Code for Thought

In this ByteSized RSE episode we talk about GIT and some of the great features it comes with. I also wanted to find out where GIT comes from, and what's with its name. My interview partner is Raniere Silva who works at Gesis, which is part of the Leibniz Institute in Germany. Git comes with loads of features: in this episode we focus on how to deal with and avoid merge conflicts, branching pa...

Meet Graham Lee, who has decided to investigate research software engineering  for his PhD thesis. I met Graham at the RSE conference in Newcastle, UK late 2022 where he presented his work in form of an "inverted" talk (i.e. driven by the audience).  Since there are not many people who make RSEs a subject of study and a PhD thesis, I caught up with Graham after the conference. In our con...

In dieser Folge ist Musik in der Tat Trumpf. 2021 haben sich das DLR und Martin Hennecke zusammengeschlossen um ein aufregendes Projekt auf die Bühne zu bringen. Das Gedicht 'The Sphinx' untermalt von Charles Ives' 'The Unanswered Question'.  Dabei war die Aufgabe, Reaktionen des Publikums mittels Biosensoren und künstlicher Intelligenz aufzunehmen und damit die live gespi...

Getting funding for software engineering in research is an ongoing challenge. The Research Software Alliance together with the eScience Centre in the Netherlands organised a 2 day workshop in Amsterdam 8-9 Nov 2022 to see how we can get on top of it. I invited the director of ReSA, Michelle Barker and Joris van Eijnatten, director of the eScience centre to talk about the workshop and the declarati...

The 6th instalment of ByteSized is about IDEs. They are mostly taken for granted these days. Hence, it might be easy to forget how much effort and time they saved when they were introduced.  After a brief history and talking about some popular IDEs, I'll be talking to Joaquin Dominguez from the US about how he uses IDEs, which ones and why. He also pointed out a relatively new one called zed...

There are a lot of excellent training programmes for researchers and RSEs, like the Code Refineries and various Carpentries. But with demand of experienced engineers growing rapidly, we have a gap in training enough RSEs. In this episode I meet with Jeremy Cohen, Radovan Bast, Weronika Filinger and Malvika Sharan to discuss training and what we can do to fill the gap.  There are a lot of training...

Hallo und herzlich willkommen zur ersten deutschsprachigen Folge von Code for Thought. Und wir beginnen diese Serie mit einem Bericht über die diesjährige Konferenz des deutschen RSE Vereins in Paderborn zwischen dem 20. und 22. Februar 2023. Circa 150 TeilnehmerInnen haben sich im Heinz Nixdorf Zentrum eingefunden, nach einer fast vierjährigen Pause.  In dieser Folge möchte ich Euch einen Einblic...

The German RSE association met for its annual conference in the north-western city of Paderborn between 20 - 22 February 2023. Ca 150 participants attended including yours truly. It was the first such conference for the German RSE community since 2019. In this episode I'd like to share some impressions and discussions I had with you. It is also the launch for a German language version of this...

Linting and static code analysis in general are important tools in software engineering. Making sure the code builds and works is all very well. But a consistent coding style minimises maintenance efforts and future development. In this episode I'll introduce several tools that can make your code analysis easier:  pylint https://www.pylint.org   flake8 https://flake8.pycqa.org/en/latest/index...

In 2021, the Society for Research Software Engineering in the UK launched its first mentoring pilot scheme. 20 mentor/mentee pairs registered for it. I spoke with the organisers of the scheme, Ania Brown and Sam Mangham to give us an overview of how this project came about. For the second part of this episode, I met with Mark Turner (Newcastle University, UK) and James Graham (King's College,...

FOSDEM, the Free and Open Source Developers' European Meeting is back as an in person event at the Université Libre in the Belgium capital, Brussels.  This is the first time I attended this conference and, indeed, the first time for reporting from a conference for this podcast.  It's impossible to cover all of the 788 events at FOSDEM, but I wanted to share my impressions with you. You c...

Open Access is one of the pillars of Open Science. In this episode I am talking to Jean-Claude Guedon from the University of Montreal (Canada). Jean-Claude is one of the authors of the declaration of the Budapest Open Access Initiative from 2002. He is also an expert on scientific communication and its history.  Who better to take us through the road that led to the Open Access declaration, what h...

In this 4th episode of our ByteSized RSE mini series, we'll talk about Continuous Integration and Deployment. Both of each play an essential part in today's software development practices and can help you in your engineering tasks. There are a number of tools available for this to get you started, and they are listed below. In addition to that, check out Martin Fowler's block post a...

For this episode I met with Nicolas Thiery from Uni Paris-Saclay in summer 2022. Nicolas is an open source activist and has been leading the Candyce project in France to promote the use of Jupyter in the classroom.  Nicolas highlights the advantages of using open source tools like Jupyter and how the pandemic accelerated their use. And that we need education software engineers as well as research...

This last episode of ByteSized RSE before the end of 2022 is about testing your Python code. Testing is an essential part of software development, and a lot of what we cover in this episode applies to any programming and scripting language.  For Python, the two big frameworks being used are unittest and PyTest. Unittest is built into Python, whereas PyTest is a module you would need to install ext...

As time moves quickly towards the end of 2022, let's talk about ageing. While in Paris in spring 2022 I had the pleasure to meet with Michael Rera, who is a biology researcher at one of the CNRS (the French national center for scientific research) institute right in the centre of Le Marais.  Michael has been studying ageing in fruit flies (and other organisms) and has been using the SMURF ass...

In this episode, the second on the theme of nuclear fusion, I meet with Simon Pinches. Simon works at ITER at the test reactor site in Cadarache, near Aix-en-Provence in Southern France. As section leader of the modelling and simulation team, he is responsible for crucial parts of the software. Contributions to the code (e.g. IMAS) are made from a wide range of different sources and we talk about...

As part of the Software Sustainability Institute's Research Software Camp on supporting mental health , SSI Research Associate and accredited mindfulness teacher Anita Banerji delivers this short breathing space mindfulness exercise. Get in touch Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto: peter@code4thought....

As part of the Software Sustainability Institute's Research Software Camp on supporting mental health , SSI Research Associate and accredited mindfulness teacher Anita Banerji delivers this 10 minute meditation. Get in touch Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto: peter@code4thought.org UK RSE Slack (ukrs...

As part of the Software Sustainability Institute's Research Software Camp on supporting mental health , SSI Research Associate and accredited mindfulness teacher Anita Banerji delivers this self-compassion meditation. Get in touch Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto: peter@code4thought.org UK RSE Slack...

In this episode of ByteSized we look at code reviews and GitHub.  Code reviews have a long tradition (see the link to Michael Fagan's paper from 1976 below).  Modern code management tools like GitHub, GitLab and others provide features to integrate code reviews with your overall development and deployment workflow. In this episode we look specifically at GitHub and how you can use the mechani...

Bastian Greshake-Tzovaras and I were accepted as Fellows of the Software Sustainability Institute around the same time. Bastian, trained in biology, has done a lot of work on "citizen science" and the Open Humans platform.  The latter of which we discuss in a bit more detail as well as two projects Bastian has been working on. Links https://www.openhumans.org Open Humans Platform https:/...

In this episode we speak to Shoaib Sufi and Rachael Ainsworth from the Software Sustainability Institute’s Community team about their Event Organisation Guide and some upcoming SSI events. The Event Organisation Guide brings together years of experience of the SSI in organising events. It covers different stages of the event organisation process from idea through feasibility, sign off, running you...

In this Halloween special, Colin Sauze, a Research Software Engineer at the University of Aberystwyth, tells us about when his code set the lab on fire. Hear about what went wrong, how his colleagues and superiors reacted, and tips for our listeners in this second edition of the Software Horror Stories series. If you have comments or suggestions, please tag @Code_4_Thought on Twitter or email us a...

This first episode of “Code for Thought ByteSized” is based on the first session in the Byte-sized RSE interactive research software training series. The session, looking at open source software licensing , took place online on Tuesday 18th October. Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project. Disclaimer: The presenters and content producers for this podcast are not...