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FLOSS for Science

FLOSSforScience

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FLOSS for Science
FLOSS for Science

FLOSS for Science

FLOSSforScience

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Open Source software in Science

Latest Episodes

EP023 Reproducible Science and Synthetic Datasets Using R

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 packages 00:15:59 Ressources to learn R 00:17:21 Introduction to synthetic datasets 00:21:54 Synthetic datasets for privacy and their limitations 00:24:52 How much time should be spent to publish datasets and code 00:26:58 Dan's view on open science practices 00:28:27 FLOSS and open science practices 00:30:49 The licence he uses for sharing code and data 00:32:06 Obtaining a DOI with the Open Science Framework 00:32:21 Journal of Open Source Software 00:34:15 The importance of publishing in open access journals 00:37:28 Publishig in open access journals and plan S 00:39:09 The lack of affordability for open access publishing 00:40:22 Preprints as a solution? 00:43:04 How to publish a perfectly reproducible paper 00:46:02 How to convince other scientists to share their data and code 00:46:42 The next big challenge of science 00:48:55 The most notable discovery in recent years 00:51:20 Favourite text processing tool 00:51:43 A topic in science he recently changed his mind about 00:52:49 Anything else? 00:53:34 How to contact Dan Quintana 00:53:56 Conclusion

55 MIN1 w ago
Comments
EP023 Reproducible Science and Synthetic Datasets Using R

EP022 Symbolic Calculation with Maxima

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 pitchfor Maxima 00:06:43 Reference manual and Maxima's documentation 00:07:52 Accessing Maxima's documentation 00:08:41 Comparison with Maple and Mathematica 00:10:50 The concept of "code equal data"? 00:12:54 Maxima's language complexity/simplicity 00:15:13 User interfaces for Maxima 00:16:24 Console interface for Maxima 00:17:12 Presentation of the resulting equations or results 00:17:46 Integrating Maxima and LaTeX 00:19:08 The origin story of Maxima 00:25:17 Licensing status before the relicensing to GPL 00:26:00 Maxima for undergrad students and researchers 00:28:33 Robert's contributions to the project and its self-organized structure 00:31:39 How many people are involved in the project 00:32:13 Communication channels for the project 00:32:52 Underlying technologies in Maxima 00:34:27 Ressources for newcomers 00:35:47 Robert's vision about FLOSS in science 00:36:26 Negative impacts of FLOSS on science 00:37:25 The most notable scientific discovery in recent years 00:39:22 Robert's favourite text processing tool 00:40:04 The social aspect of FLOSS 00:42:34 Anything else he wanted to share with us? 00:43:39 How to contact Robert 00:43:57 Outro

45 MINOCT 2
Comments
EP022 Symbolic Calculation with Maxima

EP021 High-level Scientific Computing with GNU Octave

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. 00:00:00 Message to our listeners 00:00:29 Intro 00:00:45 Introducing Juan Pablo Carbajal 00:01:32 30 seconds elevator pitch for GNU Octave 00:02:20 How does the Octave programming language compares to other common programming languages 00:03:23 Compatibility between GNU Octave and Matlab 00:06:29 Matlab's toolboxes compared to GNU Octave packages 00:07:31 Simulink models with GNU Octave 00:09:06 Parallel processing with GNU Octave 00:10:40 The issue with CUDA in GNU Octave 00:11:48 How GNU Octaves differs rom other open source Matlab equivalents 00:13:34 Syntax compatibility to ease transition and reusing code from Matlab 00:15:11 Resources to start using GNU Octave 00:16:40 GNU Octave's graphical user interface and the old QT Octave GUI 00:20:14 GNU Octave's graphical user interface compared to Matlab 00:22:11 Why GNU Octave and not simply Octave 00:23:06 GNU Octave licence 00:24:01 How often he uses GNU Octave 00:24:18 Juan's numerous contributions to the project 00:25:27 GNU octave for companies 00:27:45 Arguments for teaching with GNU Octave instead of Matlab 00:29:32 How many are involved in the project? 00:30:37 Communication channels within the project 00:31:34 Is the project actively looking for developers? 00:32:11 Skills required to contribute 00:33:14 The two-level language dilemma 00:34:59 Juan's vision about FLOSS and its importance for science 00:37:09 Possible negative impacts of FLOSS and converting non-FLOSS users 00:40:17 The most notable scientific discovery in recent years 00:41:46 Juan's favourite text processing tools 00:42:38 Things we forgot to ask about 00:43:57 Anything else to share? 00:44:25 How to contact Juan 00:44:50 Outro

46 MINSEP 4
Comments
EP021 High-level Scientific Computing with GNU Octave

EP020 Peer-reviewed Publication of Research Software

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.

63 MINAUG 6
Comments
EP020 Peer-reviewed Publication of Research Software

EP019 The Road Ahead for Scientific Linux

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.

45 MINJUL 3
Comments
EP019 The Road Ahead for Scientific Linux

EP018 Performing Arts with FLOSS

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.

55 MINJUN 5
Comments
EP018 Performing Arts with FLOSS

EP017 HPX: A cure for performance impaired parallel applications

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

46 MINMAY 1
Comments
EP017 HPX: A cure for performance impaired parallel applications

EP016 Management of High Performance Computing Infrastructures with OpenHPC

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.

52 MINAPR 3
Comments
EP016 Management of High Performance Computing Infrastructures with OpenHPC

EP015 Reproducible Research in Archaeology with rrtools

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.

73 MINMAR 5
Comments
EP015 Reproducible Research in Archaeology with rrtools

EP014 Gimp Your Images for Publication

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.

47 MINFEB 6
Comments
EP014 Gimp Your Images for Publication

Latest Episodes

EP023 Reproducible Science and Synthetic Datasets Using R

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 packages 00:15:59 Ressources to learn R 00:17:21 Introduction to synthetic datasets 00:21:54 Synthetic datasets for privacy and their limitations 00:24:52 How much time should be spent to publish datasets and code 00:26:58 Dan's view on open science practices 00:28:27 FLOSS and open science practices 00:30:49 The licence he uses for sharing code and data 00:32:06 Obtaining a DOI with the Open Science Framework 00:32:21 Journal of Open Source Software 00:34:15 The importance of publishing in open access journals 00:37:28 Publishig in open access journals and plan S 00:39:09 The lack of affordability for open access publishing 00:40:22 Preprints as a solution? 00:43:04 How to publish a perfectly reproducible paper 00:46:02 How to convince other scientists to share their data and code 00:46:42 The next big challenge of science 00:48:55 The most notable discovery in recent years 00:51:20 Favourite text processing tool 00:51:43 A topic in science he recently changed his mind about 00:52:49 Anything else? 00:53:34 How to contact Dan Quintana 00:53:56 Conclusion

55 MIN1 w ago
Comments
EP023 Reproducible Science and Synthetic Datasets Using R

EP022 Symbolic Calculation with Maxima

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 pitchfor Maxima 00:06:43 Reference manual and Maxima's documentation 00:07:52 Accessing Maxima's documentation 00:08:41 Comparison with Maple and Mathematica 00:10:50 The concept of "code equal data"? 00:12:54 Maxima's language complexity/simplicity 00:15:13 User interfaces for Maxima 00:16:24 Console interface for Maxima 00:17:12 Presentation of the resulting equations or results 00:17:46 Integrating Maxima and LaTeX 00:19:08 The origin story of Maxima 00:25:17 Licensing status before the relicensing to GPL 00:26:00 Maxima for undergrad students and researchers 00:28:33 Robert's contributions to the project and its self-organized structure 00:31:39 How many people are involved in the project 00:32:13 Communication channels for the project 00:32:52 Underlying technologies in Maxima 00:34:27 Ressources for newcomers 00:35:47 Robert's vision about FLOSS in science 00:36:26 Negative impacts of FLOSS on science 00:37:25 The most notable scientific discovery in recent years 00:39:22 Robert's favourite text processing tool 00:40:04 The social aspect of FLOSS 00:42:34 Anything else he wanted to share with us? 00:43:39 How to contact Robert 00:43:57 Outro

45 MINOCT 2
Comments
EP022 Symbolic Calculation with Maxima

EP021 High-level Scientific Computing with GNU Octave

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. 00:00:00 Message to our listeners 00:00:29 Intro 00:00:45 Introducing Juan Pablo Carbajal 00:01:32 30 seconds elevator pitch for GNU Octave 00:02:20 How does the Octave programming language compares to other common programming languages 00:03:23 Compatibility between GNU Octave and Matlab 00:06:29 Matlab's toolboxes compared to GNU Octave packages 00:07:31 Simulink models with GNU Octave 00:09:06 Parallel processing with GNU Octave 00:10:40 The issue with CUDA in GNU Octave 00:11:48 How GNU Octaves differs rom other open source Matlab equivalents 00:13:34 Syntax compatibility to ease transition and reusing code from Matlab 00:15:11 Resources to start using GNU Octave 00:16:40 GNU Octave's graphical user interface and the old QT Octave GUI 00:20:14 GNU Octave's graphical user interface compared to Matlab 00:22:11 Why GNU Octave and not simply Octave 00:23:06 GNU Octave licence 00:24:01 How often he uses GNU Octave 00:24:18 Juan's numerous contributions to the project 00:25:27 GNU octave for companies 00:27:45 Arguments for teaching with GNU Octave instead of Matlab 00:29:32 How many are involved in the project? 00:30:37 Communication channels within the project 00:31:34 Is the project actively looking for developers? 00:32:11 Skills required to contribute 00:33:14 The two-level language dilemma 00:34:59 Juan's vision about FLOSS and its importance for science 00:37:09 Possible negative impacts of FLOSS and converting non-FLOSS users 00:40:17 The most notable scientific discovery in recent years 00:41:46 Juan's favourite text processing tools 00:42:38 Things we forgot to ask about 00:43:57 Anything else to share? 00:44:25 How to contact Juan 00:44:50 Outro

46 MINSEP 4
Comments
EP021 High-level Scientific Computing with GNU Octave

EP020 Peer-reviewed Publication of Research Software

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.

63 MINAUG 6
Comments
EP020 Peer-reviewed Publication of Research Software

EP019 The Road Ahead for Scientific Linux

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.

45 MINJUL 3
Comments
EP019 The Road Ahead for Scientific Linux

EP018 Performing Arts with FLOSS

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.

55 MINJUN 5
Comments
EP018 Performing Arts with FLOSS

EP017 HPX: A cure for performance impaired parallel applications

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

46 MINMAY 1
Comments
EP017 HPX: A cure for performance impaired parallel applications

EP016 Management of High Performance Computing Infrastructures with OpenHPC

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.

52 MINAPR 3
Comments
EP016 Management of High Performance Computing Infrastructures with OpenHPC

EP015 Reproducible Research in Archaeology with rrtools

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.

73 MINMAR 5
Comments
EP015 Reproducible Research in Archaeology with rrtools

EP014 Gimp Your Images for Publication

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.

47 MINFEB 6
Comments
EP014 Gimp Your Images for Publication
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