Floss For Science

Note : 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 software licenses. We went through the GPL, LGPL, AGPL and GFDL licenses to explain some of their differences and why you may want to use one instead of another. We asked questions about the specificities of licensing your code in the context of scientific software and the issue with licenses proliferation. Some of the differences between the different versions of the GPL were presented later in the discussion to sho

In 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 Spack as well as the origin of those differences. We finished the interview with our usual quick questions. 00:00:00 Intro music 00:00:17 Introduction 00:00:36 Introducing Todd Gamblin 00:00:58 His current research topics 00:01:23 Spack as official duties 00:01:43 Spack usage at Lawrence Livermore National Laboratory 00:02:01 Other research projects 00:02:47 Profiling in HPC 00

In 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. He informed us about how you could start contributing to the project and where to discuss Python packaging. We then followed with a general discussion about FLOSS in science and the problem of long-term maintenance in academia. We concluded the interview with our usual quick questions. 00:00:00.000 Intro 00:00:23 Introducing Jason R. Coombs 00:01:28 The first programming languages he learned

In 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 details about the application process. We had a brief discussion about the history of the project and the evolution of the scope of projects that are part of the organization. After discussing the governance of the organization, we concluded the interview with our usual questions. 00:00:00 Intro 00:00:18 Introducing Leah Silen 00:02:28 Goals and mission of NumFocus 00:03:06 Exampl

In 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 this open source solution. We then had a brief discussion about SciPy and the features it provides. Ralf informed us of the positive results from Google's previous Summer of Code and Season of Docs participations. We discussed how to reach the project and the many kinds of contributions that they are looking for. We talked about the importance of FLOSS for science and attribution of research output. We finished

In 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 how to find good first time issues for newcomers. We finished the interview with out usual quick questions. 00:00:17 Introduction 00:00:26 Introducing Bhavani Ravi 00:00:49 Using machine learning models for pharmaceutical research 00:02:46 How she got involed in the pandas project 00:04:29 Her elevator pitch for pandas 00:04:43 How she use pandas in her everyday job 00:05:24 What does pandas b

In 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 engine paving the way for the integration of an official assembly workbench in future releases. We then discussed about the spread of FreeCAD in companies and universities as well as ways to contribute to the FreeCAD project. We finished the interview with out usual quick questions and with a mention of their recent presentions at FOSDEM 2020. 00:00:18 Introducing Kurt Krem

In 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 always clear and more work is needed in that area. After talking with him about the lack of sufficient preparation that students receives during their undergrad studies in regard to the tools needed to tackle research software development we finished with our usual quick questions. 00:00:00 Intro 00:00:18 Introduction and Simon Hettrick's presentation 00:00:56 His academic status at the Univer

In 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 Dan Quintana 00:01:55 The links between his research interests 00:04:00 Where does R fits in his workflow 00:05:22 His 30 seconds elevator pitch for R 00:06:28 How difficult is it to switch from SPSS to R? 00:08:05 The best time to switch to R 00:08:40 JASP and Jamovi as a gateway to R 00:10:53 Standing on the shoulders of giants with R 00:12:15 R or Python? 00:14:00 Dan's must have R packag

In 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 had an interesting discussion about the social aspects within FLOSS and other self-organized projects. 00:00:17 Introduction 00:00:26 Presentation of Robert Dodier 00:02:01 The scope of Maxima and its application for Bayesian inferences 00:02:57 Why not use R or another programming language for Bayesian inferences? 00:05:03 When did he discover Maxima? 00:05:29 Maxima's core features stability since 2003 00:06:04 His 30 seconds elevator pitch

In 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 the introduction of an integrated GUI in 2015, he noticed a continuous growth in popularity for the project. We then discussed about a few of the reasons why companies are interested by GNU Octave and why universities should teach using free/libre software. Before asking our usual quick questions, Juan talked with us about the reasons why FLOSS is important for science and the importance of expo

In 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 review. Finally, we had a discussion about the importance of FLOSS and in science and how science and FLOSS could inspire each other.

In 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 the transition to CentOS at Fermilab and CERN and the upgrade path for current users. We concluded the interview with our usual quick questions.

In 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 could or even should start creating music. The episode concludes with a small audio sample from his 2013 TEDx talk.

In 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 take advantage of hardware accelerators such as Intel Xeon Phi or GPUs. We looked at the inception of the project and the sources of contributions to the project

For 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.

For 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 FLOSS tools.

In 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.

For 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.

In 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.