Shows
FLOSS for ScienceEP031 GNU licensesNote : This interview was recorded in the summer of 2020. However, due to the pandemic we could not release the episode timely. Therefore, the current status of FSF and recent events are not discussed in this episode.
In episode 31, we interviewed Craig Topham from the Licensing and Compliance Team of the GNU Project about GNU software licenses. We started by discussing about his involvment in the compliance team at the Free Software Foundation (FSF) and what got him interested in the topic of free software. The portion of the interview centered around the GNU project with an emphasis on the GNU...2021-04-2748 minFLOSS for ScienceEP030 Spack: a package manager for supercomputersIn episode 30, we interviewed Todd Gamblin from the Lawrence Livermore National Laboratory about the Spack project. We discussed his current research project along with his involvement in Spack. We widely discussed the philosophy of Spack, some usage patterns, its capabilities for managing package management in HPC clusters as well as standalone computers and which operating systems it supports at the moment. Todd shared with us his opinion on the trend for containerized workloads to achieve reproducible science and why it may not be the goal we need to set. He highlighted for us the similarities and differences between EasyBuild and...2020-09-0352 minFLOSS for ScienceEP029 Distributing Python packages with setuptoolsIn episode 29, we interviewed Jason R Coombs from the setuptools project. We started with a discussion about his background and his interest for Python and other programming languages. Following that, we had a thorough discussion about setuptools. We covered topics such as how he got involved in the project, the nature and composition of a Python package, why packaging your code can be important even for small projects, the hidden complexity of binary packages in the Python Package Index and how to maintain compatibility between Python versions. We also had a brief segment about the security aspects of Python packages...2020-07-011h 07FLOSS for ScienceEP028 NumFocus: A Nonprofit Supporting Open SourceIn episode 28, we interviewed Leah Silen from the NumFocus organization. She introduced us to the goals and the mission of the organization. We then had a discussion about the different levels of support provided by the organization to its member projects. She informed us about the legal, financial, technological and logistical support that can be provided by NumFocus. Following that, we asked her about the revenue sources of the organization as well as the possible influence from the corporate sponsors over the decisions and governance of the organization. We also discussed of the requirements to become part of NumFocus including...2020-05-0645 minFLOSS for ScienceEP027 Scientific Computing with SciPy and NumPyIn episode 27, we interviewed Ralf Gommers from the NumPy and SciPy projects. We started our discussion by talking about his past research experience as a physicist and his transition to open source software and programming. This led him to get involved in projects such as PyWavelets, NumPy and SciPy. Following that, we had a great discussion about NumPy, its many features, its target audience and its performance. We learned why NumPy is not included in Python's standard library and its overlap with Scipy. We also compared the combination of Matlab to NumPy and Python and how users could transition to...2020-04-0859 minFLOSS for ScienceEP026 Data Analysis with pandasIn episode 26, we interviewed Bhavani Ravi about the Python data analysis library pandas. After a brief introduction about her use of machine leaning models for pharmaceutical research, we talked extensively about pandas. She told us how much pandas is important for her everyday tasks and the strict quality standards of the project. We talked about the features provided by pandas and its compatibility with other Python libraries. We then discussed the importance of FLOSS in her industry and how they are contributing back to important projects. She share with us her experience as a first time contributor to pandas and...2020-03-0427 minFLOSS for ScienceEP025 FreeCAD, a 3D Parametric ModelerIn episode 25, we interviewed Kurt Kremitzki about the paramatric 3D modelling tool FreeCAD. After discussing his previous experiences with CAD software and how he got involved in the FreeCAD project, we asked him about the current development status of the project before digging deeper into a few of the workbenches offered by FreeCAD. We also compared FreeCAD to LibreCAD and QCAD for applications only requiring 2D drawing instead of parametric 3D models and we discussed about compatibility with commercial CAD systems and standard exchange file formats. We were pleased to learn about the development status of a stable topological naming...2020-02-0551 minFLOSS for ScienceEP024 UK RSE and Software SustainabilityIn episode 24, we interviewed Simon Hettrick Professor at the University of Southampton in the UK. We started the discussion with him by asking about his transition from deveoppin high-power lasers to founding the research software engineers (RSE) association and how his experiences got him in his current position. We then discussed about the roles of RSE in research and how funding for RSE evolved over the past. The discussion went on about the RSE association, its growth over time, branches in other countries and local events. We discussed that the relation between FLOSS and more sustainable research software is not...2019-12-0452 minFLOSS for ScienceEP023 Reproducible Science and Synthetic Datasets Using RIn episode 23, we interviewed Dan Quintana from the University of Oslo. We started the discussion with him by asking the link between all his subjects of interest and where R fits into his workflow. We then had an extensive discussion about R including his must have R packages and the synthpop package for generating synthetic datasets. We then widened the discussion and talked about the multiple facets of open science and reproducibility. Dan then talked about what he sees as one of the next big challenge of science. We finished the interview with our usual quick questions.
00:00:18 Introduction
00:00:39 Presentation of...2019-11-0655 minFLOSS for ScienceEP022 Symbolic Calculation with MaximaIn episode 22, we interviewed Robert Dodier from the Maxima project. After a brief introduction and a presentation of Robert's current uses for Maxima he introduced what is Maxima and what can be achieved with it. We discussed some core concepts of Maxima's language as well as how to access the documentation within the software to help users. Then discussion went on about the interesting origin story of Maxima and its origin as a tool for AI. We then talked about the current state of the project and how can someone provide help. As well as our usual quick questions, we...2019-10-0245 minFLOSS for ScienceEP021 High-level Scientific Computing with GNU OctaveIn episode 21, we interviewed Juan Pablo Carbajal, an Argentinian physicist currently working as a postdoctoral researcher in the Department of Urban Water Management at the ETH domain in Switzerland. We had a great discussion about GNU Octave and how it can help scientists. We compared its core functions and its expandability through packages to its commercial equivalent Matlab and its toolboxes. An interesting feature of GNU Octave that we explored with Juan is the possibility to migrate code from Matlab directly to GNU Octave and to a certain point maintain code compatible with both. Juan shared with us that since...2019-09-0446 minFLOSS for ScienceEP020 Peer-reviewed Publication of Research SoftwareIn episode 20, we interviewed Arfon Smith, Editor-in-chief of the Journal of Open Source Software (JOSS) and Head of Data Science at the Space Telescope Science Institute. We talked with him about the creation of JOSS and its role in peer reviewed publications of research software. He described to us how to start a peer reviewed scientific journal and the challenges and competition that he faces. We chatted about how, by using automation, reusing existing tools and staying nimble, JOSS manages to publish with low operational costs. We also discussed about the submission process and what is reviewed during the peer...2019-08-061h 03FLOSS for ScienceEP019 The Road Ahead for Scientific LinuxIn episode 19, we interviewed Glenn Cooper the Head of experiment computing department at Fermilab about the history and future of the linux distribution Scientific Linux. The discussion started with a brief overview of current research activities at Fermilab. When then extensively talked about Scientific Linux, its goals, the reason why it was started and what made it successful. Glenn made a good argument about the need for a stable software platform in science. We then switched topics and discussed about the recent announcement in regard to the end of the project and the motivations for that. We then talked about...2019-07-0345 minFLOSS for ScienceEP018 Performing Arts with FLOSSIn episode 18, we interviewed Jesse Allison an Associate Professor of Experimental Music and Digital Media at Louisiana State University. We had a great discussion about his work to expand the experience and interactivy of music and sounds. He shared with us his view on how sciences and arts intersect in his projects. He listed some of the tools he uses to create sounds and how these can be applied to create sonic intervention. We had a chat about his past experiences regarding open source software and running a business based on it. We also questioned him whether or not anyone...2019-06-0555 minFLOSS for ScienceEP017 HPX: A cure for performance impaired parallel applicationsIn episode 17, we interviewed Adrian Serio the Scientific Program Coordinator of the STELLAR group about the C++ Standard Library for Concurrency and Parallelism (HPX). We started with a general discussion about parallel computing, where it comes from, where it is going and what can we still expect to gain. We then clarified what are C++ standards and how HPX is developed to be standard compliant. HPX was compared to other parallelism libraries such as MPI and we learned that HPX is a foundation to develop other software for domain specific applications. Adrian informed us how HPX can be used to...2019-05-0146 minFLOSS for ScienceEP016 Management of High Performance Computing Infrastructures with OpenHPCFor episode 16, we interview the Research Associate Professor Karl W. Schulz. The episode starts with a discussion about High Performance Computing and how OpenHPC facilitate the managment of computing ressources. We then open the discussion towards open source tools, how they became so important for HPC and the their importance for open science. We also discussed about the inception of the OpenHPC project and its governance structure. We end the interview with our usual question in addition to a totally new one.2019-04-0352 minFLOSS for ScienceEP015 Reproducible Research in Archaeology with rrtoolsFor episode 15, we interview the Associate Professor of Archaeology Ben Marwick. We start our discussion with an overview of some FLOSS tools he uses and how much FLOSS are used in archaeology. He shares with us his experience in regard to working completely in the open with GitHub and his hope that open science will become the norm in the future. We also discuss about rrtools and his propositions on how to greatly improve the reproducibility of science. As a closing though he shares with us his arguments why early career researchers should invest time to learn and transition to...2019-03-051h 13FLOSS for ScienceEP014 Gimp Your Images for PublicationIn episode 14, we interview Pat David a Free Software advocate, occasional photographer and engineer about the GIMP project. We talked about how GIMP can be used by scientists to enhance their images for their publications. Also, Pat shared with us his strong opinions regarding scientific communication and why free software matters. You will also learn a few interesting trivia about the origins of the GIMP project, including the content of the original announcement email.2019-02-0647 minFLOSS for ScienceEP013 Vector Graphics with InkscapeFor episode 13, we interviewed Martin Owens, a British Free Software contractor based in Boston Massachusetts, during the 2018 Kiel Inkscape Hackfest, about the Inkscape project. After a brief presentation of Inkscape, we talked about the svg file format and the compatibility of Inkscape with other commercial proprietary offerings. He presented us a list of features planned for Inkscape 1.0, the next major version. We discussed about Inkscape in science and the wider importance of free software and open science. Follow us to be informed when we will release our next episode about the GNU image manipulation program aka GIMP.2019-01-0837 minFLOSS for ScienceEP012 EasyBuild : Building Software with Ease for HPCIn Episode 12, we interviewed Kenneth Hoste, who is an HPC system administrator at Ghent University in Belgium. We talked about the problems that arise when installing scientific software on HPC systems and how the EasyBuild project that originated at HPC-UGent helps dealing with those problems, the impact of open source software in scientific research, as well as the yearly FOSDEM open source software meeting in Brussels where he is actively involved in various ways.2018-12-0555 minFLOSS for ScienceEP011 Blackbox Optimization with NOMADIn 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.2018-11-0728 minFLOSS for ScienceEP010 CGAL : The Computational Geometry Algorithms LibraryIn 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...2018-10-0340 minFLOSS for ScienceEP009 Finite element meshing with gmshIn 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.2018-09-0556 minFLOSS for ScienceEP008 Solid-Liquid Mixing ModellingFor 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...2018-08-0137 minFLOSS for ScienceEP007 A Guide to Software Licenses in ScienceFor 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...2018-07-041h 01FLOSS for ScienceEP006 Gentoo Linux for NeurosciencesIn 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...2018-06-0658 minFLOSS for ScienceEP005 LibreOffice the Swiss Army Knife of Science?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.2018-05-0239 minFLOSS for ScienceEP004 Reproducible science with RockerIn 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.2018-04-0339 minFLOSS for ScienceEP003 JabRef at JabConIn Episode 3, we interview Oliver Kopp and Jörg Lenhard about the reference management tool Jabref.2018-03-0739 minFLOSS for ScienceEP002 Modeling composite materials fatigue with PythonIn 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.2018-02-0710 minFLOSS for ScienceEP001 Introduction to the FLOSS for Science podcastIn this episode the two hosts David Brassard and Patrick Diehl of FLOSS for Science introduce themselves and they explain the aims of this podcast.2018-01-1210 min