Added PDF files with images for main files

Author: protohedgehog

content_development/MAIN.md

@@ -21,14 +21,14 @@ output:
  - [Using GitHub and Zenodo](#GitHub_Zenodo)
  - [Collaborating through Open Source](#Collaborating)
  - [Where to go from here](#Future_OSS)
- 
- 
+
+
 [IDEA: ONCE TEXT IS COMPLETE; CREATE AUDIO RECORDING FOR ALL OF THIS FOR EACH MODULE, and release as a podcast]
 
 
 ## Introduction <a name="Introduction"></a>
 
-Welcome to **Module 5** of the Open Science MOOC: **Open Research Software and Open Source**. 
+Welcome to **Module 5** of the Open Science MOOC: **Open Research Software and Open Source**.
 
 This module has been developed [in the open](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source) through collaboration by an international team of [Open Source afficianados](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/README.md#development-team-). Everything you see here has been developed in the open through interactive feedback and collaboration from the wider community. It comprises a series of videos, infographics, text-based reading (sorry), and practical tasks for you to sink you teeth into.
 
@@ -44,11 +44,11 @@ This module is designed primarily for computational researchers at the graduate
 
 > "An article about computational result is advertising, not scholarship. The actual scholarship is the full software environment, code and data, that produced the result." - J. Buckheit and D. L. Donoho, 1995.
 
-Software and technology underpin much of modern research, which is now almost inevitably computational in one way or another - search engines, social networking platforms, analytical software, and digital publishing. With this, there is an ever-increasing demand for more sophisticated Open Source Software, matched by an increasing willingness for researchers to openly collaborate on new tools. 
+Software and technology underpin much of modern research, which is now almost inevitably computational in one way or another - search engines, social networking platforms, analytical software, and digital publishing. With this, there is an ever-increasing demand for more sophisticated Open Source Software, matched by an increasing willingness for researchers to openly collaborate on new tools.
 
 The power of Open Source is in that it lowers the barriers to collaboration and adoption, therefore allowing ideas and technology to spread more rapidly. This Module will introduce the necessary tools required for transforming software into something that can be openly accessed and re-used by others.
 
-<img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/open_research_software_open_source.png" width="800" />
+<img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/open_research_software_open_source.png?raw=true" width="800" />
 
 <p align="center"><i>Image by Patrick Hochstenbach (CC0 1.0 Universal)</i></p>
 
@@ -68,7 +68,7 @@ The power of Open Source is in that it lowers the barriers to collaboration and
 
 Virtually all modern scientific research workflows rely on a range of software tools, either operating on different datasets, with different parameters, and applied iteratively in various ways (data science) or operating on different inputs and using models and methods to predict some output state (computational science). Open Source Software (OSS) is computer software in which the full source code is available under a specific license that enables other users to access, view, modify, and redistribute that code for any purpose. Because OSS requires such a license, it typically remains free of charge by default. This explicit licensing is also what differentiates OSS from free software. Re-using OSS for analysis, simulation and visualisation for research is also typically easier and more flexible compared to proprietary software. Often, whether we know it or not, we are already using OSS as part of our own research workflows.
 
-OSS fits into the broader scheme of Open Science as it helps to make the full research environment, including the software that produced the research results, fully accessible and re-usable. As such, it forms a necessary component for the best practices ([Jiménez et al., 2018](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Jim%C3%A9nez%20et%20al.%2C%202018.pdf)) and repeatability and reproducibility of research (both personally and by others), along with other components, such as sharing data ([Stodden, 2010](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Stodden%2C%202010.pdf)). 
+OSS fits into the broader scheme of Open Science as it helps to make the full research environment, including the software that produced the research results, fully accessible and re-usable. As such, it forms a necessary component for the best practices ([Jiménez et al., 2018](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Jim%C3%A9nez%20et%20al.%2C%202018.pdf)) and repeatability and reproducibility of research (both personally and by others), along with other components, such as sharing data ([Stodden, 2010](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Stodden%2C%202010.pdf)).
 
 In some cases, sharing of source code can even be conditional for the acceptance of associated research manuscripts ([Shamir et al., 2013](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Shamir%20et%20al.%2C%202013.pdf)). It is also generally perceived to increase research impact ([Vandwalle, 2012](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Vandewalle%2C%202012.pdf)).
 
@@ -124,7 +124,7 @@ The [Open Source Initiative](https://opensource.org/), one of the pioneers of OS
 
 - **License Must Be Technology-Neutral**: No provision of the license may be predicated on any individual technology or style of interface.
 
-Now, this all might be a little complex to remember. However, it can be summarised as *making software as re-usable as possible for future works, while also being freely available*. 
+Now, this all might be a little complex to remember. However, it can be summarised as *making software as re-usable as possible for future works, while also being freely available*.
 
 <br/>
 
@@ -188,7 +188,7 @@ As mentioned [above](#What_OSS), LibreOffice provides an Open Source alternative
 
 Version control is essentially a process that takes snapshots of the files in a repository, and tracks modifications to them. It records when the changes were made, what they were, and who did them. If several people are working on one file at once, any overlapping changes are detected, and must be resolved prior to continuing. This provides a much more streamlined and automated process than manually saving and recording changes as projects develop. It also avoids the inevitable lists of confusing named file versions...
 
-<p align="center"><img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/xkcd.png" width="200" /></p>
+<p align="center"><img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/xkcd.png?raw=true" width="200" /></p>
 
 <p align="center"><i>GitHub helps us to avoid, er, sub-optimal file naming conventions (source: XKCD)</i></p>
 
@@ -219,15 +219,15 @@ Especially in scientific research, Open Source Software usage and development ha
 
 For these and other reasons, Open Source tools are very commonly used in scientific research. This includes usage in fields where many researchers are amateur developers themselves and rely on tools such as [R](https://www.r-project.org/) for statistical analysis and scripting, which, in the last decade, has almost completely displaced commercial software for statistical analysis such as SPSS or JMP in a lot of fields. In fields such as bioinformatics, that involve a lot of file handling of the outputs of DNA sequencing platforms, general purpose scripting languages such as [Python](https://www.python.org/) and commonly used libraries built on top of it (such as [biopython](http://biopython.org)) have become a vital part of the toolkit of many researchers.
 
-<p align="center"><img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/python.png" width="400" /></p>
+<p align="center"><img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/python.png?raw=true" width="400" /></p>
 
 <p align="center"><i>Python</i></p>
 
 <br/>
 
 Tools such as R and Python are essentially software for writing software. Although programming is an increasingly common activity among researchers, of course not *every* scientist does this. One step away from programming is the chaining together of the inputs and outputs of various analysis tools in longer workflows. As an example from genomics, a very common workflow is to start out with high-throughput sequencing reads and then i) do basic quality control checks; ii) map the reads against a reference genome; iii) identify the points where the new data are at variance with the reference. These steps are routinely executed as a workflow where a different Open Source executable is run in a Linux command-line environment for each of the three steps. Although this is arguably not quite open source software development, it does involve the usage and production of open source artifacts (such as Linux shell scripts) for which the principles that we discuss in this module are applicable.
 
-<p align="center"><img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/r.png" width="200" /></p>
+<p align="center"><img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/r.png?raw=true" width="200" /></p>
 
 <p align="center"><i>R</i></p>
 
@@ -264,7 +264,7 @@ The most likely person who might want to re-use your software in the future is..
 
 One of the most critical aspects of this is including an informative `README` file, that accompanies almost every OSS project, and some times even more than one. It can be a good practice to include one such file in every directory, that includes a list of files, a table of contents, and what the purpose of the directory is. The `README` file is typically just plain text or markdown (again, such as all of the ones for the MOOC!), and can include critical information for how to install and run software, previous dependencies and requirements, as well as tutorials or examples.
 
-> **Did you know...** The term `README` is some times playfully ascribed to the famous scene in Lewis Carroll's Alice's Adventures In Wonderland in which Alice confronts magic munchies labeled with "Eat Me"" and "Drink Me". Potent. 
+> **Did you know...** The term `README` is some times playfully ascribed to the famous scene in Lewis Carroll's Alice's Adventures In Wonderland in which Alice confronts magic munchies labeled with "Eat Me"" and "Drink Me". Potent.
 
 The purpose here is to provide sufficient information to maximise the re-use and reproducibility of the computational environment, such that someone with no experience with the project can easily access and re-use the software ([Sandve et al., 2013](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Sandve%20et%20al.%2C%202013.PDF)). By lowering the barriers to entry, you increase the chances of others being able to re-use your work, which is one of the ultimate goals of OSS ([Ince et al., 2012](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Ince%20et%20al.%2C%202012.pdf)).
 
@@ -289,7 +289,7 @@ The 10 simple rules for making computational research more reproducible, based o
 9. Connect textual statements to underlying results.
 10. Provide public access to scripts, runs, and results.
 
-<p align="center"><img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/simple_rules.png" width="800" /></p>
+<p align="center"><img src="https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/simple_rules.png?raw=true" width="800" /></p>
 
 <p align="center"><i>Infographic adapted from Sandve et al., (2013). Feel free to download this and print it out to keep handy during your research!</i></p>
 
@@ -413,11 +413,11 @@ However, your Open Source journey does not stop here! This was just the beginnin
 * The [PLOS Open Source Toolkit](https://channels.plos.org/open-source-toolkit) provides a global forum for Open Source hardware and software research and applications.
 
 * The [NumFOCUS](http://www.numfocus.org) is a nonprofit organization that supports and promotes world-class, innovative, open source scientific software. Some of the projects they sponsor include:
-  
+
   * [IPython](http://ipython.org) and [Jupyter Notebook](https://jupyter.org) initiatives.
-  
+
   * [rOpenSci](http://ropensci.org), which promotes the open source R statistical environment for transparent and reproducible research.
-  
+
   * To gain more hands on experience with OSS, the [Software Carpentry](https://software-carpentry.org/) community holds regular workshops to improve lab-based computing skills ([Wilson et al., 2017](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Wilson%20et%20al.%2C%202017.pdf)).
 
 <br/>
@@ -463,4 +463,4 @@ However, your Open Source journey does not stop here! This was just the beginnin
 
 **Know a way this content can be improved?**
 
-Time to take your new GitHub skills for a test-run! All content development primarily happens [here](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/MAIN.md). 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! 
+Time to take your new GitHub skills for a test-run! All content development primarily happens [here](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/MAIN.md). 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!