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.