OpenScienceMOOC · jcolomb · Mar 21, 2020 · Mar 21, 2020 · Mar 26, 2020 · Mar 21, 2020
diff --git a/README.md b/README.md
@@ -13,9 +13,9 @@
 
 Welcome to Module 5 of the Open Science MOOC! Here you can find important information on the development of the module, including the latest updates to the content.
 
-**STATUS**: LIVE
+**STATUS**: ready to get LIVE
 
-This module us now LIVE on [Eliademy](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html). Check out the latest [video online here](https://www.youtube.com/watch?v=1fwGliIyAZs).
+ Check out the latest [video online here](https://www.youtube.com/watch?v=1fwGliIyAZs).
 
 The third release for this module is now also ready, and has been published on Zenodo: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1434288.svg)](https://doi.org/10.5281/zenodo.1434288)
 
@@ -25,7 +25,7 @@ Jon Tennant; Simon Worthington; Tania Allard; Philipp Zumstein; Daniel S. Katz;
 
 - [**Production Toolkit**](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/tree/master/production_toolkit) - This is where the basic protocols and outline for the module development are kept. It includes a tracking scheme as the content development progresses.
 
-Don't forget to join us in our open [Slack group](https://osmooc.herokuapp.com/)! The channel for this module is #module5opensource. You can also sign up to our mailing list [here](https://opensciencemooc.eu/contact/). To join the development team for the Open Science MOOC, anyone can openly add themselves [here](https://open-science-mooc-invite.herokuapp.com/).
+Don't forget to join us in our open [Slack group](https://osmooc.herokuapp.com/)! The channel for this module is #module5opensource. You can also sign up to our mailing list [here](https://opensciencemooc.eu/). To join the development team for the Open Science MOOC, anyone can openly add themselves [here](https://open-science-mooc-invite.herokuapp.com/).
 
 
 ## Rationale <a name="Rationale"></a>
@@ -60,7 +60,7 @@ Software and technology underpin modern science. There is an increasing demand f
 - [Module design protocol](MODULE_DESIGN_PROTOCOL.md) - The procedure for content development.
 - [Code of conduct](CODE_OF_CONDUCT.md) - The code of conduct that we expect contributors to adhere to.
 - [Key elements](key_elements.md) - Important reading materials and tools.
-- [Reading material](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/tree/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software) - Specifically reports and peer reviewed papers.
+- [Reading material](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/tree/master/Reading_Material_OSS) - Specifically reports and peer reviewed papers.
 
 Please note that all the reading materials are Open Access. Please do not upload articles which are paywalled or which are not openly licensed.
 

diff --git a/Reading_Material_OSS/README.md b/Reading_Material_OSS/README.md
@@ -1,3 +1,3 @@
 ## Reading Material
 
-This is where the core additional reading materials for this module of the MOOC are kept. All articles here are Open Access, and thus can be freely read, shared, and re-used. You can also find links to them within the [live module for this MOOC](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html).
+This is where the core additional reading materials for this module of the MOOC are kept. All articles here are Open Access, and thus can be freely read, shared, and re-used. Y
diff --git a/content_development/00mooc_mod5_Part1.html b/content_development/00mooc_mod5_Part1.html
diff --git a/content_development/00mooc_mod5_Part1.md b/content_development/00mooc_mod5_Part1.md
diff --git a/content_development/00mooc_mod5_Part2.html b/content_development/00mooc_mod5_Part2.html
diff --git a/content_development/00mooc_mod5_Part2.md b/content_development/00mooc_mod5_Part2.md
diff --git a/content_development/00mooc_mod5_Part3.html b/content_development/00mooc_mod5_Part3.html
@@ -0,0 +1,35 @@
+
+
+
+<div id="module-5-open-research-software-and-open-source-part-2" class="section level1">
+<h1>Module 5: Open Research Software and Open Source, part 2</h1>
+<div id="table-of-contents" class="section level2">
+<h2>Table of Contents</h2>
+<ul>
+<li><a href="#Collaborating">Collaborating through Open Source</a></li>
+<li><a href="#Future_OSS">Where to go from here</a></li>
+</ul>
+</div>
+<div id="collaborating-and-contributing-through-open-source" class="section level2">
+<h2>Collaborating and contributing through Open Source <a name="Collaborating"></a></h2>
+<p>Often, OSS is developed in a public, decentralised, collaborative manner between multiple contributors. The purpose of this is to enhance the diversity and scope of a project and its design, in order to become more beneficial and sustainable. Such an approach was famously likened to a ‘bazaar’ model by Eric Raymond, an early OSS proponent. One of the major guiding principles of this is that of <strong>peer production</strong>, which relies on self-organised communities to regulate the development of content, co-ordinated towards a shared goal or outcome.</p>
+<p>OSS projects rely heavily on volunteer collaboration, which often entails a constant flux of newcomers in order to become productive and sustainable (<a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Steinmacher%20et%20al.%2C%202014.pdf">Steinmacher et al., 2014</a>). Creating the right social atmosphere for a project, and a welcoming engagement environment, are often critical to successful collaboraitons in OSS.</p>
+<p><br /></p>
+</div>
+<div id="where-to-go-from-here" class="section level2">
+<h2>Where to go from here <a name="Future_OSS"></a></h2>
+<p>Hopefully now you have come to see the importance of software as a cornerstone of modern science, and the importance that OSS plays in this.</p>
+<p>The <strong>learning outcomes</strong> from this should be:</p>
+<ol style="list-style-type: decimal">
+<li><p>You will now be able to define the characteristics of OSS, and some of the ethical, legal, economic and research impact arguments for and against it.</p></li>
+<li><p>Based on community standards, you will now be able to describe the quality requirements of sharing and re-using open code.</p></li>
+<li><p>You will now be able to use a range of research tools that utilise OSS.</p></li>
+<li><p>You will now be able to transform code designed for their personal use into code that is accessible and re-usable by others.</p></li>
+<li><p>Software developers will be able to make their software citable, and software users will know how to cite the software they use.</p></li>
+</ol>
+<p><br /></p>
+<p><strong>BONUS TASK</strong></p>
+<p>Task 3 <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/Task_3.md">(also available on github)</a> will take you a step deeper into integrating Git into a typical research workflow by showing you how to integrate it with RStudio. It is recommended that you have completed the first 2 tasks before proceeding with this one.</p>
+</div>
+</div>
+
diff --git a/content_development/00mooc_mod5_Part3.md b/content_development/00mooc_mod5_Part3.md
@@ -0,0 +1,43 @@
+---
+title: "OSMOOC 5.3"
+output:
+  html_fragment
+---
+
+# Module 5: Open Research Software and Open Source, part 2
+
+## Table of Contents
+
+
+ - [Collaborating through Open Source](#Collaborating)
+ - [Where to go from here](#Future_OSS)
+
+## Collaborating and contributing through Open Source <a name="Collaborating"></a>
+
+Often, OSS is developed in a public, decentralised, collaborative manner between multiple contributors. The purpose of this is to enhance the diversity and scope of a project and its design, in order to become more beneficial and sustainable. Such an approach was famously likened to a 'bazaar' model by Eric Raymond, an early OSS proponent. One of the major guiding principles of this is that of **peer production**, which relies on self-organised communities to regulate the development of content, co-ordinated towards a shared goal or outcome.
+
+OSS projects rely heavily on volunteer collaboration, which often entails a constant flux of newcomers in order to become productive and sustainable ([Steinmacher et al., 2014](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Steinmacher%20et%20al.%2C%202014.pdf)). Creating the right social atmosphere for a project, and a welcoming engagement environment, are often critical to successful collaboraitons in OSS.
+
+<br/>
+
+## Where to go from here <a name="Future_OSS"></a>
+
+Hopefully now you have come to see the importance of software as a cornerstone of modern science, and the importance that OSS plays in this.
+
+The **learning outcomes** from this should be:
+
+1. You will now be able to define the characteristics of OSS, and some of the ethical, legal, economic and research impact arguments for and against it.
+
+2. Based on community standards, you will now be able to describe the quality requirements of sharing and re-using open code.
+
+3. You will now be able to use a range of research tools that utilise OSS.
+
+4. You will now be able to transform code designed for their personal use into code that is accessible and re-usable by others.
+
+5. Software developers will be able to make their software citable, and software users will know how to cite the software they use.
+
+<br/>
+
+**BONUS TASK**
+
+Task 3 [(also available on github)](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/Task_3.md) will take you a step deeper into integrating Git into a typical research workflow by showing you how to integrate it with RStudio. It is recommended that you have completed the first 2 tasks before proceeding with this one.
diff --git a/content_development/00mooc_mod5_Part4_appendix.html b/content_development/00mooc_mod5_Part4_appendix.html
@@ -0,0 +1,57 @@
+
+
+
+<div id="appendix" class="section level2">
+<h2>Appendix</h2>
+<p>However, your Open Source journey does not stop here! This was just the beginning, and there are some incredible resources out there if you would like to do or learn more:</p>
+<ul>
+<li><p>If you feel particularly inspired by this, you can endorse the <a href="http://sciencecodemanifesto.org/">Science Code Manifesto</a>, which is based on the five principles of code, copyright, citation, credit, and curation.</p></li>
+<li><p>To launch and develop your own project, the <a href="https://opensource.guide/">Open Source Guides</a> program offers a range of practical guides and skills to help launch and advance your OSS projects.</p></li>
+<li><p>For a detailed look at OSS-based research workflows, the <a href="https://pfern.github.io/OSODOS/gitbook/">Open Science, Open Data, Open Source</a> hand-guide by Pedro L. Fernandes and Rutger A. Vos is one of the top resources online.</p></li>
+<li><p>More formalised journal venues also exist for software-based articles, including <a href="https://openresearchsoftware.metajnl.com/">The Journal of Open Research Software</a> and <a href="https://joss.theoj.org/">The Journal of Open Source Software</a>. A list of such venues is also <a href="https://www.software.ac.uk/which-journals-should-i-publish-my-software">available</a>.</p></li>
+<li><p>The <a href="https://channels.plos.org/open-source-toolkit">PLOS Open Source Toolkit</a> provides a global forum for Open Source hardware and software research and applications.</p></li>
+<li><p>The <a href="http://www.numfocus.org">NumFOCUS</a> is a nonprofit organization that supports and promotes world-class, innovative, open source scientific software. Some of the projects they sponsor include:</p>
+<ul>
+<li><p><a href="http://ipython.org">IPython</a> and <a href="https://jupyter.org">Jupyter Notebook</a> initiatives.</p></li>
+<li><p><a href="http://ropensci.org">rOpenSci</a>, which promotes the open source R statistical environment for transparent and reproducible research.</p></li>
+<li><p>To gain more hands on experience with OSS, the <a href="https://software-carpentry.org/">Software Carpentry</a> community holds regular workshops to improve lab-based computing skills (<a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Wilson%20et%20al.%2C%202017.pdf">Wilson et al., 2017</a>).</p></li>
+</ul></li>
+</ul>
+<p><br /></p>
+<div id="further-reading" class="section level3">
+<h3>Further reading <a name="Reading"></a></h3>
+<p><em>These references here are just the beginning. They include some of the most useful general overviews of the Open Source landscape in research. However, if you want to be find something more specific to your own research field, then that path is there for you to explore!</em></p>
+<ul>
+<li><p>The Future of Research in Free/Open Source Software Development <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Scacchi%2C%202010.pdf">(Scacchi, 2010)</a>.</p></li>
+<li><p>The Scientific Method in Practice: Reproducibility in the Computational Sciences <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Stodden%2C%202010.pdf">(Stodden, 2010)</a>.</p></li>
+<li><p>The case for open computer programs <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Ince%20et%20al.%2C%202012.pdf">(Ince et al., 2012)</a>.</p></li>
+<li><p>Current issues and research trends on open-source software communities <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Martinez-Torres%20and%20Diaz-Fernandez%2C%202013.pdf">(Martinez-Torres and Diaz-Fernandez, 2013)</a>.</p></li>
+<li><p>Ten simple rules for reproducible computational research <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Sandve%20et%20al.%2C%202013.PDF">(Sandve et al., 2013)</a>.</p></li>
+<li><p>A systematic literature review on the barriers faced by newcomers to open source software projects <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Steinmacher%20et%20al.%2C%202014.pdf">(Steinmacher et al., 2014)</a>.</p></li>
+<li><p>Knowledge sharing in open source software communities: motivations and management <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Iskoujina%20and%20Roberts%2C%202015.pdf">(Iskoujina and Roberts, 2015)</a>.</p></li>
+<li><p>Software citation principles <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Smith%20et%20al.%2C%202016.pdf">(Smith et al., 2016)</a>.</p></li>
+<li><p>An introduction to Rocker: Docker containers for R <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Boettiger%20and%20Eddelbuettel%2C%202017.pdf">(Boettiger and Eddelbuettel, 2017)</a>.</p></li>
+<li><p>Good enough practices in scientific computing <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Wilson%20et%20al.%2C%202017.pdf">(Wilson et al., 2017)</a>.</p></li>
+<li><p>Four simple recommendations to encourage best practices in research software <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading_Material_OSS/Jim%C3%A9nez%20et%20al.%2C%202018.pdf">(Jiménez et al., 2017)</a>.</p></li>
+</ul>
+<p><br /></p>
+</div>
+<div id="development-team" class="section level3">
+<h3>Development Team <a name="Development_team"></a></h3>
+<ul>
+<li><a href="https://twitter.com/alex__morley">Alex Morley</a>, Open Sourceror, University of Oxford, UK.</li>
+<li><a href="https://twitter.com/KMMoerman">Kevin Moerman</a>, Open Sourceror, MIT, USA.</li>
+<li><a href="https://twitter.com/ixek">Tania Allard</a>, Open Sourceress, Data Enchantress, University of Leeds, UK.</li>
+<li><a href="https://twitter.com/mrchristian99">Simon Worthington</a>, Book Liberationist, TIB, Germany.</li>
+<li><a href="https://twitter.com/pcmasuzzo">Paola Masuzzo</a>, Open Source Batman, Italy.</li>
+<li><a href="https://twitter.com/OAforClimate">Ivo Grigorov</a>, Open Source Robin, Denmark.</li>
+<li><a href="https://twitter.com/rvosa">Rutger Vos</a>, Open Sourceror, Naturalis Biodiversity Center, the Netherlands.</li>
+<li><a href="https://twitter.com/j_colomb">Julien Colomb</a>, Open Ninja, Berlin.</li>
+<li><a href="https://twitter.com/protohedgehog">Jon Tennant</a>, Dinosaur Whisperer.</li>
+</ul>
+<p><strong>Know a way this content can be improved?</strong></p>
+<p>Time to take your new GitHub skills for a test-run! All content development primarily happens <a href="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/MAIN.md">here</a>. If you have a suggested improvement to the content, layout, or anything else, you can make it and then it will automatically become part of the MOOC content after verification from a moderator!</p>
+<p><a href="https://creativecommons.org/publicdomain/zero/1.0/"><img src="data:image/svg+xml;charset=utf-8;base64,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" alt="CC0 Public Domain Dedication" /></a></p>
+</div>
+</div>
+