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<doctype html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<title>Opening Your Research Using GitHub and OSF</title>
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<div class="reveal">
<div class="slides">
<!--SLIDE 1-->
<section>
<h2>Open Access Publishing with GitHub, arXiv, and engrXiv</h2><br/>
<div class="title-page"><p>Vicky Steeves | February 21, 2018</p></div>
<img src="imgs/dataservices.png" height="50%" width="50%" align="middle"><br/>
<hr/>
<div class="footer">
<p>Vicky's ORCID: <a href="http://orcid.org/0000-0003-4298-168X/">0000-0003-4298-168X</a><br/>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International License</a>.</p>
</div>
</section>
<!--SLIDE 2-->
<section>
<h2>Looking at scholarship holistically</h2><br/>
<div style="float:left; width:45%">
<p>We do a lot of very different things in very different ways during our research. But the final conclusion is always just a paper-- let's challenge that.</p>
</div>
<div style="float:right; width:45%">
<img src="imgs/lifecycle.png">
</div>
</section>
<!--SLIDE 3-->
<section>
<h2>A Reminder of Some Open Access Principles</h2>
<ol>
<li>Green vs. Gold Access</li>
<ul><li>Green: freely accessible, self-archived</li>
<li>Gold: researcher-paid freely available</li>
<li>Close link between publication and data archiving (i.e. archiving by journals) means data archiving may be green/gold depending on journal</li></ul>
</ol>
<p>Today, we're talking about GREEN open access. You will be self-archiving your work!</p>
</section>
<!--SLIDE 4-->
<section>
<h2>Some Minimum Requirements</h2><br/>
<p>Data and code must be:</p>
<ul><li>Persistently linked (At least URI/URL...preferabally DOI)</li>
<li>Searchable and browsable</li>
<li>Retrieved or downloaded easily</li>
<li>Citable</li>
</ul>
</section>
<!--SLIDE 5-->
<section>
<h2>The Why of<br/> Open Data & Code</h2><br/>
<p><span style="color: #42e342;">Not selfishly</span>: it helps advance your field of research!</p>
<p><span style="color: #e34242;">Selfishly</span>: citations!</p><br/>
<p>Data and code should be cited within our work for the same reasons journal articles are cited:</p>
<p><span style="color: #57068c;">to give credit where credit is due</span> (original author/producer) and to <span style="color: #57068c;">help other researchers find the material</span>.</p>
</section>
<!--SLIDE 6-->
<section>
<h2>Advantages to Tracking Citations:</h2>
<ul style="text-align:left;">
<li>Demonstrate to funders/promotion committees you & your data make big impacts in your field! </li>
<ul><li>they judge merit based on intellectual merit and wider impact</li>
<li>tangible evidence to weigh against the cost of research</li></ul><br/>
<li>Monitor usage of datasets!</li>
<ul><li>You can know what forms of data prep and data publication are most effective for sharing/open science!</li>
<li>Uncover opportunities for collaboration amongst peers</li></ul>
</ul>
</section>
<!--SLIDE 7-->
<section>
<h2>So...let's make your research citable!</h2><br/>
<p><span style="color: #57068c;">Step 1:</span> Write/version code in GitHub.</p>
<p><span style="color: #57068c;">Step 2:</span> Use the Open Science Framework to store data, documentation, etc.</p>
<p><span style="color: #57068c;">Step 3:</span> Publish & reap all your analytics!</p>
<p>Let's check out <a href="https://osf.io/zndwq/">a brief example</a> before getting into the details!</p>
</section>
<!--SLIDE 8-->
<section>
<h2>So...GitHub! <img src="imgs/github-logo.png" height="20%"></h2><br/>
<p><span style="color:#79dbf2;">GitHub</span> is a website where you can upload a copy of your Git repository. It allows people to collaborate via Git along with some other features.</p>
<p>GitHub is great because it allows folks to </p>
</section>
<!--SLIDE 9-->
<section>
<h2>Resources For Learning More</h2><br/>
<div style="float:left; width:45%">
<p><span style="color:#f05033;">Git</span></p>
<ul>
<li><a href="https://try.github.io/levels/1/challenges/1">TryGit</a>: enter commands in-browser!</li>
<li><a href="http://rogerdudler.github.io/git-guide/">Git: The Simple Guide</a>: step-by-step Git tutorial</li>
<li><a href="http://think-like-a-git.net/">Think Like A Git</a>: for someone who's been using Git, but doesn't feel they really understand it.</li>
</ul>
</div>
<div style="float:right; width:45%">
<p><span style="color:#79dbf2;">GitHub</span></p>
<ul>
<li><a href="https://guides.github.com/">GitHub Guides</a>: official help docs</li>
<li><a href="https://www.youtube.com/c/githubguides">GitHub Training Videos</a>: official video tutorials</li>
<li><a href="https://www.lynda.com/GitHub-training-tutorials/1384-0.html">Lynda.com</a>: free tutorials with NYU credentials</li>
</ul>
</div>
</section>
<!--SLIDE 10-->
<section>
<h2>What is the Open Science Framework?</h2>
<img src="imgs/osfDiagram.png" width="50%" height="60%" style="float:right; margin-left:0.5em;"><br/>
<p>A free and open source project management tool that connects researchers to the tools they are already using to make management easier through the research cycle.</p><br/>
</section>
<!--SLIDE 11-->
<section>
<h2>Why Use the OSF?</h2><br/>
<ul>
<li>Preserve your current workflow, file types, and standard operating procedures</li>
<li>Enhance those workflows by better documentation, sharing, and discovery of your research materials</li>
<li>Gather together group permissions, various storage options, bibliographic management, and publication in one place</li>
<li>OSF is the work of a non-profit, the Center for Open Science, dedicated to supporting open science using open-source tools</li>
</ul>
</section>
<!-- SLIDE 12-->
<section>
<h2>Integrations with Research Tools</h2>
<img src="imgs/osfConnections.png">
</section>
<!-- SLIDE 13-->
<section>
<h2>Getting Started: OSF at NYU</h2>
<p>Sign up at <a href="http://osf.io/">osf.io</a> using your NetID and create your account. <br/>Click on "Sign In" and at the bottom of the sign-in box, the link for "Login Through Your Institution."</p>
<img src="imgs/osf-institution-signin.png" width="40%" height="40%">
</section>
<!-- SLIDE 14-->
<section>
<h2>Setting Up a Project</h2>
<p class="fragment" data-fragment-index="1">Go to <a href="https://osf.io">https://osf.io</a> or just click "My Projects" on the top bar. <img src="imgs/osfBar.png" width="90%" height="90%"></p>
<p class="fragment" data-fragment-index="2">Click "Create Project" and fill in the form. <img src="imgs/osfCreateProject.png" width="55%" height="55%"></p>
</section>
<!--SLIDE 15-->
<section>
<h2>Don't Be Afraid of How Blank It Looks...</h2>
<img src="imgs/osfBlank.png" width="80%" height="80%">
</section>
<!--SLIDE 16-->
<section>
<h2>Let's Add Collaborators</h2>
<p class="fragment" data-fragment-index="1">Click "add" button next to the title of the page. <img src="imgs/osfCollabs.png" width="70%" height="70%"></p>
<p class="fragment" data-fragment-index="2">Search for the person to your right and add them.<img src="imgs/osfCollabs1.png" width="60%" height="60%"></p>
</section>
<!--SLIDE 17-->
<section>
<h2>Sharing</h2>
<p>Everything (files, subcomponents, wiki docs) gets a short permalink in OSF.</p><p>That makes it easy to share via e-mail, Twitter, pastebins, etc.</p>
<p>You can also share projects via a view-only link, including an option to anonymize contributors for blind peer review.</p>
<img src="imgs/osfShareOnly.png" width="40%" eight="40%">
</section>
<!--SLIDE 18-->
<section>
<h2>Setting Up Accounts</h2>
<div style="float:left; width:50%">
<p>Try adding an account of your own by clicking on your profile (top right hand corner), then "Settings," then "Configure Add-on Accounts." Click on "Connect Account" next to an addon.</p>
</div>
<div style="float:right; width:50%">
<img src="imgs/osfProfileAddons.png" >
</div>
</section>
<!--SLIDE 19-->
<section>
<h2>Back to Your Project: Select Your Project Add-ons</h2>
<p>Go to your project, click "Add-ons" in project navigation.</p>
<img src="imgs/osfProjectAddons.png">
</section>
<!--SLIDE 20-->
<section>
<h2>Adding Your Addons</h2>
<p class="fragment" data-fragment-index="1"><img src="imgs/osfProjectAddons1.png" width="90%" height="90%"></p>
<p class="fragment" data-fragment-index="2"><img src="imgs/osfProjectAddons2.png" width="60%" height="60%"></p>
</section>
<!--SLIDE 21-->
<section>
<h2>Authorizing Your Addons</h2>
<p>Read the terms, and agree if you feel comfortable.</p>
<img src="imgs/osfProjectAddonsTerms.png" width="50%" height="50%">
</section>
<!--SLIDE 22-->
<section>
<h2>Choose Your Repo</h2>
<p>Click 'Configure Add-ons' and use the drop down menu to select an existing repository, OR create a repository which will sit on your GitHub account.</p>
<img src="imgs/osfProjectAddons3.png">
</section>
<!--SLIDE 23-->
<section>
<h2>Working with Your Files</h3>
<p>Click on "Files" on Your Project Top Menu</p>
<p>From here, you can:</p>
<ul>
<li>See all files from OSF storage and any configured addons</li>
<li>Drag and drop files into any kind of storage, OSF or otherwise</li>
<li>Create folders in OSF storage for better organization</li>
</ul><br/>
<img src="imgs/osfFiles.png" width="80%" height="80%">
</section>
<!--SLIDE 24-->
<section>
<h2>Versioning Files</h2>
<p>When you click on a file in OSF storage, you can also see and download all the versions of that file that have been uploaded.</p>
<p>THE CATCH: The file has to be uploaded with the same name!</p>
<img src="imgs/osfFileVersions.png" width="90%" height="90%">
</section>
<!--SLIDE 25-->
<section>
<h2>Automating File Uploads/Downloads</h2>
<p>Now, you use scripts in R or Python to interface with OSF storage. These are the two libraries, one for R, one for Python, that can help you make your workflow more efficient!</p>
<div style="float:left; width:53%;">
<p><a href="https://github.com/chartgerink/osfr">OSFR</a>: R library to interface with OSF storage</p>
<pre><code>devtools::install_github('chartgerink/osfr')
login()</pre></code>
</div>
<div style="float:right; width:45%;">
<p><a href="https://github.com/osfclient/osfclient">OSFCLIENT</a>: Python library and command-line client for file storage on OSF</p>
<pre><code>pip install osfclient
osf clone</pre></code>
</div>
</section>
<!--SLIDE 26-->
<section>
<h2>Documenting with the Wiki</h2>
<img src="imgs/osfWiki.png" width="90%" height="90%">
<p>This also has a robust versioning. And you can compare versions side-by-side.</p>
<img src="imgs/osfWiki1.png" width="40%" height="40%">
</section>
<!--SLIDE 27-->
<section>
<h2>Best Practices with the Wiki</h2>
<p>Use the "Home" wiki page as a table of contents listing project goals, personnel, sub-components, and links to important files.</p>
<img src="imgs/osf-wiki-toc.png" width="70%" height="70%">
</section>
<!--SLIDE 28-->
<section>
<h2>So now you can:</h2>
<ol>
<li>Host your code in a GitHub repository</li>
<li>Host your data via the OSF (either in OSF storage or another add-on)</li>
<li>Download and upload data in/out of the OSF programmatically</li>
<li>Centralize all your documentation via the OSF Wiki</li>
</ol>
</section>
<!--SLIDE 29-->
<section>
<h2>Components</h2>
<p>Components are essentially "sub-projects" that can have their own set of collaborators, add-ons, and access controls.</p>
<img src="imgs/osfComponents.png" width="90%" height="90%">
</section>
<!--SLIDE 30-->
<section>
<h2>Before publishing: Prep Your Code!</h2>
<div style="text-align:left;">
<p><span style="color: #57068c;">Step 1</span>: Comment & style your code—</p>
<ul>
<li>COMMENT YOUR STUFF. PLEASE.</li>
<li>Use the <a href="https://www.python.org/dev/peps/pep-0008/">Pep 8 Python style guide</a>!</li>
</ul>
</div>
<img src="imgs/code-ett.png" align="middle" height="70%" width="70%">
</section>
<!--SLIDE 31-->
<section>
<h2>Before publishing: Prep Your Data!</h2>
<div style="text-align:left;">
<p><span style="color: #57068c;">Step 1</span>: Put your data into an open format!</p>
<ul><li>Be software agnotic!</li></ul><br/>
<img src="imgs/archival-formats.png" width="55%" height="20%" align="middle">
<p><span style="color:#57068c;">Step 2</span>: Package Your Materials</p>
<ul>
<li>Data files & scripts/analysis tools</li>
<li>Documentation & description in OSF wiki or upload metadata</li>
</ul>
</div>
</section>
<!--SLIDE 32-->
<section>
<h2>Going Public</h2>
<p>All OSF projects start private. We can make them public when we are ready and reap some benefits, like built-in analytics</p>
<img src="imgs/osfAnalytics.png" width="75%" height="75%">>
</section>
<!--SLIDE 33-->
<section>
<h2>Publishing</h2>
<p>When you want to publish your final product, you <em>register</em> it. All the files are pulled into an archive on OSF storage, and the project becomes read-only.</p>
<p>You can get a DOI for this project, and include it in a "Supplementary Materials Section" of a journal article.</p>
<img src="imgs/osfRegistration.png" width="70%" height="70%">
</section>
<!--SLIDE 34-->
<section>
<h2>Publishing via <a href="https://cos.io/our-products/osf-preprints/">domain services</a></h2>
<div style="float:left; width:49%">
<p>All you have to is go to the submission link (e.g. for engrxiv, <a href="https://osf.io/preprints/engrxiv/submit">osf.io/preprints/engrxiv/submit</a>) and select “Connect to existing OSF project”. You can then designate your front-facing document, and have your entire project seamlessly published into a domain-specific service!</p>
</div>
<div style="float:right; width:50%">
<img src="imgs/preprints.png">
</div>
</section>
<!--SLIDE 35-->
<section>
<h2>Publishing with engrxiv</h2>
<p><a href="http://blog.engrxiv.org/about/">engrxiv</a> is the open archive of engineering!</p>
<img src="imgs/engrxiv-subjects.png">
<ul>
<li><strong>Working papers</strong>: Any draft of a paper that is ready to share with interested parties, but has not yet been peer reviewed</li>
<li><strong>Preprints</strong>: Most people use this term to refer to completed papers that have not yet been peer reviewed.</li>
<li><strong>Postprints</strong>: The completed, peer-reviewed version without publisher formatting.</li>
</ul>
</section>
<!--SLIDE 36-->
<section>
<h2>Submitting to engrxiv</h2>
<div style="float:left; width:49%; font-size:21px;">
<ol>
<li>Go to <a href="https://osf.io/preprints/engrix/submit">osf.io/preprints/engrxiv/submit</a></li>
<ol><li>If you are uploading work that isn’t already on the OSF, click "Upload new"</li>
<li>If you already have work on the OSF you to submit, click "Connect to existing OSF project"</li>
<ol><li>You will select the project you want to associate</li>
<li>Either upload a new file or pick a file from the existing project.</li></ol></ol>
<li>Pick your subject headings from the menu.</li>
<li>Pick a license from the drop-down list.</li>
<li>Optionally, add:</li>
<ol><li>DOI from journal (if it relates to a published article)</li>
<li>Keywords</li>
<li>An abstract</li></ol>
<li>Add your co-authors. If they don’t have an OSF account, their names will be listed without links.</li>
<li>Submit!</li>
</ol>
</div>
<div style="float:right; width:50%"><img src="imgs/engrxiv-subjects-expand.png" height="65%" width="65%"></div>
</section>
<!--SLIDE 37-->
<section>
<h2>Holistical Publishing with engrxiv</h2>
<div style="float:left; width:50%">
<p>This is an <a href="https://engrxiv.org/k7fgk">example</a> of a project that was submitted to engrxiv. The authors submitted to engrxiv with with all code, data, and documentation RIGHT BELOW the rendered PDF. This is a powerful way to do openness -- not just free-to-read articles, but holistic and seamless access to EVERYTHING associated with a research project.</p>
</div>
<div style="float:right; width:50%">
<img src="imgs/engrxiv-ex.png">
</div>
</section>
<!--SLIDE 38-->
<section>
<h2>To sum it up:</h2><br/>
<ul>
<li>GitHub is a great place to version & collaborate on code.</li>
<li>The OSF is a great central location to document research, store data, and make it available.</li>
<li>Connecting the two lets you open up your scholarship holistically!</li>
<li>You can publish in a domain-specific space (like engrxiv) or via registering the project!</li>
<li>Your research gets more exposure, YOU get more exposure, and you benefit your field!</li>
</ul>
</section>
<!--SLIDE 39-->
<section>
<h2>Bonus: <a href="https://arxiv.org">arXiv.org</a></h2>
<p>"Started in August 1991, arXiv.org is a highly-automated electronic archive and distribution server for research articles. Covered areas include physics, mathematics, computer science, nonlinear sciences, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics. arXiv is maintained and operated by the Cornell University Library with guidance from the arXiv Scientific Advisory Board and the arXiv Member Advisory Board, and with the help of numerous subject moderators."</p>
</section>
<!--SLIDE 40-->
<section>
<h2>Bonus: submitting to arXiv.org</h2>
<p>arXiv has a great <a href="https://arxiv.org/help/submit">how-to</a> on submitting an article, but the basics are:</p>
<ul>
<li>Become a registered author -- in some fields, this requires endorsement from someone in your field.
<ul><li>Since January 17, 2004 arXiv has required that users be endorsed before submitting their first paper to a category or subject class.</li></ul></li>
<li>Submit your LaTex source or PDF files of your works, with any figures as separate files.</li>
<li>Add the title, abstract, coauthors, and license to your work. Submit!</li>
<li>Wait for moderation to publish your work.</li>
</ul>
</section>
<!-- CONCLUSION SLIDE -->
<section>
<h2>Questions?</h2><br/>
<p>Email me: <a href="mailto:[email protected]">[email protected]</a></p>
<p>Learn more about RDM: <a href="http://guides.nyu.edu/data_management">guides.nyu.edu/data_management</a></p>
<p>Get this presentation: <a href="http://guides.nyu.edu/data_management/resources">guides.nyu.edu/data_management/resources</a></p>
<p>Make an appointment: <a href="http://guides.nyu.edu/appointment">guides.nyu.edu/appointment</a></p>
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<p>Vicky's ORCID: <a href="http://orcid.org/0000-0003-4298-168X/">0000-0003-4298-168X</a><br/>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International License</a>.</p>
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