FLOSS for Science

In Episode 11, we interviewed Sébastien Le Digabel about NOMAD a blackbox optimization software. A blackbox is a system which can be viewed in terms of its inputs and outputs, without any knowledge of its internal workings. NOMAD is a software for the optimization of such problems. It implements the Mesh Adaptive Direct Search (MADS) derivative-free optimization algorithm. NOMAD is free and intended to be easy to use. It is designed for solve real-world optimization problems from the industry. It works out of the box, as long as the objective and constraints are provided.

In Episode 10, we interviewed Sébastien Loriot about CGAL. A software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics.

The library offers data structures and algorithms like triangulations, Voronoi diagrams, Boolean operations on polygons and polyhedra, point set processing, arrangements of curves, surface and volume mesh generation, geometry processing, alpha shapes, convex hull algorithms, shape analysis, AABB and KD trees...

In Episode 9, we interviewed Christophe Geuzaine about Gmsh, a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities. Gmsh is a free 3D finite element mesh generator with a built-in CAD engine and post-processor. Its design goal is to provide a fast, light and user-friendly meshing tool with parametric input and advanced visualization capabilities.

For episode 8, we interviewed Bruno Blais about his utilization of open source software in his research about solid-liquid mixing. We started our conversation by talking about the different kinds of software packages he uses in his simulation workflow. We then asked him why and when he has decided to use FLOSS tools in is research. Following that, we talked about his philosophical and practical reasons to use FLOSS. He then shared with us how he contributes to the software he is using in his daily research. Finally, we talked with him about the significance of FLOSS for the openness of science and how it affects the society as a whole. This episode is the first of series about computer simulations. Follow us to be informed when we will release our next episode about the open source meshing tool GMSH.

For Episode 7, we interviewed Karl Fogel and James Vasile about the importance of software licenses for scientists. The discussion was inspired from Chapter 9: Legal Matters: Licenses, Copyrights, Trademarks and Patents of Karl's book: Producing Open Source Software - How to Run a Successful Free Software Project. Choosing a license for ones open source project is essential and we discussed why one should ship their scientific open source code with a license. In addition, we talked about the implications of providing a license and the legal aspects of licenses. Another aspect was open source license compatibility for the integration of libraries to an existing project. We also had a discussion in regards to the expectations of academic developers.

In Episode 6, we interviewed Christian Horea about the [NeuroGentoo Overlay](https://github.com/TheChymera/neurogentoo) for Gentoo Linux which includes specific packages for Neuroscience. With this distribution many of the challenges in neuroscience software management; including: system replicability, system documentation, data analysis reproducibility, fine-grained dependency management, easy control over compilation options, and seamless access to cutting-edge software releases, are addressed. Fore more details we refer to his publication: [Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software](https://riojournal.com/article/12095/).

About Christian Horea:

Christian Horea is a Doctoral Researcher at the ETH Zurich, where he studies the ability of psychotropic drugs to modulate brain function in healthy animals. He has previously engaged in research at the University of Heidelberg, University of Oxford, Max Planck Institute for Medical Research, University of Oldenburg, and the Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences. His work has spanned the gamut of neuroscience from electrophysiology and molecular biology all the way to experimental psychology — and includes an extensive excursion into the world of Linux, Python, and software management. He has written many Free and Open Source Software packages for data analysis, metadata and lab book management, reproducible self-publishing, and data repositing. We join him on part of this exciting journey, to learn about an initiative he started — NeuroGentoo — and how he sees Free and Open Source Software, freedom in choosing and picking such software, and transparency in the choices having been made, as instrumental to the neuroscience of the present and future, and how Gentoo Linux (perhaps uniquely) makes tackling these challenges possible.

In Episode 5, we interview Katarina Behrens, a consultant and software developers of LibreOffice, LibreOffice extensions and related libraries working at CIB Group of Companies. We discuss her involvement with The Document Foundation, the capabilities of the LibreOffice suite and why an open source office suite is relevant for scientists.

In Episode 4, we interview Carl Boettinger, Assistant Professor in the Department of Environmental Science, Policy and Management at UC Berkeley. He introduces us to his work on ecological forecasting and decision making under uncertainty, with applications for global change, conservation and natural resource management. He presents to us the Rocker project and how it helps scientists produce reproducible science. Finally, we discuss with him about his view regarding FLOSS in science.

In Episode 3, we interview Oliver Kopp and Jörg Lenhard about the reference management tool Jabref.

In Episode 2, we interview Laurent Cormier, a research associate at the Ecole de Technologie Superieure in Montreal. He introduces us to his past research regarding the evaluation of the fatigue life of composite materials and the predictive model he developed with Python. He also share with us his scientific perspective on FLOSS and tools he uses in his research workflow.