98133

(206) 417-3607 | gham...@nationalscience.org | nationalscience.org

 

From: osi20...@googlegroups.com [mailto:osi20...@googlegroups.com] On Behalf Of Amy L. Nurnberger
Sent: Tuesday, April 25, 2017 8:22 AM
To: Alexander Garcia Castro
Cc: The Open Scholarship Initiative
Subject: Re: GitHub for academic research

 

Hi, Alexander,

 

When I named GitHub a development platform, I was going off of what their page said (https://github.com) "GitHub is a development platform inspired by the way you work". 

While GitHub calls their collections 'repos', they have integrations with Zenodo, and OSF has integrations with GitHub, to provide actual repository services. 

 

A nice definition for repository comes from the CASRAI dictionary: http://dictionary.casrai.org/Repository "Repositories preserve, manage, and provide access to many types of digital materials in a variety of formats. Materials in online repositories are curated to enable search, discovery, and reuse. There must be sufficient control for the digital material to be authentic, reliable, accessible and usable on a continuing basis."

 

All that said, I agree that GitHub is a great space to work in, and to Mike's point, in fact is the "GitHub for research." Your experiences also support this. At the same time, I would recommend basing work in OSF because of the many benefits it provides (Matt, this is for you to fill in...), and then linking the GitHub repo to the OSF project. Often, the intent of making work public is best supported when it is released through a repository that provides those characteristics mentioned in the CASRAI definition.

 

Best,

Amy

 

On Tue, Apr 25, 2017 at 11:08 AM, Alexander Garcia Castro <alexg...@gmail.com> wrote:

I get lost in this mailing list wrt the meaning of repositories. as a researcher I consider Github as a repository. it has additional advantages like version control; git is a version control repository. Git is not a development platform, Azure, Google app engine, cumlogic those are development platforms. 

 

I have at least one student who writes his papers using Git because he can manage the versioning, include snippets of code, etc. I have another student using overleaf and has it connected to her git -again versioning control. If I were to consider the paper as an object that I release instead of publishing it, very much following the practices of software development where they have multiple releases, then I have a git for science. One that makes it possible to release instead of just publishing -the dont publish release was put forward long ago at a FORCE11 conference in Amsterdam. Many research objects depend version control, datasets, software, manuscripts, etc. 

 

Git has been mentioned, Blockchain and the IPFS have also been mentioned (this is an area of research that I am starting now) as candidates to support scholarly communication and managing the assets that come out of research. 

On Tue, Apr 25, 2017 at 4:41 PM, Amy L. Nurnberger <anurn...@columbia.edu> wrote:

The Reproducibility Project is supported on the Open Science Framework (a scholarly commons that includes some repository & data publication services), which has integrations with GitHub (a development platform that includes a version management system, *not* a repository). Figshare is a repository. 

 

Best,

Amy

On Tue, Apr 25, 2017 at 10:32 AM, Anthony Watkinson <anthony....@btinternet.com> wrote:

What about Figshare?

 

From: osi20...@googlegroups.com [mailto:osi20...@googlegroups.com] On Behalf Of Joyce Ogburn
Sent: 25 April 2017 14:13
To: The Open Scholarship Initiative
Subject: GitHub for academic research

 

DId you all see this article in Slate about a Github for academic research? Joyce

 

http://www.slate.com/articles/technology/future_tense/2017/04/we_need_a_github_for_academic_research.html

 

Joyce L. Ogburn

Appalachian State University

218 College Street

Boone NC 28608-2026

 

Lifelong learning requires lifelong access 

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[Matt Spitzer]

Hi Eric and others,

Yes. The Open Science Framework (osf.io) was built with the explicit intention of being an automated version controlled commons for scientific (and Humanities) research projects that connects to a wide variety of services researchers already use - figshare, GitHub, Dropbox, Box, Google Drive, and others. See more here: https://cos.io/our-products/open-science-framework/

I agree with Amy that the ideal is neither a repository nor just a version mgmt system, but a layer that connects the multitude of tools together with version control, and facilitates discovery and communication for a wider variety of outputs than just a final publication. The ideal should allow a single research project to have outputs into preprint services, institutional IRs, conference proceedings, data repositories, registries, and other collections all with a common and persistent url or DOI. That is what we are iterating towards with the OSF.

While the Center for Open Science's Executive Director, Brian Nosek, was quoted, he wasn't directly interviewed for the story, otherwise I'm sure the connection would have been made more explicitly. See this exchange on that: https://twitter.com/marcusabanks/status/855166692992835585

And although Git Hub is the largest repository of open source projects, it is itself not open source. The OSF is open source and free.

Regards,

Matt

________________

Matthew Spitzer

Community Manager

Center for Open Science

https://cos.io | @osframework

|   Use the OSF for reproducible research   |   Take the Prereg Challenge!   |

On Tue, Apr 25, 2017 at 11:03 AM, Eric L Olson <eol...@gmu.edu> wrote:

Going to ping Matt Spitzer, who works on OSF.  Thoughts, Matt?

Eric

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Eric L. Olson

Outreach Coordinator, PressForward Project

Roy Rosenzweig Center for History and New Media

George Mason University

4400 University Drive
Fairfax, VA 22030

(703) 993-9277

er...@pressforward.org

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From: osi20...@googlegroups.com <osi20...@googlegroups.com> on behalf of Amy L. Nurnberger <anurn...@columbia.edu>
Sent: Tuesday, April 25, 2017 10:41:10 AM
To: The Open Scholarship Initiative
Subject: Re: GitHub for academic research

 

The Reproducibility Project is supported on the Open Science Framework (a scholarly commons that includes some repository & data publication services), which has integrations with GitHub (a development platform that includes a version management system, *not* a repository). Figshare is a repository. 

Best,

Amy

[Lorena A Barba]

The article linked by Joyce touches on many issues at once, while the rest of this thread is really asking for a few clarifications.

BTW, I was one of the 2 or 3 active researchers attending OSI 2017. My research group uses GitHub intensely. We also use figshare (I was an early adopter and figshare advisor), Zenodo, Authorea, and several other digital services and tools.

Here’s a short interview with me that appeared a few days ago on Nature TechBlogs, focused on my “digital toolbox” and reproducibility practices:

http://blogs.nature.com/naturejobs/2017/04/17/techblog-my-digital-toolbox-lorena-barba/

Some clarifications:

(1) `git` is an open-source computer program, included in every distribution of the Linux operating system (and written by Linus Torvalds, creator of Linux) that is used to track all changes made to a text-based computer file (like computer code written in any language, or manuscripts written in LaTeX). 

[Wikipedia entry: git]

Please don’t use `git` to mean GitHub. 

(2) GitHub is a hosting service for code and other digital content that provides a web-based git. Users don’t just deposit their files on GitHub: they push to GitHub every granular change made to a file, using the power of git. On the web interface, users can compare versions of a file side-by-side (red: deleted; green: added). And you can go back in history to any version.

But GitHub is so much more! It is a social network and a collaboration tool. Every GitHub repository (a set of files that belong together, in a project) has an “issue tracker” where users write things to do, their category (bug fix, question, improvement, etc.), who they assign them to, and when the issue is “closed.” Anyone in the GitHub network can comment on issue threads, and tag other uses with their @-handle who then get notified.

The most powerful collaboration feature of GitHub is the “pull request.” Essentially, it is a structured conversation around code that allows people to contribute to projects owned by others, without stepping on their toes. It is a genius implementation of computer-mediated human coordination.

Despite providing hosting, GitHub is not a “repository” in the sense used in information management (data, preprint, institutional). It does not mint DOIs, for example. And users can delete their “repos” at any time.

In my group, we develop code and content on GitHub, and then deposit on Zenodo or Figshare when we need an archival version with a DOI.

(3) Figshare is a repository for digital objects, that assigns DOIs and promises archival persistence, plus tracks views and downloads. Although you can update the object to a new version (v1, v2, v3…), it is *not* version-controlled, in the git sense. (Git repositories, which can be local or hosted, track thousands of granular changes on a file.) 

The double use of the word “repository” is unfortunate. A “git repository” has nothing to do with a hosted, archival repository for data and digital objects.

_______________________________________
Lorena A. Barba

Associate Professor, Mechanical and Aerospace Engineering

The George Washington University
twitter.com/LorenaABarba

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[mab992]

Thanks so much, OSI colleagues, for the vigorous discussion of my piece in Slate about a "GitHub for Science." This short note will not touch on all the points raised in the discussion, but I did want to mention a few things.

This piece appeared in Slate's "Future Tense" section, the part of the magazine devoted to the intersection of technology and society. I made the assumption that readers of Future Tense would be interested in the topic of how the web can change scholarship but not be as conversant in the details and tools as the OSI community. That said GitHub, although not open source itself, is one of the most widely known software services and so for this purpose it was a convenient way to frame the issue in the context of something many people would understand. I've been part of a great Twitter discussion just today about how all of the tools/services I propose are already in place and so we don't need to build anything more. I agree. The point in Slate was to make the conceptual argument for why openness and transparency is the way to go, for an audience that may be considering the issue for the first time. I was not aiming to promote any specific tools, such as the OSF or Figshare (or anything else), in this piece.

Perhaps if I am fortunate enough to do a follow-up piece it could dive into some of the nuances reflected in today's discussion.

Kind regards, Marcus Banks

marcusabanks.com 

On Tue, Apr 25, 2017 at 10:32 AM, Anthony Watkinson <anthony....@btinternet.com> wrote:

What about Figshare?

 

From: osi20...@googlegroups.com [mailto:osi20...@googlegroups.com] On Behalf Of Joyce Ogburn
Sent: 25 April 2017 14:13
To: The Open Scholarship Initiative
Subject: GitHub for academic research

 

DId you all see this article in Slate about a Github for academic research? Joyce

 

http://www.slate.com/articles/technology/future_tense/2017/04/we_need_a_github_for_academic_research.html

 

Joyce L. Ogburn

Appalachian State University

218 College Street

Boone NC 28608-2026

 

Lifelong learning requires lifelong access 

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On Tue, Apr 25, 2017 at 10:32 AM, Anthony Watkinson <anthony....@btinternet.com> wrote:

What about Figshare?

 

From: osi20...@googlegroups.com [mailto:osi20...@googlegroups.com] On Behalf Of Joyce Ogburn
Sent: 25 April 2017 14:13
To: The Open Scholarship Initiative
Subject: GitHub for academic research

 

DId you all see this article in Slate about a Github for academic research? Joyce

 

http://www.slate.com/articles/technology/future_tense/2017/04/we_need_a_github_for_academic_research.html

 

Joyce L. Ogburn

Appalachian State University

218 College Street

Boone NC 28608-2026

 

Lifelong learning requires lifelong access 

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[matt.spitzer]

Thanks to Lorena and Marcus for the additional details. I found those very helpful.

We all use Github too and it's a great tool. But the learning curve and interface can be a hurdle for some. I usually recommend that if you can use just Github and like it, for all the reasons Lorena describes, it's a perfectly reasonable solution. The key difficulty comes when you want to collaborate with others who do not use it, or you want to seamlessly connect objects there to other locations for archiving or discipline specific curation or discovery. The OSF is one solution that works for some that is inclusive of all of the use cases described. fighare is a great tool as well for a final repository of the digital objects and many use this a compliment to the OSF

Workflows are idiosyncratic, but anyone using any of these tools is already ahead of the curve on participating in open scientific communication. How do we make these same choices the norm?

Matt Spitzer

Community Manager

Center for Open Science

@matthewspitzer

@OSFramework 

[Bryan Alexander]

It's interesting to see Github appear as another "rogue solution", in the terms of our work group last week.

What is the scholarly communication ecosystem *not* doing that makes Github attractive?  What pain points does it ameliorate? 

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[Mike Taylor]

> What is the scholarly communication ecosystem *not* doing that makes Github attractive?

Version control.
Safe backups.
Collaboration with merging.
Comparison of different versions.
Project website.
Issue tracker.
Ability to accept pull-requests.
Visibility while in progress.
"Open signalling".

I think I just persuaded myself to do my own next project on GitHub :-)

-- Mike.

> Bryan Alexander
> http://bryanalexander.org/
> http://twitter.com/BryanAlexander
> Future Trends in Technology and Education, http://ftte.us/
> The Future Trends Forum, https://bryanalexander.org/the-future-trends-forum/
>

[Christopher Erdmann]

Also, OSF is not the first to be labeled as the GitHub for research:

https://www.fastcompany.com/3016677/can-the-github-for-science-convince-researchers-to-open-source-their-data

[Eric L Olson]

Of which we also have an OSI member.  Josh (if this email still works), how do you see Authorea 

fitting into this picture?

Eric

--

Eric L. Olson

Outreach Coordinator, PressForward Project

Roy Rosenzweig Center for History and New Media

George Mason University

4400 University Drive
Fairfax, VA 22030

(703) 993-9277

er...@pressforward.org

---

From: osi20...@googlegroups.com <osi20...@googlegroups.com> on behalf of Christopher Erdmann <christoph...@ncsu.edu>
Sent: Thursday, April 27, 2017 7:56:17 AM
To: Bryan Alexander
Cc: matt.spitzer; The Open Scholarship Initiative; Alexander Garcia Castro; Lorena A Barba; Amy L. Nurnberger

Subject: Re: GitHub for academic research

[The Winnower]

Hello everyone!

"The Github of Research" is exactly how we see ourselves.  In fact, each article on Authorea is a git repository. In short, we're trying to take powerful yet hard to navigate technology like git and LaTeX and making it easier to use so that it can be more widely adopted.

I think this article might be of interest to those on the thread https://www.authorea.com/users/8850/articles/164546-bringing-the-power-of-latex-and-git-to-all-researchers

best,

Josh