Free software and science : Why software licences matter for scientists

In this episode we interviewed David Brassard and Patrick Diehl about the importance of software licences for the scientific community. Patrick was also part of episode 3 which was also about open source software in research. In this episode, Patrick and Ilyass are hosting the conversation which is more focused about licenses in software, the difference between open source and free (or libre) software and their impacts on a researcher's work. David is a PhD student at Polytechnique Montreal, his work is focused on chemical engineering and material sciences but he is also very interested in open source and free software.

David actually contacted the Colper Science team following episode 3 to provide remarks and comments about the episode's content. Since David seemed pretty knowledgeable about the subject, we decided to invite him do a follow-up episode with us.

David helped us to understand the difference between libre or free software and open source software. We then talked about which among them is the most interesting for a researcher and why.
In the second part, we focused on licenses and their consequences on our work. We all constantly agree to license agreements when installing software or creating accounts for online services, David and Patrick will explain how these license agreements can sometimes be an issue for a researcher's work. We then explored different kind of licenses allowing a researcher to keep any code he might have developed free.

Contacts

References

Lab Scribbles: Real-time open access science

In this episode we interviewed Dr. Rachel Harding, a postdoctoral fellow at the Structural Genomics Consortium, University of Toronto. Rachel’s current work is focused on the structure of huntingtin, a mutated protein in individuals suffering from Huntington’s disease. During the episode we talked about Huntington’s disease, sharing your results on a regular basis on a blog, setting up a blog and the intellectual property issues related to sharing your data in such a way.

An interesting point in this area of research is that not all results are published: positive results only are actually published and reaching a positive result requires a lot of trials and errors. However those trials and errors are often neglected.
Rachel created a blog, called LabScribbles, where she records everything she does in the lab, all her positive results but also trials and errors. Rachel explains this workflow, how it helps her improve her method in the lab, how it helps other researchers, how it helps her exchange with them, and even create a community around her work.

We also explored the intellectual property issues related to the Labscribbles a blog. In Rachel’s case, her funding comes from the Cure for Huntington’s Disease Initiative Foundation, a non-profit biomedical organisation. Depending on your employer and organization, it might be forbidden to share your research in such a way, but Rachel was able to explain, in her opinion, how such intellectual property are not a real issue (in most cases).

Bonus: "Open Access Materials"

References:

Working in the open and using it to do public good with Monica Granados

In this episode we interviewed Monica Granados, a postdoctoral fellow at the University of Guelph & Wildlife Conservation Society Canada. Monica explained how she was introduced to open science and how practicing in the open helped her advance her projects. She is developing a mobile app with Jacob Ritchie, a computer science graduate student at the University of Toronto to make fish consumption advisory data more accessible to the public including the indigenous communities of the northern parts of Ontario. If you’d like to to know more about the project or would like to contribute to the app development, click here.

Monica also discussed her recent open access article, Stabilizing mechanisms in a food web with an introduced omnivore. She explains how important it is to share raw data for reproducibility and how working in the open changed the way she prepared, delivered and published her manuscripts.

Working in the open has improved the way Monica does research and now gives workshops to other researchers on how to practice in the open. Monica also shares these and other tutorials through her github repository which can be accessed here.

Bonus

Monica explains how improv' can help a researcher become a better science communicator.

If you like to know more about Monica and her projects, check out the links below:

Monica Granados: Github; Google Scholar; Twitter; Email;
Projects:

Open Source Software in Science

Patrick Diehl is a Postdoctoral fellow at the Laboratory for Multiscale Mechanics at Polytechnique Montreal. During his studies in computer science he got in touch with Linux and Open Source software in his work life and daily life. Since his PhD he switched completely to Fedora and tries from there on to use open source alternatives for most applications.

In this episode, we first explored the meaning and different definitions of open source available. It was possible to realize that open source by itself is not enough and that it is necessary to have a license with it to clearly define how it can be used and distributed. We then started exploring different usages all researchers have of their computers, such as writing e-mails, managing bibliographic references or storing and backing up files. For each usage, Patrick helped us discover one or several open source alternatives, he also provided a description of the open source alternatives their advantages and limitations and how hard it would actually be to switch from a proprietary equivalent to the open source one. A table summarizing the complete list of softwares explored during the episode is provided after the Soundcloud episode in this post.
We also discussed, through the episode, why it is important and makes sense for a researcher to use open source software instead of proprietary ones.

Complete list of Software

Here, is an overview of all open source software mentioned in the pod cast and a complete list can be found here.

Open source alternatives1
Proprietary OpenSource OS
Outlook Thunderbird,Evolution All
Photoshop GIMP,Krita All
Endnote JabRef All
Microsoft Office Libre Office All
Auto Desk Maya Blender All
Abaqus/Ansys FEniCS All
Dropbox Seafile All
Matlab GNU Otave ,Python,R All
Maple Maxima All
Autodesk LibreCAD All
Solidworks/Catia FreeCAD All
Slack IRC,RocketChat ,Mastodon All
Comsol Elmer,OpenFOAM All
IE, Google Chrome Firefox,Chromium All
Skype Mumble, Jitsi No
Open source software for specialized research applications

In this sections, Patrick also provides a list of

Usage Software OS
Meshing Gmsh All
Document preparation LaTeX All
Vectorgraphics Inkscape All
UML diagrams Umlet All
Molecular dynamics Lammps All
Plotting Matplotlib All
Numerical algorithms & toolboxes SciPy All
Media Player VLC,mplayer All
Video editing KdenLive,Openshot All

After listening to this episode, you should have all the knowledge you need to switch to a fully open source environment ! If you have any additional questions before you start working open, please use the comments area at the bottom of this page to ask them, Patrick will be glad to answer them.

If you enjoyed this episode and would like to hear more about open source software, let us know in the comments, we'll prepare a sequel :)

A week after

A week after we recorded this podcast episode, Kambiz started working on switching from Windows OS to a Linux distribution, here are few words from him:

I installed Linux (Ubuntu) a few days ago. The installation was easy. You can use this video to install it using a USB key. For normal usages, such as internet browsing and installing software you need, it was very easy to adapt. Regarding sound editing, I am using Audacity which is a great software. Regarding video editing, I used to use Adobe Premiere which was very good but heavy for my computer. I started using Kdenlive and I found it awesome. It crashes a lot though, but when I re-open it, it recovers well the project.
So far my Ubuntu setup is much faster than my Windows one. I don’t know if it gets slow with time or not, but will let you know if it does.

Bonus

Patrick talks about encryption and how we can easily start sending encrypted e-mails as researchers.

References
  1. We like to thank David Brassard for extedning the list.

Building an open source platform for crowdsourced open data sharing

In this episode, we interviewed Bastian Greshake, PhD student in Applied Bioinformatics at the University of Frankfurt am Main, in Germany.

If you are a researcher in a field somehow related to genetics, you might have already used OpenSNP to explore SNPs (Single Nucleotide Polymorphisms) in an open dataset. In that case, you probably already know Bastian and his work. Bastian started working on OpenSNP, a platform which allows users to upload their genotyping data and make it available to the community. The platform also allows users to share their phenotypes in order to help scientists discover new genetic associations. It also automatically gets the latest open access articles about genetic variations to inform users and researchers about SNPs.

OpenSNPfeatures

Bastian explained how to start an open source project, the issues related to these kind of projects. We also explored how to get more users for an open source project without any advertising budget, and how to get more contributors to help you develop a similar project. In the second part, Bastian helped us understand the issues related with sharing open data results with the community and how himself and his team are protecting themselves against any legal risks by ensuring that users clearly know what they are putting themselves into when using the platform.

A very clear paper explaining most of the elements we discussed during this podcast episode was written by Bastian and his co-authors, the paper was published (obviously open access) in the journal PLOS ONE and is a highly recommended read by the ColperScience team for anyone interested by working around open source or open data in research. The survey amongst the openSNP users that is referred to during the episode can also be found there.

If you have any questions or remarks, please post a comment at the bottom of this page, or contact us directly through Twitter. Thanks for listening !

Bonus !

Bastian talks about gamification and how it could help certain projects involving massive data.

References