Blog

EP023 Reproducible Science and Synthetic Datasets Using R

Nov 6, 2019. | By: Admin

Outline

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.

About Dan Quintana:

Dan Quintana is a Senior Researcher at the Norwegian Center for Mental Disorders Research at the University of Oslo. While his primary research focus is in the field of biological psychiatry, he also works in the in the emerging discipline of meta-research, whose goal is to evaluate and improve research practices. He also co-hosts ‘Everything Hertz’, a bi-monthly podcast on methodology, scientific transparency, and research life in the biobehavioral sciences.

Links

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EP022 Symbolic Calculation with Maxima

Oct 2, 2019. | By: Admin

Outline

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.

About Robert Dodier:

Robert Dodier has a background in mathematics, computer science, and engineering. At present he’s writing software for a medical app for smart phones. In times past he has worked on machine learning, agent systems, and forecasting electrical demand, among other topics. He has a special interest in Bayesian inference and decision analysis.

About Maxima:

Maxima is derived from the Macsyma system, developed at MIT in the years 1968 through 1982 as part of Project MAC. MIT turned over a copy of the Macsyma source code to the Department of Energy in 1982; that version is now known as DOE Macsyma. A copy of DOE Macsyma was maintained by Professor William F. Schelter of the University of Texas from 1982 until his death in 2001. In 1998, Schelter obtained permission from the Department of Energy to release the DOE Macsyma source code under the GNU Public License, and in 2000 he initiated the Maxima project at SourceForge to maintain and develop DOE Macsyma, now called Maxima.

Links

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EP021 High-level Scientific Computing with GNU Octave

Sep 4, 2019. | By: Admin

Outline

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 exposing non-FLOSS users to the benefits of FLOSS.

About Juan Pablo Carbajal:

Juan Pablo is a physicist from Argentina, currently living in Switzerland. He has been using GNU Octave for more than 15 years. GNU Octave is one of the FLOSS tools he uses for research and development (applied complex systems). He is also a promoter of education and training using FLOSS. He provides GNU Octave technical training at CERN, and in his small non-profit, which also promotes programming and robotics among teenagers using FLOSS. In his free time he contributes to GNU Octave, maintains a few small packages, and provides help in the mailing list. You can know more about Juan Pablo on his website.

About GNU Octave:

GNU Octave is a high-level language, primarily intended for numerical computations using a language that is mostly compatible with Matlab. Octave has extensive tools for solving common numerical linear algebra problems, finding the roots of nonlinear equations, integrating ordinary functions, manipulating polynomials, and integrating ordinary differential and differential-algebraic equations. It is easily extensible and customizable via user-defined functions written in Octave’s own language, or using dynamically loaded modules written in C++, C, Fortran, or other languages.

Links

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EP020 Peer-reviewed Publication of Research Software

Aug 6, 2019. | By: Admin

Outline

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.

About Arfon Smith:

Arfon Smith is the Head of the Data Science Mission Office at Space Telescope Science Institute in Baltimore. Previously he was at GitHub, helping to bring open source to academia.

A lapsed academic with a passion for new models of scientific collaboration, he’s used big telescopes to study dust in space, built sequencing pipelines in Cambridge and has engaged millions of people in online citizen science by co-founding the Zooniverse.

He’s also been known to publish the odd paper and has also accidentally built a few academic journals in his time too including, most recently, the Journal of Open Source Software.

About Journal of Open Source Software:

The Journal of Open Source Software (JOSS) is an open source, developer-friendly journal for research software packages. It’s designed to make it as easy as possible to create a software paper for your work. If a piece of software is already well documented, then paper preparation (and submission) should take no more than an hour. The primary purpose of a JOSS paper is to enable citation credit to be given to authors of research software and we have a rigorous peer review process and a first-class editorial board (http://joss.theoj.org/about#editorial_board) highly experienced at building (and reviewing) high-quality research software.

Links

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EP019 The Road Ahead for Scientific Linux

Jul 3, 2019. | By: Admin

Outline

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.

About Scientific Linux:

Scientific Linux is a Linux distribution intended to provide a platform for scientific computing and specifically for high-energy physics computing. Because experiments in that field can run for years or even decades, a stable operating system that allows for security patching and major bug fixes, but otherwise remains stable, so that physics results do not have to be re-validated frequently is needed. The first version, Scientific Linux 3, was based on Red Hat Enterprise Linux 3 and was released in 2004 in conjunction with CERN. Scientific Linux has been widely adopted by physics labs like Fermilab, by many university departments, and by others in the community.

About Glenn Cooper:

Glenn Cooper started as an astronomer and taught physics and astronomy at several colleges and universities. He moved into computing, winding up at Fermilab, “America’s particle physics and accelerator laboratory”. He is currently leading a department that manages most of the computers used by experiments at Fermilab, as well as many used by the CMS experiment at the CERN laboratory in Europe. Besides managing computers and their operating systems, they also manage batch computing software on many of the computers. Finally, they build, distribute, and support Scientific Linux.

Links

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EP018 Performing Arts with FLOSS

Jun 5, 2019. | By: Admin

Outline

In episode 18, we interviewed Jesse Allison an Associate Professor of Experimental Music & 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.

About Jesse Allison:

Jesse Allison is a leader in sonic art technology, thought, and practice. Dr. Allison holds the position of Associate Professor of Experimental Music & Digital Media at Louisiana State University. As part of the Cultural Computing focus of the Center for Computation & Technology, he performs research into ways that technology can expand what is possible in the sonic arts. Prior to coming to LSU, he helped to found the Institute for Digital Intermedia Art at Ball State University and Electrotap

Links

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EP017 HPX: A cure for performance impaired parallel applications

May 1, 2019. | By: Admin

Outline

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

About Adrian Serio:

Adrian Serio is the Scientific Program Coordinator for the STELLAR group at Louisiana State University. In this role, he assists in the development of HPX, a distributed C++ runtime system for parallelism and concurrency. Adrian was surprised to find himself working in HPC after graduating with a bachelor degree in biological engineering in 2011. Nevertheless, he loves working in a university setting where he gets exposed to cutting edge research and work with an international team of collaborators.

About the C++ Standard Library for Concurrency and Parallelism (HPX):

High Performance ParalleX (HPX) is an environment for high performance computing. It is currently under active development by the STELLAR group at Louisiana State University. Focused on scientific computing, it provides an alternative execution model to conventional approaches such as MPI. HPX aims to overcome the challenges MPI faces with increasing large supercomputers by using asynchronous communication between nodes and lightweight control objects instead of global barriers, allowing application developers to exploit fine-grained parallelism.

Links

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EP016 Management of High Performance Computing Infrastructures with OpenHPC

Apr 3, 2019. | By: Admin

Outline

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.

About OpenHPC:

OpenHPC is a collaborative, community effort that initiated from a desire to aggregate a number of common ingredients required to deploy and manage High Performance Computing (HPC) Linux clusters including provisioning tools, resource management, I/O clients, development and administration tools, and a variety of scientific libraries. Packages provided by OpenHPC have been pre-built with HPC integration in mind with a goal to provide re-usable building blocks for the HPC community. OpenHPC was formalized as a Linux Foundation collaborative project in June 2016 and has over 35 institutional members from academia, national labs, and industry.

About Karl W. Schulz:

Karl W. Schulz received his Ph.D. from the University of Texas (UT) in 1999. After completing a one-year post-doc, he transitioned to the commercial software industry working for the CD-Adapco group as a Senior Project Engineer to develop and support engineering software in the field of computational fluid dynamics (CFD). After several years in industry, Karl returned to UT in 2003, joining the research staff at the Texas Advanced Computing Center (TACC), a leading research center for advanced computational science, engineering and technology. During his 10-year tenure at TACC, Karl was actively engaged in HPC research, scientific curriculum development and teaching, technology evaluation and integration, and strategic initiatives serving on the Center’s leadership team. Karl also served as the Chief Software Architect for the PECOS Center within the Institute for Computational Engineering and Sciences (ICES), a research group focusing on the development of next-generation software to support multi-physics simulations and uncertainty quantification.

In 2014, Karl joined the Data Center Group at Intel where he led the technical design and release of OpenHPC. He continues to remain actively engaged in the project and is currently serving as the overall Project Lead. In 2018, Karl returned to UT as a Research Associate Professor in an interdisciplinary role within ICES and the Women’s Health Department at the Dell Medical School.

Links

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EP015 Reproducible Research in Archaeology with rrtools

Mar 5, 2019. | By: Admin

Outline

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.

About Ben Marwick:

Ben Marwick is an Associate Professor of Archaeology at the University of Washington, Seattle. His other local affiliations include the eScience Institute, the Burke Museum, the Center for Statistics and Social Sciences, the Quaternary Research Center, and the Southeast Asia Center. Ben’s main research activities combine models from evolutionary ecology with analyses of archaeological evidence to investigate past human behaviour. Specific interests include the hominin colonisation of mainland Southeast Asia, forager technologies and ecology in Australia, mainland Southeast Asia and elsewhere. He also analyses how archaeology engages with local communities and popular culture. Ben has a special interest in techniques and methods for reproducible research, especially using open source software. To support this, he has lead the development of the rrtools package for the R programming language, which simplifies many of the tasks of writing a reproducible manuscript.

Links

  • rrtools: Tools for Writing Reproducible Research in R
  • Marwick, B. J Archaeol Method Theory (2017) 24: 424. https://doi.org/10.1007/s10816-015-9272-9
  • Marwick B, Boettiger C, Mullen L. 2018. Packaging data analytical work reproducibly using R (and friends) PeerJ Preprints 6:e3192v2 https://doi.org/10.7287/peerj.preprints.3192v2
  • Eglen SJ, Marwick B, Halchenko YO, Hanke M, Sufi S, Gleeson P, Silver RA, Davison AP, Lanyon L, Abrams M, Wachtler T. Toward standard practices for sharing computer code and programs in neuroscience. Nature neuroscience. 2017 May 25;20(6):770.

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EP014 Gimp Your Images for Publication

Feb 6, 2019. | By: Admin

Outline

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.

About GIMP:

The GNU Image Manipulation Program, GIMP, has been a fixture of the Free Software world since 1995. It has long been a standard cross-platform tool available to FL/OSS users for manipulating graphics and images, and is also the namesake of the GTK project (the GIMP Toolkit). For over twenty years GIMP has been available to help users create and modify all manner of graphics for scientific computing, photography, and digital arts.

About Pat David:

Pat David is a Free Software advocate, occasional photographer, and digital dabbler. He has been a member of the GIMP team for many years now, and did the recent re-design of the GIMP website. He is also the founder of the Free Software photography community PIXLS.US. His time is usually spent annoying, then helping, various FL/OSS projects (in that order).

Links

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EP013 Vector Graphics with Inkscape

Jan 8, 2019. | By: Admin

Outline

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.

About Inkscape:

A Free and Open Source SVG vector image editor available for multiple platforms. A popular way of creating physical objects, intricate visualisations and beautiful artworks.

About Martin Owens:

Martin is a British Free Software contractor based in Boston, Massachusetts.

Links

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EP012 EasyBuild : Building Software with Ease for HPC

Dec 5, 2018. | By: Admin

Outline

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.

About Kenneth Hoste :

Kenneth Hoste, a.k.a. ‘boegel’, is a computer scientist and Free & Open Source Software (FOSS) enthusiast from Belgium. He holds a Masters (2005) and PhD (2010) in Computer Science from Ghent University. His dissertation topic was “Analysis, Estimation and Optimization of Computer System Performance Using Machine Learning”.

Since October 2010, he is a member of the HPC team at Ghent University (Belgium) where he is mainly responsible for user support & training. As a part of his job, he is also the lead developer and release manager of EasyBuild, a software build and installation framework for (scientific) software on High Performance Computing (HPC) systems.

In his free time, he is a family guy and a fan of loud music, frequently attending gigs and festivals. He enjoys helping people & sharing his expertise, and likes joking around. He has a weak spot for stickers.

For more details, we refer to his social media:

Links:

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EP011 Blackbox Optimization with NOMAD

Nov 7, 2018. | By: Admin

Outline

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.

About Sébastien Le Digabel:

Sébastien Le Digabel received the M.Sc.A. degree and the Ph.D. degree in applied mathematics from Polytechnique Montreal, Montreal, Quebec, Canada in 2002 and 2008 respectively, and worked as a postdoctoral fellow at the IBM Watson Research Center and the University of Chicago in 2010 and 2011. He is currently an Associate Professor in the Department of Mathematics and Industrial Engineering at Polytechnique Montreal and a regular member of the GERAD research center. His research interests include the analysis and development of algorithms for derivative-free and blackbox optimization, and the design of related software. All of his work on derivative-free optimization is included in the NOMAD software, a free package for blackbox optimization.

Links:

  • Nomad website
  • Le Digabel, S., 2011. Algorithm 909: NOMAD: Nonlinear Optimization with the MADS algorithm. ACM Transactions on Mathematical Software 37 (4), 44:1–44:15. DOI
  • NOMAD’s user guide

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EP010 CGAL : The Computational Geometry Algorithms Library

Oct 3, 2018. | By: Admin

Outline

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…

Check out for a detailed list of available modules.

About Sébastien Loriot:

Sébastien is co-author of several CGAL packages and is also part of the editorial board of the library. He is mainly working on various operations on polyhedral surfaces within GeometryFactory.

Links:

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EP009 Finite element meshing with gmsh

Sep 5, 2018. | By: Admin

Outline

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. Gmsh is built around four modules: geometry, mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface, in ASCII text files using Gmsh’s own scripting language (.geo files), or using the C++, C, Python or Julia API.

About Christophe Geuzaine:

Christophe Geuzaine received his PhD degree in 2001 from the Faculty of Applied Sciences at the University of Liège in Belgium. After post-doctoral positions at the California Institute of Technology and with the Belgian National Science Foundation, he became an assistant professor of Mathematics at Case Western Reserve University in the US in 2005. In 2007 he came back to the University of Liège, where he is now full professor in the department of Electrical Engineering and Computer Science. He is the founder and head of the Applied and Computational Electromagnetics research group within the Montefiore Institute.

Prof. Geuzaine’s research encompasses modeling, analysis, algorithm development, and simulation for problems arising in various areas of engineering and science, with current applications in electromagnetic, biomedical and geophysical problems. He has authored numerous papers in the fields of scientific computing and is the co-creator of the popular open source mesh generator Gmsh and the multi-physics finite element solver GetDP.

Links:

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EP008 Solid-Liquid Mixing Modelling

Aug 1, 2018. | By: Admin

Outline

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 finite element simulations, meshing and geometry analysis. Follow us to be informed when we will release our next episode about the open source meshing tool GMSH.

About Bruno Blais:

Bruno Blais is a Research Officer with the Automotive and Surface Transportation Portfolio of the National Research Council of Canada (NRC AST) and an associate professor at the Department of Chemical Engineering at Polytechnique Montreal. He has earned a B. Eng. in Chemical Engineering, a Grande École Engineering Diploma from ENSTA Paristech, a master in Fundamental Fluid Mechanics from ENSTA and a Ph.D. in Chemical Engineering from Polytechnique Montreal. Bruno is a Vanier Graduate Scholar (2012-2016) and has received the Govenor’s General gold academic medal for his thesis work on numerical modelling of multiphase flow. He has also received the best thesis award from Ecole Polytechnique (2017) and the North American Mixing Forum (2016-2017). Bruno has also received other recognition such as the Da Vinci Profile of Ecole Polytechnique (2012) and the Master Île-de-France international Scholarship (2011-2012). Bruno’s expertise lies in the development, verification, and validation of high performance digital models for fluid mechanics, heat transfer, and complex multi-physical and multi-scale phenomena. His research interests are in computational fluid mechanics (CFD), reacting flow, granular and solid-fluid flow modelling, topology optimization as well as high-performance computing on distributed high-performance architecture and on GPU. He has been an active collaborator of the CFDEM project, an open source platform for granular and solid-fluid flows, since 2013.

Links

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EP007 A Guide to Software Licenses in Science

Jul 4, 2018. | By: Admin

Outline

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.

About Karl Fogel:

Karl Fogel is an open source software developer, author, and consultant. In 2005 he wrote “Producing Open Source Software: How to Run a Successful Free Software Project” (O’Reilly Media, online at producingoss.com, based partly on his experiences in the Subversion project. He has worked at CollabNet, Google, Canonical, O’Reilly Media, and Code for America / Civic Commons, all as an open source specialist. He is now a partner at Open Tech Strategies, LLC, where he helps organizations launch and engage with open source projects. He is also an Open Internet Tools Project Fellow at the New America Foundation, a former member of the board of directors of the Open Source Initative, and a member of the Apache Software Foundation. He is @kfogel on Identi.ca and Twitter, and his home page is red-bean.com/kfogel.

About James Vasile:

James Vasile has fifteen years experience as a user, developer, advocate and advisor in the free and open source software world. His expertise is in software licensing and community-building, as well as non-profit and small business startup. He focuses on free software and open source production, although his work and interests often take him far beyond the world of software. Much of what James does involves teaching people how to build successful businesses around free software and ensuring licensing alignment in multisource FOSS stacks.

Previously, James was a Senior Fellow at the Software Freedom Law Center, where he advised and supported a wide range of free software efforts. A former Director of the FreedomBox Foundation, James remains active in several technology development efforts.

James was a founding board member of Open Source Matters, the non-profit behind Joomla. He began his career at Cravath, Swaine & Moore. You can learn more about him from his GitHub activity and his LinkedIn profile, or by connecting with him on Twitter.

Links:

  • Fogel, K. (2005). Producing open source software: How to run a successful free software project. “ O’Reilly Media, Inc.”. Link
  • Short notice: Some Common Issues in Open Source Licensing. Link
  • More resources about starting and managing open source projects. Link

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EP006 Gentoo Linux for Neurosciences

Jun 6, 2018. | By: Admin

Outline

In Episode 6, we interviewed Christian Horea about the NeuroGentoo Overlay 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.

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.

For more details, we refer to his social media:

Links:

  • NeuroGentoo Overlay @ github
  • Christian, Horea & Saab, Bechara & Rudin, Markus. (2017). Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software. Research Ideas and Outcomes. 3. e12095. 10.3897/rio.3.e12095.

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EP005 LibreOffice the Swiss Army Knife of Science?

May 2, 2018. | By: Admin

Outline

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.

About Katarina Behrens:

Katarina Behrens (aka Bubli) is one of LibreOffice core developers.

She got involved with free and open-source software more than a decade ago, contributing l10n to Debian project. Employed by SUSE later, she worked on YaST, openSUSE’s installation and configuration tool and in 2010, she became
member of SUSE LibreOffice team.

After a brief intermezzo in computer security business, she was hired by CIB (a German company delivering document management systems) in 2015 to work on LibreOffice full-time again. Apart from squashing LibreOffice bugs that disturb CIB customers’ good night’s sleep, she engages in mentoring (Google Summer of Code) and finds seeing her mentees succeed to be an ultimately rewarding experience.

Links

You can get more information about LibreOffice using this link. If you want to get involved in the project you can get more information’s here and a video can also be found on Youtube.

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For the definition of Denkmalschutz, you can consult this link

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EP004 Reproducible science with Rocker

Apr 3, 2018. | By: Admin

Outline

In Episode 4, we interviewed Carl Boettinger about Rocker:

Rocker is an open source community project providing Docker containers for R users. Rocker containers help users to easily share and deploy customized and reproducible R environments on local and remote machines. Rocker images have been downloaded over three million times and are maintained by Carl Boettiger & Dirk Eddelbuettel with many contributions from the user community.

About Carl Boettinger

Carl Boettinger is an Assistant Professor in the Department of Environmental Science, Policy and Management at UC Berkeley. He works on problems in ecological forecasting and decision making under uncertainty, with applications for global change, conservation and natural resource management. He is particularly interested in how we can predict or manage ecological systems that may experience regime shifts: sudden and dramatic changes that challenge both our models and available data. The rapid expansion in both computational power and the available ecological and environmental data enables and requires new mathematical, statistical and computational approaches to these questions. Ecology has much to learn about what are and are not useful from advances in informatics & computer science, just as it has from statistics and mathematics. Traditional approaches to ecological modeling and resource management such as stochastic dynamic systems, Bayesian inference, and optimal control theory must be adapted both to take advantage of all available data while also dealing with its imperfections. His approach blends ecological theory with the synthesis of heterogeneous data and the development of software – a combination now recognized as data science.

Links

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EP003 JabRef at JabCon

Mar 7, 2018. | By: Admin

Outline

In Episode 3, we interview Oliver Kopp and Jörg Lenhard about Jabref:

JabRef is an open-source, cross-platform citation and reference management tool licensed under the MIT license, which works on Windows, Linux and Mac OS X. It is available free of charge and is actively developed. JabRef supports you in every step of your research work. Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. Bibliographies generated by LaTeX and BibTeX from a BibTeX file can be formatted to suit any reference list specifications by the use of different BibTeX and BibLaTeX style files.

About Oliver Koop :

Oliver Kopp studied Software Engineering and defended his PhD in the field of cross-partner business process management. Currently, he researches as PostDoc in the area of architectural decision records. For him, the key success factor for turning research into practice is sustainable open source software. Thus, it is a natural fit that he is project lead at Eclipse Winery, which provides a framework for research on modeling TOSCA-based (Cloud) applications.

About Jörg Lenhard :

Jörg Lenhard is a post-doctoral research fellow at the Software Engineering Research Group of Karlstad University, Sweden. He obtained his PhD in Computer Science from the University of Bamberg, Germany, where he also completed his Bachelor and Master studies, along with several exchanges to the University of Skövde and the Blekinge Institute of Technology in Sweden. Jörg’s passion lies in the development of high-quality software, which is where his research and teaching activities are centered. This is also the reason why he participates in open source software development and JabRef. Next to his academic publications, he recently authored a text book on code quality for Java beginners titled Java by Comparison: Become a Java Craftsman in 70 Examples.

Links

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EP002 Modeling composite materials fatigue with Python

Feb 7, 2018. | By: Admin

Outline

In Episode 2, we interview Laurent Cormier, a research associate at the École de Technologie Supérieure in Montréal. 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.

About Laurent Cormier :

Laurent Cormier owns a Bachelor’s degree (2006) and a research Master’s degree (2009) in mechanical engineering and received his Ph.D in engineering in 2017 from the École de technologie supérieure (ETS) in Montréal. He currently is a postdoctoral researcher working on high voltage capacitor manufacturing technology, a research associate in composite materials and a lecturer at the same institution.

His previous research topics include experimental characterization and analytical modeling of temperature and northern climates’ effects on the static strength, fatigue durability and viscoelastic behaviour of composites. These research topics were part of multiple projects, including the Wind Energy Strategic Network (WESNet) from the Natural Sciences and Engineering Research Council of Canada (NSERC), the Upwind program from the European Commission Sixth Framework Programme and industrial partnerships.

He also has a strong interest in Science, its methods, its philosophy and the transmission of knowledge. Photography, literature and politics are also part of his broader interests.

Links

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EP001 Introduction to the FLOSS for Science podcast

Jan 12, 2018. | By: Admin

Outline

In this episode the two hosts David Brassard and Patrick Diehl of FLOSS for Science introduce themselves and they explain the aims of this podcast.

Links

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