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.


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

  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.


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.


Open Access and Non-Traditional Scholarly Communications with Jane Burpee

In this episode, we interviewed Jane Burpee, associate librarian and coordinator of data curation and scholarly communication at the University of McGill.

We met Jane at the Humanities and Social Sciences Library of McGill University, in a room full of books about arts and humanities to talk about Open Access (OA) and non-traditional methods of scholarly communication.

The first part of this episode is about OA and its importance in research and publishing. Jane explained how researchers can help the OA movement by sharing their published articles in repositories. During the interview, Jane discussed how authors can find out about their rights regarding publishers' copyright and self-archiving policies using the Sherpa/Romeo website.
As a librarian, Jane was also able to explain how libraries can facilitate making articles open access. If you are interested in making a paper you co-authored available as OA document, you can simply contact the library of your University. They should be able to help you put the paper in a repository which will make it OA available as soon as the copyright restrictions of the journal become null. If your library doesn’t offer this service, you can simply contact a librarian (ie. at McGill) to use the repository they offer.
The concepts of preprint, postprint, green OA and gold OA are also clearly explained, which is highly useful in order to move toward a more open research world.

In the second part, we talked about a publication Jane co-authored in the Journal of Scholarly and Research Communication about new and emerging methods of scholarly communications. In this interview, she gave us a brief summary of the article and introduced a few different ways being used by scholars to communicate their research findings. Different subjects such as video journals (e.g., JoVE) and the effect of social media on scholarly communication was discussed. Examples of creativity in transferring the information to the audience were given such as a recent discussion on CBC’s As it Happens with a Harvard University student who successfully submitted rap album as his senior thesis.

Bonus: double dipping

Webinar: Modern Scientific Publishing

Colper Science is proud to present our first podcast episode. Our first episode is the audio version of the webinar we presented live the 2nd of May at École Polytechnique Montréal.

The webinar was an introduction to a novel peer-reviewed and open access publishing system which provides a discussion platform to trigger critical thinking and intellectual exchange among researchers and also non-academics. It aims to improve the quality and reproducibility of research articles, facilitate scientific exchange, and build a bridge between the general public and peer-reviewed scientific content.

You can listen to the audio version on this webpage, and while you're at it, use this opportunity to subscribe to our podcast's RSS feed here.

The Colper Science podcast will mainly be about Open Science, each episode will feature someone connected to the open science world. We intend to discover with you different aspects of the open science world.

The YouTube video:

The intro song credit: Lobo Loco - Crumpet River A (ID 519)-

Join us next month for the next episode !