https://flossforscience.com Open Source software in Science Thu, 29 Apr 2021 21:01:54 +0000 en-US hourly 1 http://jekyllrb.com Interviews with scientists who are using or developing free and libre open source software FLOSSforScience no FLOSSforScience flossforscience@gmail.com flossforscience@gmail.com (FLOSSforScience) https://flossforscience.comhttps://raw.githubusercontent.com/FLOSSforScience/FLOSSforScience.github.io/master/assets/img/logo.png https://flossforscience.com https://flossforscience.com/podcast/season3-epsiode-5 https://flossforscience.com/podcast/season3-epsiode-5#comments Tue, 27 Apr 2021 00:00:00 +0000 https://flossforscience.com/51957127dbd460fac1affbe062d692a0ffa845711f8b8d5c61e80f078f6b5826 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 show the improvements brought in the version 3 in regard to the compliance and patent sections. We asked him about his take on the philosophical differences between GNU style licenses and the MIT/BSD licenses in regard to the debate between user and developper freedom. We followed by going through some myths surrounding the GNU licenses and a general discussion about freedom and privacy. We finished the interview with our usual quick questions. 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 show the improvements brought in the version 3 in regard to the compliance and patent sections. We asked him about his take on the philosophical differences between GNU style licenses and the MIT/BSD licenses in regard to the debate between user and developper freedom. We followed by going through some myths surrounding the GNU licenses and a general discussion about freedom and privacy. We finished the interview with our usual quick questions. An interview with Craig Topham 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 show the improvements brought in the version 3 in regard to the compliance and patent sections. We asked him about his take on the philosophical differences between GNU style licenses and the MIT/BSD licenses in regard to the debate between user and developper freedom. We followed by going through some myths surrounding the GNU licenses and a general discussion about freedom and privacy. We finished the interview with our usual quick questions. FLOSSforScience no 0:48:42 https://flossforscience.com/podcast/season3-epsiode-7 https://flossforscience.com/podcast/season3-epsiode-7#comments Thu, 03 Sep 2020 00:00:00 +0000 https://flossforscience.com/13716329014667f17da4b9650965be78d5dd34aa171d2fd448ae451f6f6caaa0 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 00:04:24 His role as leader of software packaging technology for the exascale computing project 00:04:58 One-minute elevator pitch for Spack 00:05:34 Spack's usage philosophy compared to other package managers 00:06:59 Installation from source code or binary? 00:07:28 Spack's usage in the top500 super computers 00:07:49 Geographical distribution of users 00:08:18 Number of packages in the repo and some examples 00:09:05 Managing computer clusters with Spack's automation capabilities 00:11:04 Module files in Spack 00:12:32 Syntax of a Spack package file 00:13:43 Configuration of compiler flags 00:15:00 Importing python libraries in the Spack files 00:15:48 The procedure to submit a package 00:16:27 Review process for new packages 00:17:34 Reasons for rejection of Spack packages 00:18:01 Operating systems supported by Spack 00:18:23 WSL and Spack 00:18:58 Restricting packages to certain hardware and software configurations 00:20:04 Build testing and nightly builds 00:21:28 Working with containers in a Spack environment 00:22:25 Deploying prebuilt containers 00:23:05 About the "universality" of containers 00:24:16 His opinion on containerized applications for reproducible science 00:26:17 Spack's log file to document reproducibility 00:27:13 Reproducing older results 00:28:10 Specifying requirements on compilers 00:30:39 Post-installation verification test 00:31:10 Using Spack on a standalone computer instead of HPC systems 00:32:56 Differences between EasyBuild and Spack 00:34:24 EasyBuild in the top500 00:34:49 Transitionning between EasyBuild and Spack 00:35:38 Other alternatives 00:36:23 Using EasyBuild and Spack on the same system 00:38:36 When did the project start? 00:39:53 External contributions to Spack 00:40:53 How many core developpers? 00:41:30 Organization of the community and governance model 00:43:06 Who decides which package is accepted in the repo? 00:44:38 Spack's choice of software license 00:47:09 Todd's vision about the importance of FLOSS for the openness of science 00:48:13 Possible negative impacts of FLOSS 00:48:58 Most notable recent scientific discovery 00:49:14 Favourite text processing tool 00:49:25 A topic in science about which he recently changed his mind about 00:49:58 Anything else we forgot to ask? 00:50:09 How to contact Todd 00:50:46 Conclusion 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 00:04:24 His role as leader of software packaging technology for the exascale computing project 00:04:58 One-minute elevator pitch for Spack 00:05:34 Spack's usage philosophy compared to other package managers 00:06:59 Installation from source code or binary? 00:07:28 Spack's usage in the top500 super computers 00:07:49 Geographical distribution of users 00:08:18 Number of packages in the repo and some examples 00:09:05 Managing computer clusters with Spack's automation capabilities 00:11:04 Module files in Spack 00:12:32 Syntax of a Spack package file 00:13:43 Configuration of compiler flags 00:15:00 Importing python libraries in the Spack files 00:15:48 The procedure to submit a package 00:16:27 Review process for new packages 00:17:34 Reasons for rejection of Spack packages 00:18:01 Operating systems supported by Spack 00:18:23 WSL and Spack 00:18:58 Restricting packages to certain hardware and software configurations 00:20:04 Build testing and nightly builds 00:21:28 Working with containers in a Spack environment 00:22:25 Deploying prebuilt containers 00:23:05 About the "universality" of containers 00:24:16 His opinion on containerized applications for reproducible science 00:26:17 Spack's log file to document reproducibility 00:27:13 Reproducing older results 00:28:10 Specifying requirements on compilers 00:30:39 Post-installation verification test 00:31:10 Using Spack on a standalone computer instead of HPC systems 00:32:56 Differences between EasyBuild and Spack 00:34:24 EasyBuild in the top500 00:34:49 Transitionning between EasyBuild and Spack 00:35:38 Other alternatives 00:36:23 Using EasyBuild and Spack on the same system 00:38:36 When did the project start? 00:39:53 External contributions to Spack 00:40:53 How many core developpers? 00:41:30 Organization of the community and governance model 00:43:06 Who decides which package is accepted in the repo? 00:44:38 Spack's choice of software license 00:47:09 Todd's vision about the importance of FLOSS for the openness of science 00:48:13 Possible negative impacts of FLOSS 00:48:58 Most notable recent scientific discovery 00:49:14 Favourite text processing tool 00:49:25 A topic in science about which he recently changed his mind about 00:49:58 Anything else we forgot to ask? 00:50:09 How to contact Todd 00:50:46 Conclusion An interview with Todd Gamblin 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 00:04:24 His role as leader of software packaging technology for the exascale computing project 00:04:58 One-minute elevator pitch for Spack 00:05:34 Spack's usage philosophy compared to other package managers 00:06:59 Installation from source code or binary? 00:07:28 Spack's usage in the top500 super computers 00:07:49 Geographical distribution of users 00:08:18 Number of packages in the repo and some examples 00:09:05 Managing computer clusters with Spack's automation capabilities 00:11:04 Module files in Spack 00:12:32 Syntax of a Spack package file 00:13:43 Configuration of compiler flags 00:15:00 Importing python libraries in the Spack files 00:15:48 The procedure to submit a package 00:16:27 Review process for new packages 00:17:34 Reasons for rejection of Spack packages 00:18:01 Operating systems supported by Spack 00:18:23 WSL and Spack 00:18:58 Restricting packages to certain hardware and software configurations 00:20:04 Build testing and nightly builds 00:21:28 Working with containers in a Spack environment 00:22:25 Deploying prebuilt containers 00:23:05 About the "universality" of containers 00:24:16 His opinion on containerized applications for reproducible science 00:26:17 Spack's log file to document reproducibility 00:27:13 Reproducing older results 00:28:10 Specifying requirements on compilers 00:30:39 Post-installation verification test 00:31:10 Using Spack on a standalone computer instead of HPC systems 00:32:56 Differences between EasyBuild and Spack 00:34:24 EasyBuild in the top500 00:34:49 Transitionning between EasyBuild and Spack 00:35:38 Other alternatives 00:36:23 Using EasyBuild and Spack on the same system 00:38:36 When did the project start? 00:39:53 External contributions to Spack 00:40:53 How many core developpers? 00:41:30 Organization of the community and governance model 00:43:06 Who decides which package is accepted in the repo? 00:44:38 Spack's choice of software license 00:47:09 Todd's vision about the importance of FLOSS for the openness of science 00:48:13 Possible negative impacts of FLOSS 00:48:58 Most notable recent scientific discovery 00:49:14 Favourite text processing tool 00:49:25 A topic in science about which he recently changed his mind about 00:49:58 Anything else we forgot to ask? 00:50:09 How to contact Todd 00:50:46 Conclusion FLOSSforScience no 0:52:26 https://flossforscience.com/podcast/season3-episode-6 https://flossforscience.com/podcast/season3-episode-6#comments Wed, 01 Jul 2020 00:00:00 +0000 https://flossforscience.com/66ff8ae1bf6ca9d3ae8996a79c89c27b4d8664bf6613367962e573353d4fb886 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 and how he got into Python 00:03:46 New interesting programming languages 00:05:07 His favourite past Python projects 00:06:53 His one minute elevator pitch for setuptools 00:08:00 The relation between setuptools, PIP and Anaconda 00:10:43 How he got involved with the setuptools project 00:14:43 What is a Python package ? 00:16:07 What can be included in a package? 00:16:36 At which point is it beneficial to create a package ? 00:18:04 Managing compatibility with multiple versions of Python 00:20:33 Advantages of packages for small projects 00:22:46 How much work is required to create a package ? 00:25:05 Files required to create a Python package 00:27:45 Licenses and readme for Python packages 00:30:51 The nature of distribution archives 00:31:27 Compatibility of binary archives 00:32:39 Eggs and wheel files 00:34:32 Dealing with non portable packages in the Python Package Index across multiple operating systems 00:37:49 Uploading packages to the Python Package Index 00:39:12 Review for broken or malicious code 00:40:08 Vulneraility from package removal in the Python Package Index 00:43:24 Package name collisions 00:45:13 How many packages are in the Python Package Index 00:45:25 Alternatives to the main Python Package Index 00:46:35 Other packaging tools 00:47:39 How many developpers are involved in the project 00:48:31 Communication channels and discussions about Python packaging 00:49:53 Openings for new contributors 00:50:59 Skills required to contribute 00:52:24 The challenge of long term maintenance of packages in academia 00:55:43 His vision about the importance of FLOSS for the openess of science 00:59:18 Disadvantage of using FLOSS 01:01:24 The most notable scientific discovery in recent years 01:02:13 Favourite text processing tool 01:03:23 A topic in science about which he recently changed his mind 01:04:50 Contact informations 01:05:23 Conclusion 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 and how he got into Python 00:03:46 New interesting programming languages 00:05:07 His favourite past Python projects 00:06:53 His one minute elevator pitch for setuptools 00:08:00 The relation between setuptools, PIP and Anaconda 00:10:43 How he got involved with the setuptools project 00:14:43 What is a Python package ? 00:16:07 What can be included in a package? 00:16:36 At which point is it beneficial to create a package ? 00:18:04 Managing compatibility with multiple versions of Python 00:20:33 Advantages of packages for small projects 00:22:46 How much work is required to create a package ? 00:25:05 Files required to create a Python package 00:27:45 Licenses and readme for Python packages 00:30:51 The nature of distribution archives 00:31:27 Compatibility of binary archives 00:32:39 Eggs and wheel files 00:34:32 Dealing with non portable packages in the Python Package Index across multiple operating systems 00:37:49 Uploading packages to the Python Package Index 00:39:12 Review for broken or malicious code 00:40:08 Vulneraility from package removal in the Python Package Index 00:43:24 Package name collisions 00:45:13 How many packages are in the Python Package Index 00:45:25 Alternatives to the main Python Package Index 00:46:35 Other packaging tools 00:47:39 How many developpers are involved in the project 00:48:31 Communication channels and discussions about Python packaging 00:49:53 Openings for new contributors 00:50:59 Skills required to contribute 00:52:24 The challenge of long term maintenance of packages in academia 00:55:43 His vision about the importance of FLOSS for the openess of science 00:59:18 Disadvantage of using FLOSS 01:01:24 The most notable scientific discovery in recent years 01:02:13 Favourite text processing tool 01:03:23 A topic in science about which he recently changed his mind 01:04:50 Contact informations 01:05:23 Conclusion An interview with Jason R Coombs 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 and how he got into Python 00:03:46 New interesting programming languages 00:05:07 His favourite past Python projects 00:06:53 His one minute elevator pitch for setuptools 00:08:00 The relation between setuptools, PIP and Anaconda 00:10:43 How he got involved with the setuptools project 00:14:43 What is a Python package ? 00:16:07 What can be included in a package? 00:16:36 At which point is it beneficial to create a package ? 00:18:04 Managing compatibility with multiple versions of Python 00:20:33 Advantages of packages for small projects 00:22:46 How much work is required to create a package ? 00:25:05 Files required to create a Python package 00:27:45 Licenses and readme for Python packages 00:30:51 The nature of distribution archives 00:31:27 Compatibility of binary archives 00:32:39 Eggs and wheel files 00:34:32 Dealing with non portable packages in the Python Package Index across multiple operating systems 00:37:49 Uploading packages to the Python Package Index 00:39:12 Review for broken or malicious code 00:40:08 Vulneraility from package removal in the Python Package Index 00:43:24 Package name collisions 00:45:13 How many packages are in the Python Package Index 00:45:25 Alternatives to the main Python Package Index 00:46:35 Other packaging tools 00:47:39 How many developpers are involved in the project 00:48:31 Communication channels and discussions about Python packaging 00:49:53 Openings for new contributors 00:50:59 Skills required to contribute 00:52:24 The challenge of long term maintenance of packages in academia 00:55:43 His vision about the importance of FLOSS for the openess of science 00:59:18 Disadvantage of using FLOSS 01:01:24 The most notable scientific discovery in recent years 01:02:13 Favourite text processing tool 01:03:23 A topic in science about which he recently changed his mind 01:04:50 Contact informations 01:05:23 Conclusion FLOSSforScience no 1:07:17 https://flossforscience.com/podcast/season3-epsiode-4 https://flossforscience.com/podcast/season3-epsiode-4#comments Wed, 06 May 2020 00:00:00 +0000 https://flossforscience.com/ea49c20854f6ab2785e87f2e2b03daae5a7fd5c53ef68716c11c4ab1eb4a3577 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 Examples of supported projects 00:03:39 Status of sponsorded and affiliated projects 00:05:04 Advantages of one status over the other 00:05:48 Legal challenges for open source scientific projects 00:07:19 Financial support for scientific open source projects 00:10:13 Assistance to apply for external grants 00:11:01 Paying developers from outside of US? 00:11:43 Revenue sources for NumFocus 00:12:21 Levels of corporate sponshorships 00:13:14 The influence of corporate sponsors 00:13:56 Motivations of corporate sponsors 00:15:02 Some of the sponsors of the NumFocus organization 00:16:05 Technological support for projects 00:17:03 Events previously supported by the organization 00:18:09 The kind of support that can be provided for events 00:19:22 Requirements for new projects 00:21:10 Clarification about the meaning of being a scientific oriented project 00:23:11 Requirements about the team size and strong governance within projects 00:24:58 The application process 00:26:18 Duration of support 00:26:44 Timeframe to receive a response for an application 00:28:30 Feedback in the case of rejection 00:29:12 Are there downsides of becoming a part of NumFocus? 00:30:32 Additional administrative overhead? 00:32:01 Location of NumFocus staff members 00:33:00 Foudation of NumFocus and initial projects 00:34:05 Opening to projects outside of the Python ecosystem 00:34:54 Favourite project? 00:35:46 Initial role in NumFocus 00:36:53 Term duration for positions at the board of directors 00:37:24 Selection process for the board of directors 00:38:31 Leah's vision about FLOSS and its importance for the openness of science 00:39:04 Negative impacts of FLOSS 00:39:33 Most notable scientific discovery in recent years 00:39:59 Favourite text processing tool 00:40:37 A topic in science about which she changed her mind about 00:41:36 Anything else we forgot to ask about? 00:42:54 How to contact Leah Silen 00:43:14 Outro 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 Examples of supported projects 00:03:39 Status of sponsorded and affiliated projects 00:05:04 Advantages of one status over the other 00:05:48 Legal challenges for open source scientific projects 00:07:19 Financial support for scientific open source projects 00:10:13 Assistance to apply for external grants 00:11:01 Paying developers from outside of US? 00:11:43 Revenue sources for NumFocus 00:12:21 Levels of corporate sponshorships 00:13:14 The influence of corporate sponsors 00:13:56 Motivations of corporate sponsors 00:15:02 Some of the sponsors of the NumFocus organization 00:16:05 Technological support for projects 00:17:03 Events previously supported by the organization 00:18:09 The kind of support that can be provided for events 00:19:22 Requirements for new projects 00:21:10 Clarification about the meaning of being a scientific oriented project 00:23:11 Requirements about the team size and strong governance within projects 00:24:58 The application process 00:26:18 Duration of support 00:26:44 Timeframe to receive a response for an application 00:28:30 Feedback in the case of rejection 00:29:12 Are there downsides of becoming a part of NumFocus? 00:30:32 Additional administrative overhead? 00:32:01 Location of NumFocus staff members 00:33:00 Foudation of NumFocus and initial projects 00:34:05 Opening to projects outside of the Python ecosystem 00:34:54 Favourite project? 00:35:46 Initial role in NumFocus 00:36:53 Term duration for positions at the board of directors 00:37:24 Selection process for the board of directors 00:38:31 Leah's vision about FLOSS and its importance for the openness of science 00:39:04 Negative impacts of FLOSS 00:39:33 Most notable scientific discovery in recent years 00:39:59 Favourite text processing tool 00:40:37 A topic in science about which she changed her mind about 00:41:36 Anything else we forgot to ask about? 00:42:54 How to contact Leah Silen 00:43:14 Outro An interview with Leah Silen 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 Examples of supported projects 00:03:39 Status of sponsorded and affiliated projects 00:05:04 Advantages of one status over the other 00:05:48 Legal challenges for open source scientific projects 00:07:19 Financial support for scientific open source projects 00:10:13 Assistance to apply for external grants 00:11:01 Paying developers from outside of US? 00:11:43 Revenue sources for NumFocus 00:12:21 Levels of corporate sponshorships 00:13:14 The influence of corporate sponsors 00:13:56 Motivations of corporate sponsors 00:15:02 Some of the sponsors of the NumFocus organization 00:16:05 Technological support for projects 00:17:03 Events previously supported by the organization 00:18:09 The kind of support that can be provided for events 00:19:22 Requirements for new projects 00:21:10 Clarification about the meaning of being a scientific oriented project 00:23:11 Requirements about the team size and strong governance within projects 00:24:58 The application process 00:26:18 Duration of support 00:26:44 Timeframe to receive a response for an application 00:28:30 Feedback in the case of rejection 00:29:12 Are there downsides of becoming a part of NumFocus? 00:30:32 Additional administrative overhead? 00:32:01 Location of NumFocus staff members 00:33:00 Foudation of NumFocus and initial projects 00:34:05 Opening to projects outside of the Python ecosystem 00:34:54 Favourite project? 00:35:46 Initial role in NumFocus 00:36:53 Term duration for positions at the board of directors 00:37:24 Selection process for the board of directors 00:38:31 Leah's vision about FLOSS and its importance for the openness of science 00:39:04 Negative impacts of FLOSS 00:39:33 Most notable scientific discovery in recent years 00:39:59 Favourite text processing tool 00:40:37 A topic in science about which she changed her mind about 00:41:36 Anything else we forgot to ask about? 00:42:54 How to contact Leah Silen 00:43:14 Outro FLOSSforScience no 0:45:10 https://flossforscience.com/podcast/season3-epsiode-3 https://flossforscience.com/podcast/season3-epsiode-3#comments Wed, 08 Apr 2020 00:00:00 +0000 https://flossforscience.com/764b98ad5a87227ff22a529ec46b5b34be2014978bb5760ec1d935ddaf09e0ce 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 the interview with our classic quick questions and a reflection from Ralf about the need for more sustainability in open source software development as volunteer effort may not be sufficient in the future. 00:00:00 Intro 00:00:18 Introduction 00:00:33 Introducing Ralf Gommers 00:02:05 Research during his PhD and and PostDoc 00:03:20 When he started to use open source tools 00:03:52 Learning to code 00:04:39 PyWavelets, another sideproject he likes 00:05:55 His elevator pitch for NumPy 00:06:55 Vector arrays in Python before NumPy 00:07:49 How he got involved in the NumPy project 00:10:13 Traget users for NumPy 00:11:36 NumPy as part of the standard library? 00:13:24 Features provided by NumPy 00:14:22 Major differences between Python built-in list and NumPy's array 00:16:01 Structured data 00:16:45 Why appending a row to an array is made hard 00:18:09 Multithreaded code with NumPy 00:19:48 Distributed array processing 00:20:50 GPU computation with Python and NumPy 00:22:16 Linear algebra functions in NumPy 00:23:25 Overlap between SciPy and NumPy for linear algebra 00:23:55 Python speed as an interpreted language 00:25:43 Python with NumPy compared to Matlab 00:28:07 How easy is the transition between Matlab and Python Numpy 00:29:26 Performance difference between Matlab and Python 00:31:00 Commercial applications of NumPy 00:32:15 Contributions from the industry ans incentives to contribute 00:34:10 Elevator pitch for SciPy 00:35:37 Overview of some of the submodules in SciPy 00:38:11 The size of the communities 00:39:33 Participation in Google Summer of Code 00:40:24 Participation in Google Season of Docs 00:41:48 Communication channels in the project 00:43:25 Where to ask for support? 00:44:48 Possible contributions 00:46:25 Skills usefull to contribute to the NumPy project 00:48:12 Identifying possible contributions 00:48:52 The importance of FLOSS for science 00:52:02 Possible negative impact of FLOSS on science 00:52:49 Crediting contributions in science 00:53:42 Most notable scientific discovery in recent years 00:54:49 His favourite text processing tool 00:55:30 Volunteer effort may not be sufficient anymore 00:56:58 Contact informations for Ralf Gommers 00:57:27 Outro 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 the interview with our classic quick questions and a reflection from Ralf about the need for more sustainability in open source software development as volunteer effort may not be sufficient in the future. 00:00:00 Intro 00:00:18 Introduction 00:00:33 Introducing Ralf Gommers 00:02:05 Research during his PhD and and PostDoc 00:03:20 When he started to use open source tools 00:03:52 Learning to code 00:04:39 PyWavelets, another sideproject he likes 00:05:55 His elevator pitch for NumPy 00:06:55 Vector arrays in Python before NumPy 00:07:49 How he got involved in the NumPy project 00:10:13 Traget users for NumPy 00:11:36 NumPy as part of the standard library? 00:13:24 Features provided by NumPy 00:14:22 Major differences between Python built-in list and NumPy's array 00:16:01 Structured data 00:16:45 Why appending a row to an array is made hard 00:18:09 Multithreaded code with NumPy 00:19:48 Distributed array processing 00:20:50 GPU computation with Python and NumPy 00:22:16 Linear algebra functions in NumPy 00:23:25 Overlap between SciPy and NumPy for linear algebra 00:23:55 Python speed as an interpreted language 00:25:43 Python with NumPy compared to Matlab 00:28:07 How easy is the transition between Matlab and Python Numpy 00:29:26 Performance difference between Matlab and Python 00:31:00 Commercial applications of NumPy 00:32:15 Contributions from the industry ans incentives to contribute 00:34:10 Elevator pitch for SciPy 00:35:37 Overview of some of the submodules in SciPy 00:38:11 The size of the communities 00:39:33 Participation in Google Summer of Code 00:40:24 Participation in Google Season of Docs 00:41:48 Communication channels in the project 00:43:25 Where to ask for support? 00:44:48 Possible contributions 00:46:25 Skills usefull to contribute to the NumPy project 00:48:12 Identifying possible contributions 00:48:52 The importance of FLOSS for science 00:52:02 Possible negative impact of FLOSS on science 00:52:49 Crediting contributions in science 00:53:42 Most notable scientific discovery in recent years 00:54:49 His favourite text processing tool 00:55:30 Volunteer effort may not be sufficient anymore 00:56:58 Contact informations for Ralf Gommers 00:57:27 Outro An interview with Ralf Gommers 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 the interview with our classic quick questions and a reflection from Ralf about the need for more sustainability in open source software development as volunteer effort may not be sufficient in the future. 00:00:00 Intro 00:00:18 Introduction 00:00:33 Introducing Ralf Gommers 00:02:05 Research during his PhD and and PostDoc 00:03:20 When he started to use open source tools 00:03:52 Learning to code 00:04:39 PyWavelets, another sideproject he likes 00:05:55 His elevator pitch for NumPy 00:06:55 Vector arrays in Python before NumPy 00:07:49 How he got involved in the NumPy project 00:10:13 Traget users for NumPy 00:11:36 NumPy as part of the standard library? 00:13:24 Features provided by NumPy 00:14:22 Major differences between Python built-in list and NumPy's array 00:16:01 Structured data 00:16:45 Why appending a row to an array is made hard 00:18:09 Multithreaded code with NumPy 00:19:48 Distributed array processing 00:20:50 GPU computation with Python and NumPy 00:22:16 Linear algebra functions in NumPy 00:23:25 Overlap between SciPy and NumPy for linear algebra 00:23:55 Python speed as an interpreted language 00:25:43 Python with NumPy compared to Matlab 00:28:07 How easy is the transition between Matlab and Python Numpy 00:29:26 Performance difference between Matlab and Python 00:31:00 Commercial applications of NumPy 00:32:15 Contributions from the industry ans incentives to contribute 00:34:10 Elevator pitch for SciPy 00:35:37 Overview of some of the submodules in SciPy 00:38:11 The size of the communities 00:39:33 Participation in Google Summer of Code 00:40:24 Participation in Google Season of Docs 00:41:48 Communication channels in the project 00:43:25 Where to ask for support? 00:44:48 Possible contributions 00:46:25 Skills usefull to contribute to the NumPy project 00:48:12 Identifying possible contributions 00:48:52 The importance of FLOSS for science 00:52:02 Possible negative impact of FLOSS on science 00:52:49 Crediting contributions in science 00:53:42 Most notable scientific discovery in recent years 00:54:49 His favourite text processing tool 00:55:30 Volunteer effort may not be sufficient anymore 00:56:58 Contact informations for Ralf Gommers 00:57:27 Outro FLOSSforScience no 0:59:05 https://flossforscience.com/podcast/season3-epsiode-2 https://flossforscience.com/podcast/season3-epsiode-2#comments Wed, 04 Mar 2020 00:00:00 +0000 https://flossforscience.com/0ec9f46c45094e6fbdb8790721d9c09d4f811bda7f31e972e3d8eb6761168435 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 bring that is lacking in basic Python 00:06:53 Preparing data for machine learning algorithms 00:08:12 The performance of pandas 00:09:21 Data formats supported by pandas 00:11:03 Data structures provided by pandas 00:11:42 Data analysis tools provided by pandas 00:12:32 Using pandas data structures with scikit-learn 00:12:55 Plotting data from pandas 00:13:39 Transition to Python version 2 00:14:51 Commercial usage of pandas 00:15:16 Companies contributing back to pandas 00:16:02 Exposition of students to pandas 00:16:42 Tutorials to start with pandas 00:18:26 Python libraries dependencies of pandas 00:18:55 Main communication channels 00:19:44 Her experience contributing to pandas 00:21:14 Skills to contribute to the project 00:21:49 List of good first issues 00:22:21 Tasks for non-programmers 00:23:12 FLOSS and the industry 00:24:16 The most notable scientific discovery in recent years 00:24:33 Her favourite text processing tool 00:25:06 Anything else? 00:25:38 How to contact Bhavani 00:25:57 Outro 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 bring that is lacking in basic Python 00:06:53 Preparing data for machine learning algorithms 00:08:12 The performance of pandas 00:09:21 Data formats supported by pandas 00:11:03 Data structures provided by pandas 00:11:42 Data analysis tools provided by pandas 00:12:32 Using pandas data structures with scikit-learn 00:12:55 Plotting data from pandas 00:13:39 Transition to Python version 2 00:14:51 Commercial usage of pandas 00:15:16 Companies contributing back to pandas 00:16:02 Exposition of students to pandas 00:16:42 Tutorials to start with pandas 00:18:26 Python libraries dependencies of pandas 00:18:55 Main communication channels 00:19:44 Her experience contributing to pandas 00:21:14 Skills to contribute to the project 00:21:49 List of good first issues 00:22:21 Tasks for non-programmers 00:23:12 FLOSS and the industry 00:24:16 The most notable scientific discovery in recent years 00:24:33 Her favourite text processing tool 00:25:06 Anything else? 00:25:38 How to contact Bhavani 00:25:57 Outro An interview with Bhavani Ravi 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 bring that is lacking in basic Python 00:06:53 Preparing data for machine learning algorithms 00:08:12 The performance of pandas 00:09:21 Data formats supported by pandas 00:11:03 Data structures provided by pandas 00:11:42 Data analysis tools provided by pandas 00:12:32 Using pandas data structures with scikit-learn 00:12:55 Plotting data from pandas 00:13:39 Transition to Python version 2 00:14:51 Commercial usage of pandas 00:15:16 Companies contributing back to pandas 00:16:02 Exposition of students to pandas 00:16:42 Tutorials to start with pandas 00:18:26 Python libraries dependencies of pandas 00:18:55 Main communication channels 00:19:44 Her experience contributing to pandas 00:21:14 Skills to contribute to the project 00:21:49 List of good first issues 00:22:21 Tasks for non-programmers 00:23:12 FLOSS and the industry 00:24:16 The most notable scientific discovery in recent years 00:24:33 Her favourite text processing tool 00:25:06 Anything else? 00:25:38 How to contact Bhavani 00:25:57 Outro FLOSSforScience no 0:27:35 https://flossforscience.com/podcast/season3-episode1 https://flossforscience.com/podcast/season3-episode1#comments Wed, 05 Feb 2020 00:00:00 +0000 https://flossforscience.com/ba5dcb1ae0dc58325333e763d037dd08dbb1110dfa771e43c12574a674561b7a 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 Kremitzki 00:02:16 How he got involved with FreeCAD 00:03:22 His previous CAD experience before working on FreeCAD 00:04:35 One minute elevator pitch for FreeCAD 00:05:50 Current general development status of FreeCAD 00:07:12 BIM with FreeCAD 00:09:24 What are workbenches in FreeCAD? 00:10:46 Core FreeCAD workbenches 00:11:40 Technical drawing with FreeCAD 00:13:44 FEM libraries integrated within FreeCAD 00:16:15 Multiphysics simulations 00:18:16 Model updates recalculations 00:19:04 Technical drawings and annotations 00:19:49 FreeCAD for 2D CAD drawing vs other FLOSS alternatives 00:21:08 Compatibility with commercial CAD systems and standard exchange file formats 00:23:41 Performance of STEP files conversion 00:24:54 FreeCAD's native file format 00:25:44 Version control with FreeCAD 00:27:01 File formats that are supported by FreeCAD 00:29:16 Integration of Python in FreeCAD 00:30:56 Assemblies with FreeCAD 00:33:29 Stable topological naming 00:35:10 Manual approach for static assemblies 00:36:30 When to expect a stable assembly workbench 00:37:20 How to test assemblies right now 00:38:33 FreeCAD's software license 00:39:16 Companies using FreeCAD 00:39:42 Universities using FreeCAD 00:40:16 FreeCAD's use in science and citations of FreeCAD 00:42:29 How many people are involved in the project 00:43:04 Main communication channels 00:43:54 How to contribute to FreeCAD 00:45:45 Kurt's vision of FLOSS and its importance for the openness of science 00:47:13 Most notable scientific discovery in recent years 00:47:47 Favourite text processing tool 00:48:11 A topic he changed his mind about in science 00:48:28 FreeCAD at FOSDEM 2020 00:49:33 How to contact Kurt 00:49:54 Outro 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 Kremitzki 00:02:16 How he got involved with FreeCAD 00:03:22 His previous CAD experience before working on FreeCAD 00:04:35 One minute elevator pitch for FreeCAD 00:05:50 Current general development status of FreeCAD 00:07:12 BIM with FreeCAD 00:09:24 What are workbenches in FreeCAD? 00:10:46 Core FreeCAD workbenches 00:11:40 Technical drawing with FreeCAD 00:13:44 FEM libraries integrated within FreeCAD 00:16:15 Multiphysics simulations 00:18:16 Model updates recalculations 00:19:04 Technical drawings and annotations 00:19:49 FreeCAD for 2D CAD drawing vs other FLOSS alternatives 00:21:08 Compatibility with commercial CAD systems and standard exchange file formats 00:23:41 Performance of STEP files conversion 00:24:54 FreeCAD's native file format 00:25:44 Version control with FreeCAD 00:27:01 File formats that are supported by FreeCAD 00:29:16 Integration of Python in FreeCAD 00:30:56 Assemblies with FreeCAD 00:33:29 Stable topological naming 00:35:10 Manual approach for static assemblies 00:36:30 When to expect a stable assembly workbench 00:37:20 How to test assemblies right now 00:38:33 FreeCAD's software license 00:39:16 Companies using FreeCAD 00:39:42 Universities using FreeCAD 00:40:16 FreeCAD's use in science and citations of FreeCAD 00:42:29 How many people are involved in the project 00:43:04 Main communication channels 00:43:54 How to contribute to FreeCAD 00:45:45 Kurt's vision of FLOSS and its importance for the openness of science 00:47:13 Most notable scientific discovery in recent years 00:47:47 Favourite text processing tool 00:48:11 A topic he changed his mind about in science 00:48:28 FreeCAD at FOSDEM 2020 00:49:33 How to contact Kurt 00:49:54 Outro An interview with Kurt Kremitzki 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 Kremitzki 00:02:16 How he got involved with FreeCAD 00:03:22 His previous CAD experience before working on FreeCAD 00:04:35 One minute elevator pitch for FreeCAD 00:05:50 Current general development status of FreeCAD 00:07:12 BIM with FreeCAD 00:09:24 What are workbenches in FreeCAD? 00:10:46 Core FreeCAD workbenches 00:11:40 Technical drawing with FreeCAD 00:13:44 FEM libraries integrated within FreeCAD 00:16:15 Multiphysics simulations 00:18:16 Model updates recalculations 00:19:04 Technical drawings and annotations 00:19:49 FreeCAD for 2D CAD drawing vs other FLOSS alternatives 00:21:08 Compatibility with commercial CAD systems and standard exchange file formats 00:23:41 Performance of STEP files conversion 00:24:54 FreeCAD's native file format 00:25:44 Version control with FreeCAD 00:27:01 File formats that are supported by FreeCAD 00:29:16 Integration of Python in FreeCAD 00:30:56 Assemblies with FreeCAD 00:33:29 Stable topological naming 00:35:10 Manual approach for static assemblies 00:36:30 When to expect a stable assembly workbench 00:37:20 How to test assemblies right now 00:38:33 FreeCAD's software license 00:39:16 Companies using FreeCAD 00:39:42 Universities using FreeCAD 00:40:16 FreeCAD's use in science and citations of FreeCAD 00:42:29 How many people are involved in the project 00:43:04 Main communication channels 00:43:54 How to contribute to FreeCAD 00:45:45 Kurt's vision of FLOSS and its importance for the openness of science 00:47:13 Most notable scientific discovery in recent years 00:47:47 Favourite text processing tool 00:48:11 A topic he changed his mind about in science 00:48:28 FreeCAD at FOSDEM 2020 00:49:33 How to contact Kurt 00:49:54 Outro FLOSSforScience no 0:51:30 https://flossforscience.com/podcast/season2-episode12 https://flossforscience.com/podcast/season2-episode12#comments Wed, 04 Dec 2019 00:00:00 +0000 https://flossforscience.com/e7ab7db1efcdd526fb7990a0111aa5e98a65326065543eec1abece9ad6e2a127 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 University of Southampton 00:01:53 His transition from developping high power compact lasers to RSE 00:03:31 About his PhD and general comments about PhD defenses 00:04:21 Any relations between laser and his current research area? 00:07:57 1 minute elevator pitch for UK RSE 00:08:32 The growing importance of software and the effect on funding 00:14:03 Defining what is a RSE 00:17:35 How many RSE in UK? 00:18:20 The state of preparation of the research community for brexit 00:20:05 When was the RSE association founded? 00:20:16 How to become a member of RSE UK and the growth rate of the association 00:22:44 Other RSE branches 00:24:42 Relations between RSE associations 00:25:40 Regional RSE organizations and RSE groups 00:27:09 Local meetups groups 00:28:00 Crediting research software development 00:31:39 Is FLOSS the norm or the exception for RSE? 00:35:09 Does FLOSS helps providing better and more sustainable research software? 00:38:55 Curriculum for new researchers 00:43:50 The state of research software licensing 00:46:13 Most notable recent scientific discovery 00:48:13 His favourite text processing tool 00:48:58 A topic in science he changed his mind about 00:50:13 How to contact Simon 00:50:37 Conclusion 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 University of Southampton 00:01:53 His transition from developping high power compact lasers to RSE 00:03:31 About his PhD and general comments about PhD defenses 00:04:21 Any relations between laser and his current research area? 00:07:57 1 minute elevator pitch for UK RSE 00:08:32 The growing importance of software and the effect on funding 00:14:03 Defining what is a RSE 00:17:35 How many RSE in UK? 00:18:20 The state of preparation of the research community for brexit 00:20:05 When was the RSE association founded? 00:20:16 How to become a member of RSE UK and the growth rate of the association 00:22:44 Other RSE branches 00:24:42 Relations between RSE associations 00:25:40 Regional RSE organizations and RSE groups 00:27:09 Local meetups groups 00:28:00 Crediting research software development 00:31:39 Is FLOSS the norm or the exception for RSE? 00:35:09 Does FLOSS helps providing better and more sustainable research software? 00:38:55 Curriculum for new researchers 00:43:50 The state of research software licensing 00:46:13 Most notable recent scientific discovery 00:48:13 His favourite text processing tool 00:48:58 A topic in science he changed his mind about 00:50:13 How to contact Simon 00:50:37 Conclusion An interview with Simon Hettrick 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 University of Southampton 00:01:53 His transition from developping high power compact lasers to RSE 00:03:31 About his PhD and general comments about PhD defenses 00:04:21 Any relations between laser and his current research area? 00:07:57 1 minute elevator pitch for UK RSE 00:08:32 The growing importance of software and the effect on funding 00:14:03 Defining what is a RSE 00:17:35 How many RSE in UK? 00:18:20 The state of preparation of the research community for brexit 00:20:05 When was the RSE association founded? 00:20:16 How to become a member of RSE UK and the growth rate of the association 00:22:44 Other RSE branches 00:24:42 Relations between RSE associations 00:25:40 Regional RSE organizations and RSE groups 00:27:09 Local meetups groups 00:28:00 Crediting research software development 00:31:39 Is FLOSS the norm or the exception for RSE? 00:35:09 Does FLOSS helps providing better and more sustainable research software? 00:38:55 Curriculum for new researchers 00:43:50 The state of research software licensing 00:46:13 Most notable recent scientific discovery 00:48:13 His favourite text processing tool 00:48:58 A topic in science he changed his mind about 00:50:13 How to contact Simon 00:50:37 Conclusion FLOSSforScience no 0:52:23 https://flossforscience.com/podcast/season-2-episode-11 https://flossforscience.com/podcast/season-2-episode-11#comments Wed, 06 Nov 2019 00:00:00 +0000 https://flossforscience.com/360ea6b0f9d02eac28efc3dda39ca8e3e1989a13ce6a87b800dbf18c95804750 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 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 An interview with Dan Quintana 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 FLOSSforScience no 0:55:36 https://flossforscience.com/podcast/season-2-episode-10 https://flossforscience.com/podcast/season-2-episode-10#comments Wed, 02 Oct 2019 00:00:00 +0000 https://flossforscience.com/d9a2381cd853681b557680e252f614d313359ed608e1cc0666ac1993e4100eb7 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 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 An interview with Robert Dodier 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 FLOSSforScience no 0:45:36 https://flossforscience.com/podcast/season-2-episode-9 https://flossforscience.com/podcast/season-2-episode-9#comments Wed, 04 Sep 2019 00:00:00 +0000 https://flossforscience.com/562305a86bc282406a0704ab991e53b1af6b90c6e5f5a2cd9ceb930f3b8b9cf7 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 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 An interview with Juan Pablo Carbajal 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 FLOSSforScience no 0:46:30 https://flossforscience.com/podcast/season-2-episode-8 https://flossforscience.com/podcast/season-2-episode-8#comments Tue, 06 Aug 2019 00:00:00 +0000 https://flossforscience.com/44b4ccf05c579e320fed5dac97246b460e251c4d0e6cf9463cb71e9bf12d5ed1 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 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. An interview with Arfon Smith from the Journal of Open Source 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. FLOSSforScience no 1:03:24 https://flossforscience.com/podcast/season-2-episode-7 https://flossforscience.com/podcast/season-2-episode-7#comments Wed, 03 Jul 2019 00:00:00 +0000 https://flossforscience.com/aa203abbcc36bd89b3e4908275f7f084028896902fcf03701ef679cb5f588de4 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 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. An interview with Glenn Cooper 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. FLOSSforScience no 0:45:22 https://flossforscience.com/podcast/season-2-episode-6 https://flossforscience.com/podcast/season-2-episode-6#comments Wed, 05 Jun 2019 00:00:00 +0000 https://flossforscience.com/b4ee57b99dc01ea39d4e7c32612f006e1d06dffb2589e9cf3409a3777ee9fbc5 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 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. An interview with Jesse Allision 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. FLOSSforScience no 0:55:19 https://flossforscience.com/podcast/season-2-episode-5 https://flossforscience.com/podcast/season-2-episode-5#comments Wed, 01 May 2019 00:00:00 +0000 https://flossforscience.com/89dba3fae680c37778034e534345450dd5ca4d7dc66c160b39daf9be220e83eb 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 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 An interview with Adrian Serio 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 FLOSSforScience no 0:46:36 https://flossforscience.com/podcast/season-2-episode-4 https://flossforscience.com/podcast/season-2-episode-4#comments Wed, 03 Apr 2019 00:00:00 +0000 https://flossforscience.com/9b7e6d0550a68779213724570a715b1dbe6a47bad9a63808781966ca6137759a 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 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. An interview with Karl W. Schulz 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. FLOSSforScience no 0:52:57 https://flossforscience.com/podcast/season-2-episode-3 https://flossforscience.com/podcast/season-2-episode-3#comments Tue, 05 Mar 2019 00:00:00 +0000 https://flossforscience.com/0475c22464c90bab2682162fe7f509e0a21192bcb1a9136963abb6a2c6e9c504 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. 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. An interview with Ben Marwick 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. FLOSSforScience no 1:13:52 https://flossforscience.com/podcast/season-2-episode-2 https://flossforscience.com/podcast/season-2-episode-2#comments Wed, 06 Feb 2019 00:00:00 +0000 https://flossforscience.com/1a3b3cee9c13042e83d7c6904cc0887dae9591592fd682ecfd5027bdeb013bad 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. 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. An interview with Pat David 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. FLOSSforScience no 0:47:23 https://flossforscience.com/podcast/season-2-episode-1 https://flossforscience.com/podcast/season-2-episode-1#comments Tue, 08 Jan 2019 00:00:00 +0000 https://flossforscience.com/a659707a4660d8494594a2d6b14cabcb53898675f63d18a045fc7697adad7a9a 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. 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. An interview with Martin Owens 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. FLOSSforScience no 0:37:36 https://flossforscience.com/podcast/season-1-episode-12 https://flossforscience.com/podcast/season-1-episode-12#comments Wed, 05 Dec 2018 00:00:00 +0000 https://flossforscience.com/ce47ff96ab236efd28512a8108da88013b31e7eb3da21e99c9130f9aefa34dec 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. 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. An interview with Kenneth Hoste 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. FLOSSforScience no 55:47 https://flossforscience.com/podcast/season-1-episode-11 https://flossforscience.com/podcast/season-1-episode-11#comments Wed, 07 Nov 2018 00:00:00 +0000 https://flossforscience.com/b4d848cbd2b630d43c49f65609d398666496b6a10d7c1452a9984ace00430dbc In Episode 11, we interviewed Sébastien Le Digabel about NOMAD a blackbox optimization software. A blackbox is a system which can be viewed in terms of its inputs and outputs, without any knowledge of its internal workings. NOMAD is a software for the optimization of such problems. It implements the Mesh Adaptive Direct Search (MADS) derivative-free optimization algorithm. NOMAD is free and intended to be easy to use. It is designed for solve real-world optimization problems from the industry. It works out of the box, as long as the objective and constraints are provided. In Episode 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. An interview with Sébastien Le Digabel 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. FLOSSforScience no 28:18 https://flossforscience.com/podcast/season-1-episode-10 https://flossforscience.com/podcast/season-1-episode-10#comments Wed, 03 Oct 2018 00:00:00 +0000 https://flossforscience.com/7a584f41a937a85608bf9074868c91bfc85772ae25a495cadfa4ece7ace66615 In Episode 10, we interviewed Sébastien Loriot about CGAL. A software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics. The library offers data structures and algorithms like triangulations, Voronoi diagrams, Boolean operations on polygons and polyhedra, point set processing, arrangements of curves, surface and volume mesh generation, geometry processing, alpha shapes, convex hull algorithms, shape analysis, AABB and KD trees... In Episode 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... An interview with Sébastien Loriot from the CGAL project 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... FLOSSforScience no 40:35 https://flossforscience.com/podcast/season-1-episode-09 https://flossforscience.com/podcast/season-1-episode-09#comments Wed, 05 Sep 2018 00:00:00 +0000 https://flossforscience.com/dfb620a9bb37b9f6465e567effb11458bdc533cf6232ca41be6f04f2fd709a68 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. 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. An interview with Christophe Geuzaine 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. FLOSSforScience no 56:45 https://flossforscience.com/podcast/season-1-episode-8 https://flossforscience.com/podcast/season-1-episode-8#comments Wed, 01 Aug 2018 00:00:00 +0000 https://flossforscience.com/94ea28ec123c51807c4f1eec37ae3ea7adf458957654671f57e08cdb15fa190a For episode 8, we interviewed Bruno Blais about his utilization of open source software in his research about solid-liquid mixing. We started our conversation by talking about the different kinds of software packages he uses in his simulation workflow. We then asked him why and when he has decided to use FLOSS tools in is research. Following that, we talked about his philosophical and practical reasons to use FLOSS. He then shared with us how he contributes to the software he is using in his daily research. Finally, we talked with him about the significance of FLOSS for the openness of science and how it affects the society as a whole. This episode is the first of series about computer simulations. Follow us to be informed when we will release our next episode about the open source meshing tool GMSH. For episode 8, we interviewed Bruno Blais about his utilization of open source software in his research about solid-liquid mixing. We started our conversation by talking about the different kinds of software packages he uses in his simulation workflow. We then asked him why and when he has decided to use FLOSS tools in is research. Following that, we talked about his philosophical and practical reasons to use FLOSS. He then shared with us how he contributes to the software he is using in his daily research. Finally, we talked with him about the significance of FLOSS for the openness of science and how it affects the society as a whole. This episode is the first of series about computer simulations. Follow us to be informed when we will release our next episode about the open source meshing tool GMSH. An interview with Bruno Blais For episode 8, we interviewed Bruno Blais about his utilization of open source software in his research about solid-liquid mixing. We started our conversation by talking about the different kinds of software packages he uses in his simulation workflow. We then asked him why and when he has decided to use FLOSS tools in is research. Following that, we talked about his philosophical and practical reasons to use FLOSS. He then shared with us how he contributes to the software he is using in his daily research. Finally, we talked with him about the significance of FLOSS for the openness of science and how it affects the society as a whole. This episode is the first of series about computer simulations. Follow us to be informed when we will release our next episode about the open source meshing tool GMSH. FLOSSforScience no 0:37:51 https://flossforscience.com/podcast/season-1-episode-7 https://flossforscience.com/podcast/season-1-episode-7#comments Wed, 04 Jul 2018 00:00:00 +0000 https://flossforscience.com/1ed15f75ba274b68beb6860ce566521590c2a2c0861f614574c37b7b9ccca513 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. 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. An interview with Karl Fogel and James Vasile 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. FLOSSforScience no 1:01:24 https://flossforscience.com/podcast/season-1-episode-6 https://flossforscience.com/podcast/season-1-episode-6#comments Wed, 06 Jun 2018 00:00:00 +0000 https://flossforscience.com/a45d9910f8db37ff0a74eccc23a8c7e61600e39cada36a1dab6387e198cad3f4 In Episode 6, we interviewed Christian Horea about the [NeuroGentoo Overlay](https://github.com/TheChymera/neurogentoo) for Gentoo Linux which includes specific packages for Neuroscience. With this distribution many of the challenges in neuroscience software management; including: system replicability, system documentation, data analysis reproducibility, fine-grained dependency management, easy control over compilation options, and seamless access to cutting-edge software releases, are addressed. Fore more details we refer to his publication: [Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software](https://riojournal.com/article/12095/). About Christian Horea: Christian Horea is a Doctoral Researcher at the ETH Zurich, where he studies the ability of psychotropic drugs to modulate brain function in healthy animals. He has previously engaged in research at the University of Heidelberg, University of Oxford, Max Planck Institute for Medical Research, University of Oldenburg, and the Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences. His work has spanned the gamut of neuroscience from electrophysiology and molecular biology all the way to experimental psychology — and includes an extensive excursion into the world of Linux, Python, and software management. He has written many Free and Open Source Software packages for data analysis, metadata and lab book management, reproducible self-publishing, and data repositing. We join him on part of this exciting journey, to learn about an initiative he started — NeuroGentoo — and how he sees Free and Open Source Software, freedom in choosing and picking such software, and transparency in the choices having been made, as instrumental to the neuroscience of the present and future, and how Gentoo Linux (perhaps uniquely) makes tackling these challenges possible. In Episode 6, we interviewed Christian Horea about the [NeuroGentoo Overlay](https://github.com/TheChymera/neurogentoo) for Gentoo Linux which includes specific packages for Neuroscience. With this distribution many of the challenges in neuroscience software management; including: system replicability, system documentation, data analysis reproducibility, fine-grained dependency management, easy control over compilation options, and seamless access to cutting-edge software releases, are addressed. Fore more details we refer to his publication: [Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software](https://riojournal.com/article/12095/). About Christian Horea: Christian Horea is a Doctoral Researcher at the ETH Zurich, where he studies the ability of psychotropic drugs to modulate brain function in healthy animals. He has previously engaged in research at the University of Heidelberg, University of Oxford, Max Planck Institute for Medical Research, University of Oldenburg, and the Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences. His work has spanned the gamut of neuroscience from electrophysiology and molecular biology all the way to experimental psychology — and includes an extensive excursion into the world of Linux, Python, and software management. He has written many Free and Open Source Software packages for data analysis, metadata and lab book management, reproducible self-publishing, and data repositing. We join him on part of this exciting journey, to learn about an initiative he started — NeuroGentoo — and how he sees Free and Open Source Software, freedom in choosing and picking such software, and transparency in the choices having been made, as instrumental to the neuroscience of the present and future, and how Gentoo Linux (perhaps uniquely) makes tackling these challenges possible. An interview with Christian Horea In Episode 6, we interviewed Christian Horea about the [NeuroGentoo Overlay](https://github.com/TheChymera/neurogentoo) for Gentoo Linux which includes specific packages for Neuroscience. With this distribution many of the challenges in neuroscience software management; including: system replicability, system documentation, data analysis reproducibility, fine-grained dependency management, easy control over compilation options, and seamless access to cutting-edge software releases, are addressed. Fore more details we refer to his publication: [Gentoo Linux for Neuroscience - a replicable, flexible, scalable, rolling-release environment that provides direct access to development software](https://riojournal.com/article/12095/). About Christian Horea: Christian Horea is a Doctoral Researcher at the ETH Zurich, where he studies the ability of psychotropic drugs to modulate brain function in healthy animals. He has previously engaged in research at the University of Heidelberg, University of Oxford, Max Planck Institute for Medical Research, University of Oldenburg, and the Sechenov Institute of Evolutionary Physiology and Biochemistry of the Russian Academy of Sciences. His work has spanned the gamut of neuroscience from electrophysiology and molecular biology all the way to experimental psychology — and includes an extensive excursion into the world of Linux, Python, and software management. He has written many Free and Open Source Software packages for data analysis, metadata and lab book management, reproducible self-publishing, and data repositing. We join him on part of this exciting journey, to learn about an initiative he started — NeuroGentoo — and how he sees Free and Open Source Software, freedom in choosing and picking such software, and transparency in the choices having been made, as instrumental to the neuroscience of the present and future, and how Gentoo Linux (perhaps uniquely) makes tackling these challenges possible. FLOSSforScience no 58:27 https://flossforscience.com/podcast/season-1-episode-5 https://flossforscience.com/podcast/season-1-episode-5#comments Wed, 02 May 2018 00:00:00 +0000 https://flossforscience.com/f8ecf0a788a3c7e9402656d74ffcd0eaa44f0d36d93294dc056a57353ae8e712 In Episode 5, we interview Katarina Behrens, a consultant and software developers of LibreOffice, LibreOffice extensions and related libraries working at CIB Group of Companies. We discuss her involvement with The Document Foundation, the capabilities of the LibreOffice suite and why an open source office suite is relevant for scientists. In Episode 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. An interview with Katarina Behrens 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. FLOSSforScience no 39:56 https://flossforscience.com/podcast/season-1-episode-4 https://flossforscience.com/podcast/season-1-episode-4#comments Tue, 03 Apr 2018 00:00:00 +0000 https://flossforscience.com/a6e6624d95f6c9d7ca3f8687f467bb703e4e92ec6c0414dc6fb849850f302292 In Episode 4, we interview Carl Boettinger, Assistant Professor in the Department of Environmental Science, Policy and Management at UC Berkeley. He introduces us to his work on ecological forecasting and decision making under uncertainty, with applications for global change, conservation and natural resource management. He presents to us the Rocker project and how it helps scientists produce reproducible science. Finally, we discuss with him about his view regarding FLOSS in science. In Episode 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. An interview with Carl Boettinger In Episode 4, we interview Carl Boettinger, Assistant Professor in the Department of Environmental Science, Policy and Management at UC Berkeley. He introduces us to his work on ecological forecasting and decision making under uncertainty, with applications for global change, conservation and natural resource management. He presents to us the Rocker project and how it helps scientists produce reproducible science. Finally, we discuss with him about his view regarding FLOSS in science. FLOSSforScience no 39:46 https://flossforscience.com/podcast/season-1-episode-3 https://flossforscience.com/podcast/season-1-episode-3#comments Wed, 07 Mar 2018 00:00:00 +0000 https://flossforscience.com/484fa7cf99b4c64e8f169743dca41b59cf621def In Episode 3, we interview Oliver Kopp and Jörg Lenhard about the reference management tool Jabref. In Episode 3, we interview Oliver Kopp and Jörg Lenhard about the reference management tool Jabref. An interview with Oliver Kopp and Jörg Lenhard In Episode 3, we interview Oliver Kopp and Jörg Lenhard about the reference management tool Jabref. FLOSSforScience no 39:56 https://flossforscience.com/podcast/season-1-episode-2 https://flossforscience.com/podcast/season-1-episode-2#comments Wed, 07 Feb 2018 01:00:00 +0000 https://flossforscience.com/204efffe623ab7cc39e821a46fc39a6062ff44cd8413d4d8a4ef730e275dbb5b In Episode 2, we interview Laurent Cormier, a research associate at the Ecole de Technologie Superieure in Montreal. He introduces us to his past research regarding the evaluation of the fatigue life of composite materials and the predictive model he developed with Python. He also share with us his scientific perspective on FLOSS and tools he uses in his research workflow. In Episode 2, we interview Laurent Cormier, a research associate at the Ecole de Technologie Superieure in Montreal. He introduces us to his past research regarding the evaluation of the fatigue life of composite materials and the predictive model he developed with Python. He also share with us his scientific perspective on FLOSS and tools he uses in his research workflow. An interview with Laurent Cormier In Episode 2, we interview Laurent Cormier, a research associate at the Ecole de Technologie Superieure in Montreal. He introduces us to his past research regarding the evaluation of the fatigue life of composite materials and the predictive model he developed with Python. He also share with us his scientific perspective on FLOSS and tools he uses in his research workflow. FLOSSforScience no 10:48 https://flossforscience.com/podcast/season-1-episode-1 https://flossforscience.com/podcast/season-1-episode-1#comments Fri, 12 Jan 2018 13:59:59 +0000 https://flossforscience.com/454393ac623ec4173b3a93c0bb2d943b2f81074979185bf8c4350cd9812c2677 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. 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. Content and aims of the podcast. 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. FLOSSforScience no 10:48