Code for Thought: Recent Episodes
RSE
Welcome to Code for Thought, the podcast on software, engineering, research and anything in between. Find out more about our work, the technologies we use (and why) and meet us at workshops and conferences.
English Edition: My guest Bill Kurth and I will go on a space exploration of a special kind: the Voyager probes. Launched in 1977 just a few weeks apart they have now reached interstellar space. Some of the data they send back to Earth are audio - which can tell us a lot about the outer planets like Jupiter or indeed interstellar space, where both Voyagers are now.
Links
- https://science.nasa.gov/mission/voyager/
- https://science.jpl.nasa.gov/projects/voyager/
- https://doi.org/10.1038/s41550-021-01363-7 a paper on persistent plasma waves in interstellar space
- https://science.nasa.gov/blogs/voyager/2025/05/14/nasas-voyager-1-revives-backup-thrusters-before-command-pause/ reviving Voyager's thrusters
- https://space-audio.org some of the sounds we heard during the episode (Uni. of Iowa/US)
- https://www.sleepbot.com/ambience/album/planets.html Symphonies of the Planets old homepage
- https://www.nasa.gov/communicating-with-missions/dsn/ The Deep Space Network
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Edition française: Guillaume Levrier est chercheur associé à la Bibliothèque nationale de France - Francois Mitterand. Il est l'auteur d'une application Open Source appelée Pandorae. Une application pour simplifier, normaliser et explorer les documents ou données numériques.
Bonne écoute
- https://github.com/Guillaume-Levrier/PANDORAE Pandorae sur GitHub
- https://politique.science
- https://hal.science/hal-04309075v1/document
- https://heritrix.readthedocs.io/en/latest/getting-started.html
- https://fluxcd.io
- https://www.electronjs.org
- https://d3js.org
- https://www.istex.fr
- https://www.zotero.org
- https://respadon.hypotheses.org
- https://fosdem.org/2025/schedule/event/fosdem-2025-5223-closed-data-open-software-building-new-ways-into-the-french-web-archives/
- https://www.bnf.fr/fr/consulter-les-archives-de-linternet
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
My guest this week, Rémi Delaporte-Mathurin from MIT, Cambridge, Massachusetts/US, will tell us about the first Open Source Software in Fusion Energy (OSSFE) conference from earlier 2025 - but also why it is important to use and develop open source software in the field and the difficulties he met during his career.
Links:
- https://ossfe.github.io/OSSFE_2025/ The conference website
- https://ossfe.github.io/OSSFE_2025/plot some conference stats
- https://www.youtube.com/@OSSFE-conf OSSFE YouTube channel
- https://github.com/OSSFE the main website of OSSFE
- https://join.slack.com/t/ossfeworkspace/shared_invite/zt-31yacoitt-yl1aAPLxkm5NkCdv8VpfNg Slack channel for OSSFE
- https://ossfe.github.io/OSSFE_2026/ next year's conference
- https://zenodo.org/communities/ossfe OSSFE on Zenodo
- https://www.linkedin.com/in/remidelaportemathurin/ Rémi on LinkedIn
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Better Software - Better Research! This is the mission of the Software Sustainability Institute (SSI) since 2010. To support this, the SSI has been running a fellowship programme. In this episode you'll hear from 3 different fellows from the 2025 cohort about their motivation and plans for their fellowship. Maybe you want to join, too? You can apply for next year's fellowship - 2026 - until 6 October 2025.
Links:
- https://www.software.ac.uk/programmes/fellowship-programme the fellowship programme's website. Please, go to this page if you think about applying!
- https://mdsimpson42.github.io/converse/ Mike's ConveRSE page on mental health
- https://book.the-turing-way.org The Turing Way Handbook
- https://obsproject.com The tool to create videos
- https://github.com/DeepLabCut/DeepLabCut DeepLabCut app
- https://github.com/talmolab/sleap The SLEAP app
And here are the fellows
- https://www.software.ac.uk/fellowship-programme/esther-plomp Esther Plomp
- https://www.software.ac.uk/fellowship-programme/mike-simpson Mike Simpson
- https://www.software.ac.uk/fellowship-programme/niko-sirmpilatze Niko Sirmpilatze
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Meet Christian Gutschow, particle physicist and research software engineer at UCL (University College London, UK). Christian is one of the scientists working on the ATLAS experiment at CERN. And together we try to give you a glimpse of what is going on in this massive experiment that tries to unlock the secrets of matter. Software plays a crucial part in this - and at all levels.
Links:
- https://atlas.cern/about an overview of the ATLAS experiment
- https://profiles.ucl.ac.uk/33100-christian-gutschow Chris' profile at UCL
- https://opendata.atlas.cern/docs/documentation/monte_carlo/introduction_MC Monte Carlo simulations at ATLAS
- https://home.cern/science/computing/grid the LHC computing grid
- https://www.hepdata.net the repository of High Energy Physics (HEP) experimental data
- https://atlaspo.cern.ch/public/ATLASOrganisation/index.html
Some publications with Chris as author or contributor:
- https://arxiv.org/abs/1401.7610 some rare Standard Model processes
- https://arxiv.org/abs/2403.02793 dark matter signatures
- https://arxiv.org/abs/1803.00950 Monte-Carlo modelling (theoretical physics)
- https://arxiv.org/abs/2309.13154 GPU acceleration/common file format for HPC
- https://arxiv.org/abs/1912.05451 project RIVET to preserve data, see also
- https://arxiv.org/abs/2404.15984
- https://fosdem.org/2025/schedule/event/fosdem-2025-4809-efficient-histogramming-for-high-performance-computing-in-c-with-yoda/ efficient histogramming - a presentation at FOSDEM 25
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
The Code Refinery has been training researchers on how to write better software since 2016. In this episode Samantha Wittke, Richard Darst and Radovan Bast tell us how it all started, how CodeRefinery is run and what's in store for the future.
Do look out for their workshops for September and October 2025.
Links:
- https://coderefinery.org/ The CodeRefinery home page
- https://coderefinery.github.io/2025-09-09-workshop/ list of the forthcoming workshops Sept/Oct
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Welcome to Season 10 of Code for Thought. To warm us up for the forthcoming winter and autumn season, here a list of the episodes and content you can look forward to.
The season will start in earnest on 2 September.
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English edition: In the last episode of this season of Code for Thought, I want to take you on a tour through the MetOffice in Exeter, UK. My host Dimitri Theodorakis and some colleagues of his talk us through some of the exciting work happening there.
Links:
- https://www.metoffice.gov.uk/research overview of research at the MetOffice
- https://en.wikipedia.org/wiki/Tempest_prognosticator the "leech barometer"
- https://www.metoffice.gov.uk/research/approach/modelling-systems/unified-model the Unified Model for weather and climate modelling
- https://github.com/cylc/cylc-flow the workflow engine, mentioned a few times in the episode
- https://github.com/MetOffice/stc other open source tools
- https://niwa.co.nz/climate-and-weather/niwa-weather one of the collaborators of the MetOffice
- https://www.ywt.org.uk/oil-tanker-collision the oil tanker collision from March 2025 we talked about in the episode
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Deutsche Ausgabe: Vera Karlsbauer und Jonas Hagenberg arbeiten am Max-Planck Institut für Psychiatrie in München. Aber Software und Datenverarbeitung spielt auch dort eine große Rolle. Vera und Jonas erzählen uns etwas über ihre Arbeit und über den Code Klub den sie gegründet haben um anderen Forschenden und Studierenden den Zugang und Umgang mit Software etwas zu erleichtern.
Links:
- https://www.psych.mpg.de/2931418/deutsch_pm_jonas_hagenberg_comic.pdf Ein Poster zum Thema Depression und Mikroben
- https://www.psych.mpg.de Das Max Planck Institut für Psychiatrie in München
- https://pure.mpg.de/pubman/faces/ViewItemOverviewPage.jsp?itemId=item_3428878_1 der Code Klub am Institut
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
FOSDEM is the annual event for all things free and open source software in Europe happening over the 1st weekend in February in Brussels. In this episode I want to talk about one "dev room" (developer room) in particular: the one on Open Research, that has been running since 2020.
Over the course of a day, we heard from a variety of speakers on topics ranging from climate change to human choreography in computing.
Curious? Have a listen
Links:
- https://fosdem.org/2025/schedule/track/research/ the link to all the talks at the Open Research devroom at FOSDEM25
- https://research-fosdem.github.io/2025-online-schedule there was an "unofficial" devroom online on 15 Feb, 2 weeks later
- Interested in joining the effort on semantic climate? Here's the speaker's email: Peter.murray.rust@googlemail.com
- https://codeforthought.buzzsprout.com/1326658/episodes/13216530-en-open-data-open-software-with-teresa-gomez-diaz Previous episode with Teresa Gomez-Diaz (Uni Paris Gustav Eiffel)
Announcements:
- https://docs.google.com/forms/d/e/1FAIpQLSdV75CnxOjw4Xd7AYad8ChZir1OPnW8ex7yUsOCldqRDzdUaQ/viewform Survey from Maxence in Karlsruhe/Germany
- https://www.fiz-karlsruhe.de/en/bereiche/lebenslauf-und-publikationen-maxence-azzouz-thuderoz Maxence profile
- https://github-pages.arc.ucl.ac.uk/Education/rseworkshop/ UCL workshop 23 - 27 July (in person)
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Parallel programming is hard. Say Hi to Parsl a Python library and tool that aims to make the task a bit easier. I spoke with two of the key people on the project, Dan Katz and Ben Clifford.
- https://github.com/parsl/parsl the GitHub repo of Parsl
- https://funcx.org FuncX
- http://montage.ipac.caltech.edu Montage programme mentioned in the discussion
- https://github.com/Caltech-IPAC/Montage it's GitHub project
- https://www.astropy.org AstroPy a popular lib in Astrophysics
- https://numfocus.org Numfocus in the US, which supports a number of open source projects
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Meine Gäste Carina Haupt und Christoph Steinkamp vom DLR beschäftigen sich mit der Frage, inwieweit der Einsatz von Large Language Models (wie z.B. ChatGPT) bei Forschungsprojekten und deren Softwareentwicklung helfen? Große Versprechungen - aber kleine Brötchen?
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
John MacFarlane and Albert Krewinkel from Pandoc take us through the history and development of this very popular Swiss-army knife for digital documents and document publishing. Pandoc is, of course, open source. And if you want to contribute, don't be shy!
- https://github.com/jgm/pandoc GitHub repo
- https://www.lua.org Lua language
- https://pandoc.org/lua-filters.html Lua filters and Pandoc
- https://www.haskell.org Pandoc is written in Haskell
- https://joss.readthedocs.io/en/latest/paper.html JOSS and Pandoc
- https://johnmacfarlane.net/tools all the tools from John MacFarlane
- https://github.com/tarleb Albert's GitHub
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Brad Frost is the author of a book called Atomic Design, in which he tries to help UI/UX designers improve their workflow and approach and create digital apps.
We also talk about the changing roles of designers and design in a world where we get new gadgets all the time. As Brad says in his book: let's go atomic
Links:
- https://bradfrost.com Brad's home page
- https://atomicdesign.bradfrost.com here the book
- https://www.webcomponents.org
- https://www.w3.org/History.html bit of history re the WWW
- https://www.w3.org/History/1989/proposal.html
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Dr Elisabeth Lobe und Dr Peter Schuhmacher vom DLR geben uns einen (nicht ganz so) kleinen Einblick in die Welt von Quantencomputern und an welchen Themen sie daran arbeiten. Ein spannendes Gebiet auf dem viel passiert!
Hier eine Reihe von Links
- https://qci.dlr.de/en/alqu/ Die Quanteninitiative und die daran beteiligten Projekte
- https://qci.dlr.de/en/quantum-computing-basic-knowledge-in-five-video-lectures/ ein paar Einführungsvideos
- https://gitlab.com/quantum-computing-software/quark ein bisschen Software
- https://www.ibm.com/quantum/qiskit Qiskit von IBM
- https://openqasm.com OpenQasm
- https://www.qir-alliance.org Quantum Intermediate Representation
More general stuff:
- https://en.wikipedia.org/wiki/Quantum_algorithm
- https://ionq.com/resources/what-is-hybrid-quantum-computing
- https://www.classiq.io/insights/quantum-algorithms-shors-algorithm
- https://en.wikipedia.org/wiki/Deutsch–Jozsa_algorithm
- https://azure.microsoft.com/en-us/resources/cloud-computing-dictionary/what-is-a-qubit
- https://en.wikipedia.org/wiki/DiVincenzo%27s_criteria Di Vincenzo Kriterien für Quanten Rechner
- https://en.wikipedia.org/wiki/Quantum_logic_gate
- https://en.wikipedia.org/wiki/Adiabatic_theorem
- https://en.wikipedia.org/wiki/Quantum_error_correction
- https://de.wikipedia.org/wiki/Quantengatter
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
My guest is John Stevenson from the British Geological Survey (BGS) and there is a lot to cover in this episode: John's switch from science to engineering; how to move from proprietary to open source software - and the hot stuff: volcanos. And what John did in volcanology.
Here are a few links:
- https://www.bgs.ac.uk/people/stevenson-john/ John's profile at the BGS
- https://volcanologistsoutsideacademia.wordpress.com/2018/08/29/spotlight-john-a-stevenson-ph-d/
- https://all-geo.org/volcan01010/every-post-ever/ John's blog posts
- https://fosstodon.org/@volcan01010 John's profile on Mastodon
- https://github.com/volcan01010/ GitHub for John
- https://en.wikipedia.org/wiki/Elisabeth_Kübler-Ross a reference for the 5 stages of grief
Volcanos
- https://icelandicvolcanos.is Iceland has a lot of volcanos
- https://rischi.protezionecivile.gov.it/en/volcanic/volcanoes-italy/ Volcanos in Italy
- https://en.wikipedia.org/wiki/2010_eruptions_of_Eyjafjallajökull the big eruption from 2010
- http://www.pompeii.org.uk/s.php/tour-the-two-letters-written-by-pliny-the-elder-about-the-eruption-of-vesuvius-in-79-a-d-history-of-pompeii-en-238-s.htm the letters by Pliny the Younger describing the eruption of Vesuvius in 79AD
Tools mentioned
- https://www.sonatype.com
- https://qgis.org
- https://www.geopackage.org
- https://merginmaps.com
- https://www.redhat.com/en
- https://www.debian.org
- https://www.centos.org
- https://thehackernews.com/2024/04/malicious-code-in-xz-utils-for-linux.html Linux security vulnerability found in 2024
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
How can you transition from photo-type or exploratory research software to production code? Can you? I've been discussing this with my guest Duncan McGregor. In the first part of our discussion we touch on how you can effectively analyse large data sets that are distributed over different locations with tools like Dask.
Links:
- https://www.youtube.com/@PairingWithDuncan Duncan's YouTube channel
- https://www.oneeyedmen.com Duncan's website
- https://github.com/dmcg and his GitHub
- https://www.dask.org Dask
- https://github.com/aws-solutions-library-samples/distributed-compute-on-aws-with-cross-regional-dask cross regional programming with Dask
- https://aws.amazon.com/blogs/big-data/build-efficient-cross-regional-i-o-intensive-workloads-with-dask-on-aws/
- https://blog.dask.org/2022/07/19/dask-multi-cloud
- https://zarr.readthedocs.io/en/stable/ Zarr format
- https://en.wikipedia.org/wiki/NetCDF NetCDF
- https://www.ecmwf.int European Centre for Medium Range Weather Forecasts
- https://github.com/ecmwf
- https://www.eumetsat.int
- https://pangeo.io
- https://testbook.readthedocs.io/en/latest/ Unit testing with Jupyter
- https://github.com/nteract/testbook
Conferences/Events:
- https://dhrse2025.er.kcl.ac.uk King's College London: summer school for digital humanities. 30 June - 4 July, London
- https://www.software.ac.uk/workshop/collaborations-workshop-2025-cw25 The annual Collaborations Workshop of the Software Sustainability Institute UK, 13-15 May, University of Sterling, Scotland
- https://www.helmholtz-hirse.de/events/2025_06_13-rsehpcatisc.html The RSE workshop (13 June) at the ISC conference in Hamburg, Germany
- https://nordic-rse.org Nordic RSE Conference, Gothenburg, Sweden 20-21 May
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English Edition: In this last episode for the ByteSized RSE "miniseries" we talk about AI assisted coding - and the (long) history how engineers tried to come up with assisting tools to make our code better and more robust. My guest is Liam Gao from Imperial College, London, UK.
Links:
- https://github.com/features/copilot GitHub Co-Pilot
- https://huggingface.co HuggingFace another AI tool
- https://spacelift.io/blog/ai-coding-assistant-tools a summary of current tools (non exhaustive)
- https://platform.openai.com/docs/guides/prompt-engineering OpenAI's take on prompt engineering
- https://www.promptingguide.ai
- https://web.archive.org/web/20121022091418/http://www.stanford.edu/~learnest/spelling.pdf some of the attempts to come up with spelling checks
- https://en.wikipedia.org/wiki/Code_completion
- https://www.gnu.org/software/emacs/ Good old Emacs
- https://en.wikipedia.org/wiki/Vi_(text_editor) vi editor (not for the faint hearted)
- https://winworldpc.com/product/turbo-pascal/7x Borland's Turbo Pascal with IDE
- https://survey.stackoverflow.co/2024/ Stackoverflow survey from 2024 with ca 65000 respondents
And here the YouTube clips mentioned
- https://www.youtube.com/watch?v=MvEXkd3O2ow Cypher musing why he didn't take the "blue pill"
- https://www.youtube.com/watch?v=L0mRMp2kbQY Star Trek TNG, S3E6 - Geordie LaForge talking to the computer
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Deutsche Ausgabe: Das Hermes Projekt versucht das Publizieren von Software zu vereinfachen und auch zu automatisieren. Stephan Druskat und Michael Meinel, beide vom DLR und dem deRSE e.V. erklären uns was es damit auf sich hat.
Links:
- https://hermes.software-metadata.pub/en/latest/ Hermes homepage
- https://docs.software-metadata.pub/en/latest/ Hermes workflow
- https://arxiv.org/abs/2201.09015 das Paper zu Hermes
- https://invenio-software.org/products/rdm/
- https://dataverse.org dataverse von Harvard
- https://zenodo.org Zenodo
- https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content Zenodo und GitHub
- https://citation-file-format.github.io Citation File Format
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English Edition: This episode is all about 'green computing' and how we can check the impact of our computing efforts. Helping me with that are Kirsty Pringle (SSI), Loic Lannelongue (University of Cambridge, UK) and Andy Turner from the EPCC in Edinburgh (UK).
Tools discussed in this episode:
- https://www.green-algorithms.org Green Algorithms home page with the online calculator
- https://codecarbon.io Code Carbon - a Python library
Other:
- https://www.software.ac.uk/GreenDiSC Green Disc certification
- Green Computing Special Interest group (SIG) contact
- https://socrse.github.io/green-sig/ home page of the SIG with contact details
- UK RSE Slack channel: #green-sig
- https://post.parliament.uk/research-briefings/post-pn-0677/ Parliamentary report on ICT energy consumption and greenhouse gas emissions
- https://app.electricitymaps.com/map map of energy sources for electricity (fossil fuel, nuclear, renewables etc)
- https://www.nationalgrid.com/stories/energy-explained/what-are-scope-1-2-3-carbon-emissions Emmisions scopes explained
ERRATA: I mentioned in the episode that Kirsty is working at the EPCC - but she works at the SSI (Software Sustainability Institute, UK). Sorry about the confusion.
The sound effects are from Hindenburg audio editing software.
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Edition française: le projet RésIn - réseau d'ingénieurs RésIn est une collaboration entre Science Po et l'Université Paris Cité pour valoriser le travail des ingénieurs pluridisciplinaires.
Audrey Banyex et Diégo Antolinos-Basso (maintenant à l'Université de Neuchâtel, Suisse) nous expliquent pourquoi créer ce réseau et à quoi il sert.
Liens:
- https://medialab.sciencespo.fr/activites/resin/ le descriptif du projet RésIn
- https://resin.medialab.sciences-po.fr/ l'annuaire professionnel
- https://vimeo.com/showcase/11270732 le viméo qui héberge les captations et interviews faites dans le cadre du projet
- https://medialab.sciencespo.fr/activites/metat-atelier-de-methodes/ L'atelier de méthodes (MetAt)
- https://metsem.hypotheses.org/ Le séminaire de méthodologie (MetSem)
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English Edition: How can repository services like GitHub or GitLab help you manage your project. Listen to my conversation with three guests, Gemma Turon (Ersilia), Ben Clifford (Parsl) and Mike Simpson (Uni Newcastle) how they use GitHub PM tools effectively in their work.
Links:
- https://ersilia.io Ersilia project - Gemma Turon
- https://github.com/ersilia-os GitHub pages for Ersilia
- https://parsl-project.org - Parsl project - Ben Clifford
- https://github.com/Parsl/parsl - Parsl on GitHub
- https://www.youtube.com/watch?v=uQYQ_F8auEQ - Mike Simpson's talk at RSE Con 2023 'Colouring Cities: from prototype to Platform'
- https://www.youtube.com/watch?v=vP9k8mAXod4 - a session on Project Management and people at RSE Con 2024 - also with Mike
- https://docs.github.com/en/issues/planning-and-tracking-with-projects/learning-about-projects/best-practices-for-projects GitHub guidelines for using Projects (GitHub tool)
- https://www.software.ac.uk/blog/task-management-humans-self-care blog post from Mike
ByteSized RSE is supported by the Universe-HPC project.
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Deutsche Ausgabe: Ende November 2024 fand in Berlin ein Austausch von Ausbildern und Tutoren bei Helmholtz statt - unter dem Namen TEACH. Wie kann man dem wachsenden Bedarf and Weiterbildung gerecht werden und welche Mittel und Tools helfen dabei. In diesem kleinen Rückblick spreche ich mit den OrganisatorInnen und Sprechern der Veranstaltung: Prof Silke Schworm, Jolanta Zjuba, Fredo Erxleben und Anna-Lisa Döring.
Links:
- https://events.hifis.net/event/1472/timetable/#20241121.detailed Das Programm der Veranstaltung mit Beiträgen zum Herunterladen
- https://www.helmholtz-hida.de HIDA, der Dachverband bei dem die Tagung stattfand
- https://www.hifis.net HIFIS auch eine Helmholtz Platform
- https://www.helmholtz.de/hida-files/user_upload/pdf_dokumente/Helmholz-Incubator-Folder_2022.pdf Übersicht der Helmholtz Platformen
- https://www.uni-regensburg.de/humanwissenschaften/erziehungswissenschaft-medien/team/prof-dr-silke-schworm/index.html Prof Silke Schworm
- https://www.youtube.com/watch?v=xKralSEhZq0
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English Edition: together with Meag Doherty and Zihao Lu I want to shine a light on UX/UI design in research and put the capital "D" back into it. The way we design our software and research projects shapes the way not only the way they are being used, but also how successful they will be.
Links:
- https://www.figma.com/ Figma tool for wireframing
- https://balsamiq.com Balsamiq wireframe
- https://www.bjfogg.com BJ Fogg home page with a mention of Persuasion Technology from 2002
- https://en.wikipedia.org/wiki/A/B_testing A and B testing
- https://kdl.kcl.ac.uk King's College Digital Laboratory (KDL)
I'd like to thank the UNIVERSE-HPC project for the support of this podcast.
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Edition française: Nous sommes ravi d'accueillir Florian Angeletti d'INRIA, qui est très connu pour son travail sur OCamL (anciennement Objective CamL), le langage multi-paradigme. OCamL est Open Source et très utilisé dans le métier de la recherche. Mais aussi dans certains secteurs industriels.
- https://ocaml.org
- https://dev.realworldocaml.org
- https://perso.quaesituri.org/florian.angeletti/
- https://gallium.inria.fr/blog/
- https://github.com/Octachron
- https://github.com/coq/coq
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
I met Deborah at the Research Software Engineering 2024 conference in Newcastle, UK, where she gave an impassioned speech about her drive to carve out a new career and new opportunities in STEM. Here she talks about how she got here and the obstacles she faces.
My apologies, I initially uploaded the raw version of the interview. This should now be corrected
- https://we-are-ols.org Open Life Sciences
- https://www.outreachy.org the Outreachy programme
- https://rsecon24.society-rse.org/programme/emerging-voice-plenary/ Deb's talk at RSE Con 24.
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Deutsche Ausgabe: Vom 2.-4. Dezember 2024 fand in Hannover die Tagung zum Thema Digitale Kompetenzen in der Wissenschaft statt. Mit von der Partie waren ca 35 TeilnehmerInnen aus der Landschaft der Forschungssoftware EntwicklerInnen. Bei den Arbeitskreisen kamen dabei interessante und spannende Vorschläge heraus, wie Ihr hoffentlich in dieser Folge hören könnt.
Links:
- https://www.volkswagenstiftung.de/de/foerderung/foerderangebot/themenwoche-digitale-kompetenzen-der-wissenschaft-beendet Die Webseite zur Themenwoche in Hannover
- https://events.hifis.net/event/1741/ die deRSE e.V. Konferenz in Karlsruhe 25. ß 27. Februar 2025
- https://de-rse.org/de/index.html der deRSE e.V.
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Happy New Year and Welcome to Season 9 of Code for Thought. The season opens with a ByteSized RSE session - the short online courses with companion episodes for all of you who do science and write code. ByteSized RSE is sponsored by the Universe HPC project.
Subject for this episode is data visualisation and how you could use the perception features of our brain (see Gestalt psychology) to tell a compelling story with your data. My guest is Kirsty Pringle from the Software Sustainability Institute in the UK.
- https://www.interaction-design.org/literature/topics/gestalt-principles Gestalt principles by a user design group
- https://en.wikipedia.org/wiki/Gestalt_psychology a good summary of Gestalt psychology
- https://en.wikipedia.org/wiki/Data_and_information_visualization a summary of data visualisation
- https://matplotlib.org the Python Matplotlib library
- https://d3js.org the D3 Javascript library
- https://root.cern the Root analysis tool by CERN
- https://www.software.ac.uk the Software Sustainability Institute
- https://www.universe-hpc.ac.uk the Universe-HPC project
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English Edition: In this last episode of 2024 I want to remember David Mills and his work on the Network Time Protocol (NTP). The tool that keeps our machines in sync. David Mills worked closely with Harlan Stenn from the Network Time Foundation on NTP and I was very fortunate to grab some of Harlan's time to talk to him about NTP and David Mills' contribution.
Some links (by far not an exhaustive list):
- https://www.eecis.udel.edu/~mills/ David Mills homepage at the Uni. of Delaware (which still exists). There are a lot of links to his work on NTP
- https://eecs.engin.umich.edu/stories/remembering-alum-david-mills-who-brought-the-internet-into-perfect-time
- https://www.ntp.org/ The Network Time Protocol homepage with tons of details and specifications on how it all works
- https://www.nwtime.org The Network Time Foundation
- https://www.eecis.udel.edu/~mills/database/brief/arch/arch.pdf a presentation on how NTP works
- https://www.nwtime.org/bio/harlan-stenn/ Harlan Stenn's Bio
- https://datatracker.ietf.org/doc/html/rfc778 I think this is the first RFC of the early version of NTP
- https://www.ntp.org/reflib/rfc/ This contains a list of all RFCs related to NTP
The sounds you're hearing are from Phill Niblock, musician, composer, artist and his recording you can get on the internet archive
https://archive.org/details/phill-niblock-music-by-phill-niblock
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English Edition: Arnaud Legrand, Christophe Pouzat and Konrad Hinsen, three French researchers, who went through the pain of making research data and software reproducible. Out of that pain grew a set of online courses. I met with them to discuss how they developed the courses, the steps they had to go through and what the courses cover.
- https://www.fun-mooc.fr/en/courses/reproducible-research-methodological-principles-transparent-scie/
- https://www.fun-mooc.fr/en/courses/reproducible-research-ii-practices-and-tools-for-managing-comput/
- https://khinsen.net
- https://orgmode.org
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Edition française: GNU Guix est un gestionnaire de paquets pour GNU/Linux. Ghislain a rencontré Pierre-Antoine Bouttier, Ludovic Courtes et Simon Tournier de GUIX pour discuter de la façon dont GUIX peut aider à la reproductibilité.
- https://guix.gnu.org/fr/
- https://10years.guix.gnu.org/video/guix-as-a-tool-for-computational-science/
- https://10years.guix.gnu.org/video/using-guix-for-scientific-reproducible-and-publishable-experiments/
- https://hpc.guix.info/events/2023/workshop/video/what-is-guix-/
- https://hpc.guix.info/events/2023/workshop/video/everyone-can-learn-how-to-guix/
- https://hpc.guix.info/events/2023/workshop/video/reproducible-virtual-machine-management-with-guix/
- https://hpc.guix.info/events/2023/workshop/video/reconciling-high-performance-computing-with-the-use-of-third-party-libraries-/
Dans un contexte HPC
- https://inria.hal.science/hal-01161771/en
- https://inria.hal.science/hal-03604971/
Plus généralement
- https://guix.gnu.org/en/publications/
Simon Tournier
- https://replay.jres.org/w/3TuYmocHwKtzs7q1VtL1GB
- https://www.nature.com/articles/s41597-022-01720-9
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English edition [EN]: Niklaus Wirth is one of the computing pioneers and his work inspired many other technologies and a generation of engineers. In this episode I discuss one of his many contributions: the programming language Pascal. And we hear from 3 people who worked and learnt with Pascal in their career: Irving Reid, Todd Jacobs and Charles Forsythe.
Links:
- https://computerhistory.org/profile/niklaus-wirth/
- https://people.inf.ethz.ch/wirth/
- https://amturing.acm.org/award_winners/wirth_1025774.cfm Turing Award for N Wirth
- https://people.inf.ethz.ch/wirth/CompilerConstruction/index.html Book on Compiler Construction
- http://pascal.hansotten.com/ucsd-p-system/more-on-p-code/ p-code machines
- http://pascal.hansotten.com/standard-pascal-and-validation/ Standard Pascal
- https://www.embarcadero.com/products/delphi Delphi
- https://en.wikipedia.org/wiki/UCSD_Pascal UCSD Pascal
- https://www.youtube.com/watch?v=Yj3DMUn6cck Kathleen Jenssen (co-author of the Pascal book) at the 80th birthday reception for N Wirth
- https://www.fidonet.org Fidonet bulletin board
- http://www.retroarchive.org/swag/index.html Software Archiving group (Pascal)
Not everyone was enamoured with Pascal. Here is a link to B Kernighan's post on 'Pascal...is a toy language' http://www.lysator.liu.se/c/bwk-on-pascal.html
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English edition [EN]: We're kickstarting a round of new ByteSized RSE online classes and podcast episodes with an episode on containers. Focusing on Podman (used in the online class) and Docker. My guest for this episode is Simon Li from the Uni. Dundee.
Many thanks to Universe HPC for supporting this podcast.
Containers:
- https://docs.docker.com Docker
- https://www.docker.com/pricing/faq/ Info regarding the Docker licenses
- https://docs.docker.com/get-started/docker-overview/ An overview of how Docker works
- https://podman.io Podman homepage
- https://podman-desktop.io/docs/migrating-from-docker migrating from Docker to Podman
- https://www.redhat.com/en/blog/run-containers-mac-podman running Podman on a Mac
- https://www.redhat.com/en/blog/run-podman-windows running Podman on Windows
- https://github.com/containers/podman/blob/main/docs/tutorials/podman-for-windows.md more on Podman for Windows
- https://containerd.io another container tool
- https://repo2docker.readthedocs.io/en/latest/index.html repro2docker, the tool Simon mentioned
- https://kubernetes.io Kubernetes
- https://apptainer.org Apptainer (formerly Singularity)
Container history:
- https://www.aquasec.com/blog/a-brief-history-of-containers-from-1970s-chroot-to-docker-2016/ brief overview
- https://www.youtube.com/watch?v=wW9CAH9nSLs the presentation from 2013 when Docker was introduced at PyCon that year
- https://utcc.utoronto.ca/~cks/space/blog/unix/ChrootHistory a brief history of the chroot(2) command of Unix
- https://freebsdfoundation.org/freebsd-project/resources/introduction-to-freebsd-jails/
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 (ukrse.slack.com): @code4thought or @piddie
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This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Deutsche Version: In dieser letzten Folge vor Weihnachten treffe ich mich mit Priv. Doz. Dr Georg Hager vom Rechenzentrum der Universität Erlangen-Nürnberg. Georg Hager gibt uns einen kleinen Überblick in die Entwicklung von HPC Rechnern, also Hochleistungsrechnern und wir sprechen über die Herausforderung bzgl. Software Entwicklung und wie man Personal and HPC Rechner heranführt.
Links:
- https://hpc.fau.de/person/georg-hager/
- https://www.nhr-verein.de/en Der NHR e.V.
- https://en.wikipedia.org/wiki/Vector_processor Vektor Rechner
- https://ieeexplore.ieee.org/document/508045 "Cluster" von PCs, das Beowulf System
- https://en.wikipedia.org/wiki/Myrinet Myrinet Netzwerk
- https://en.wikipedia.org/wiki/InfiniBand Infiniband Netzwerk
- https://www.openmp.org Open MP für paralleles Programmieren
- https://developer.nvidia.com/cuda-toolkit NVIDIA CUDA toolkit
Etwas zur Geschichte von älteren Modellen
- https://de.wikipedia.org/wiki/Z23 Der Zuse 2023 Rechner
- https://horst-zuse.hier-im-netz.de/Konrad_Zuse_index_english_html/rechner_z23.html Konrad Zuse und der Z23
- https://www.reddit.com/r/pcmasterrace/comments/n4wwp4/the_zuse_z23_at_the_university_of_erlangen_fully/?rdt=55435 der Z23 am Rechenzentrum in Erlangen
- https://en.wikipedia.org/wiki/Magnetic-core_memory Magnetische Speicher
- https://en.wikipedia.org/wiki/Drum_memory Trommelspeicher
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English Edition:
- https://www.esciencecenter.nl Home page of the eScience Center
- https://www.esciencecenter.nl/calls-for-proposals/fellowship-open-call/ Fellowship programme at the eScience Center
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 (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
- LinkedIn: https://www.linkedin.com/in/pweschmidt/ (personal Profile)
- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
L'édition française: On a beaucoup de promesse sur l'usage du calcul quantique. Ghislain Vaillant discute avec Sabine Mehr et Félix Givois de GENCI (Grand Equipement National de Calcul Intensif) pour jeter un coup d'œil aux coulisses de cette technologie fascinante.
- https://www.genci.fr/connaitre-genci/calcul-haute-performance-intelligence-artificielle-et-calcul-quantique
- https://www.genci.fr/actualites/france-hybrid-hpc-quantum-initiative-hqi-genci-et-le-cea-annoncent-la-selection-de-0
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- UK RSE Slack (ukrse.slack.com): @code4thought or @piddie
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English Edition [EN]: In this episode I am looking at two different champion schemes: one at Imperial College London, focussing on research software and the other at Cambridge University for research data. My guests are Jeremy Cohen and Mike Bearpark from Imperial and Clair Castle, Sacha Jones and Lutfi Ben Othman from Cambridge University.
Imperial:
- https://www.imperial.ac.uk/computational-methods/rse/call-for-rs-champions-2024/ Champion scheme at Imperial
- https://www.ukri.org/news/new-funding-to-support-research-technical-professionals/ UKRI funding
- https://profiles.imperial.ac.uk/m.bearpark Profile Mike Bearpark
- https://profiles.imperial.ac.uk/jeremy.cohen Profile Jeremy Cohen
Cambridge
- https://www.data.cam.ac.uk/ The data home page
- https://www.data.cam.ac.uk/intro-data-champions Introduction to the Champion scheme at Cambridge
- https://www.data.cam.ac.uk/research-data-management-team the Research Data Management team at Cambridge University
Get in touch
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- Email mailto:peter@code4thought.org
- UK RSE Slack (ukrse.slack.com): @code4thought or @piddie
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- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
Deutsche Ausgabe: Diesmal geht es an die TU Braunschweig, von wo aus Jan Linxweiler uns über seine Arbeit am Suresoft Projekt erzählt - und uns erklärt warum es wichtig ist, nachhaltige Software für die Wissenschaft zu schreiben.
Links
- https://suresoft.dev Die Homepage des Suresoft Projektes
- https://zenodo.org/communities/suresoft/ Suresoft on Zenodo
- https://doi.org/10.24355/dbbs.084-202210121528-0 Suresoft Konzept Papier
- https://www.dfg.de/de Homepage der Deutschen Forschungsgemeinschaft
- https://www.tu-braunschweig.de Die TU Braunschweig
- https://www.fau.de die Friedrich-Alexander Universität Erlangen-Nürnberg
- https://de-rse.org/de/index.html der deRSE e.V. - Verein der EntwicklerInnen von Forschungssoftware
Get in touch
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Contact Details/ Coordonnées / Kontakt:
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- UK RSE Slack (ukrse.slack.com): @code4thought or @piddie
- Bluesky: https://bsky.app/profile/code4thought.bsky.social
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- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English edition: My guest this week is Kurt Lust from the University of Antwerp (Belgium) and part of the user support team of LUMI (Large Unified Modern Infrastructure). Acc to the website, LUMI is Europe's fastest supercomputer. Kurt tells us what it takes to run a machine like that and all the gotchas that he and his colleagues encounter.
Links
- https://www.lumi-supercomputer.eu/about-lumi/ LUMI website (About)
- https://eurohpc-ju.europa.eu/index_en EuroHPC Joint Undertaking site
- https://klust.github.io Kurt Lust on GitHub
Get in touch
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- Email mailto:peter@code4thought.org
- UK RSE Slack (ukrse.slack.com): @code4thought or @piddie
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- LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
English Edition: Meet Kenneth Hoste and Alan O'Cais who will tell us about EESSI,The European Environment for Scientific Software Installation for high performance computing (HPC).
Links:
- https://www.eessi.io Home page of EESSI
- https://docs.easybuild.io EESSI docs
- https://github.com/boegel Kenneth's GitHub page
- https://cernvm.cern.ch our friend CERN VM/VMFS
- https://lmod.readthedocs.io/en/latest/ LMOD docs
- https://docs.easybuild.io Easybuild
- https://www.multixscale.eu MultiXscale website
- https://eurohpc-ju.europa.eu/kick-10-centres-excellence-hpc-support-transition-towards-exascale-2023-01-26_en
- https://www.eessi.io/docs/blog/#eessi-nominated-for-hpcwire-readers-choice-awards-2024 EESSI nominated for HPC Wire award
- https://www.izum.si/en/vega-en/ VEGA HPC system
- https://www.it4i.cz/en/infrastructure/karolina Karolina HPC system
- https://ssl.linklings.net/conferences/pearc/pearc19_program/views/includes/files/pap139s3-file1.pdf Canadian proposal
- ttps://ubcbraincircuits.readthedocs.io/en/latest/data_storage/compute_canada.html Compute Canada
Get in touch
Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!
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L'édition française: Alice Brenon est une doctorande et chercheuse du CNRS en informatique linguistique au LIRIS (Laboratoire d'InfoRmatique en Image et Systèmes d'information) à Lyon. Alice décrit son engagement dans le projet GEODE (“Encyclopedic GEOgraphical DiscoursE: Writing about Geography in France from the Enlightenment to the Age of Wikipedia”). Dans ce cadre, elle a développé plusieurs outils logiciels dont certains sont en Haskell.
Nous vous souhaitons une bonne écoute.
Liens
- https://perso.liris.cnrs.fr/abrenon/ Alice Brenon
- https://liris.cnrs.fr/these/these-alice-brenon
- https://gitlab.inria.fr/abrenon/soprano/
- https://geode-project.github.io projet Géode sur GitHub
- https://archive.softwareheritage.org/browse/content/sha1_git:5675074b84f915278fc2137190bdc44d514a6740/?origin_url=https://gitlab.inria.fr/abrenon/soprano/&path=LICENSE
- https://www.collexpersee.eu/projet/disco-lge/
- https://guix.gnu.org projet GUIX
- https://www.haskell.org Haskell langage de programmation
- https://editions-rnti.fr/?inprocid=1002717 Classification automatique d'articles encyclopédiques
Get in touch
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Contact Details/ Coordonnées / Kontakt:
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Meet 6 of the research software champions at Imperial College London (UK) who help to create better research - through better software: Allen Xavier, Lukas Kopecky, Jakub Lala, Benjamin Scharpf, Sara Patti and Sneha Jhal.
Links
- https://www.imperial.ac.uk/computational-methods/rse/call-for-rs-champions-2024/ The call for the 2024 champion scheme cohort
- https://imperialcollegelondon.github.io/rs-community-newsletters/2024-03.html The newsletter announcing the championship
- https://www.imperial.ac.uk/computational-methods/rse/ The RSE group at Imperial College
- https://www.ukri.org/news/new-funding-to-support-research-technical-professionals/ UKRI initiative to nurture research technical professionals
- https://www.tandfonline.com/doi/full/10.1080/14703297.2023.2237943#abstract An article about the size of doctoral programmes at UK academic institutions in the year 2020-2021
My thanks go to Imperial College London (UK) for supporting this episode and this podcast.
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[EN] English Edition: "Green computing" had a strong showing at the annual conference for Research Software Engineering in Newcastle, UK, early September 2024. I talk to the presenters, poster creator and organisers of the birds of the feather session on the subject. In addition you hear from Charlotte Pascoe and Poppy Townsend from the UKRI on their project to get us to net zero. And finally, from the platinum sponsor of the conference: CloudKubed https://www.cloudkubed.com.
Also note https://eng.ox.ac.uk/netdrive/ from UKRI, who work towards a sustainable, digital research infrastructure.
Links:
- https://rsecon24.society-rse.org RSE Conference 2024 site
- https://www.green-algorithms.org Green Algorithms home page
- https://codecarbon.io Code Carbon library
- https://github.com/GreenScheduler/cats CATS scheduler
- https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?SUBED1=GREENRESEARCHSOFTWARE mailing list for the Special Interest Group (SIG) on greener computing
- https://net-zero-dri.ceda.ac.uk The UKRI net zero for the digital research infrastructure project
- https://zenodo.org/records/8199984 The report on the scoping project UKRI - Net Zero for Digital Research Infrastructure
- https://www.nature.com/articles/s43588-023-00461-y.epdf GREENER principles for computing article
- https://www.cell.com/patterns/fulltext/S2666-3899(21)00188-4 Estimating the contribution from ICT re greenhouse gas emissions
- https://climate.ec.europa.eu/eu-action/transport/reducing-emissions-aviation_en The EU report on emissions from the transport sector
- https://app.electricitymaps.com/map Electricity maps
- https://www.nationalgrid.com/stories/energy-explained/what-are-scope-1-2-3-carbon-emissions explaining scope 1,2,3 emissions
- https://ghgprotocol.org the Greenhouse Gas protocol
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Deutsche Ausgabe: in der ersten DE Ausgabe nach der Sommerpause geht es gleich um 2 Open Source Projekte: MTEX und PyRolL. Mit von der Partie sind die Entwickler und Autoren der Softwarepakete Ralf Hielscher (MTEX) und Christoph Renzing (PyRolL), beide von der TU Bergakademie Freiberg, Sachsen.
Links:
- https://mtex-toolbox.github.io MTEX
- https://tu-freiberg.de/en/node/2702/prof-dr-rer-nat-ralf-hielscher Prof Ralf Hielscher, TU Freiberg
- https://github.com/pyroll-project PyRolL auf GitHub
- https://pyroll.readthedocs.io/en/latest/ Dokumentation
- https://joss.theoj.org/papers/10.21105/joss.06200 PyRolL bei dem Journal for Open Source Software (JOSS)
- https://www.linkedin.com/in/christoph-renzing-584077214/ Christoph Renzing
- https://tu-freiberg.de Homepage der TU/Bergakademie Freiberg
- https://www.freiberg.de/stadt-und-buerger/stadt/stadtportrait/geschichte-chronik etwas zur Geschichte von Freiberg
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ENGLISH EDITION: There are a lot of "large" things at CERN, including the amount of data produced and the software needed to manage and analyse them. In this episode I talk to Laura Promberger and Jakob Blomer from the CERN virtual machine/file system VM/VMFS project about how this set of tools is helping researchers.
And not just physicists, as CERN VM/VMFS is also used in other areas of the high performance computing community.
Links:
- https://cernvm.cern.ch Home page for CERN VM/VMFS
- https://ep-rnd.web.cern.ch/index.php/person/jakob-blomer Jakob Blomer
- https://www.researchgate.net/profile/Laura-Promberger Laura Promberger publications
- https://www.eessi.io the EESSI library
- https://www.zlib.net/zlib_tech.html ZLIB compression library
- https://github.com/facebook/zstd Facebook's zstd compression library
- https://alliancecan.ca/en Digital Alliance of Canada (one of the CERN VM/VMFS users)
- https://home.cern/science/accelerators/high-luminosity-lhc "High-luminosity" LHC (large hadron collider)
- https://cern70.cern CERN 70th birthday home page
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L'édition française: Ça y est - le premier épisode de Code for Thought en français.
Comment reproduire et évaluer l'apprentissage automatique? Publier les résultats de recherche avec les données et le code source? Avec Pascal Monasse, chercheur chez IMAGINE (Laboratoire d'informatique Gaspard Monge) et éditeur de journal IPOL - Image Processing On Line.
Animé par: Ghislain Vaillant. Réalisé par: Peter Schmidt
Liens:
- https://imagine-lab.enpc.fr Laboratoire IMAGINE
- https://imagine-lab.enpc.fr/staff-members/pascal-monasse/
- http://www.ipol.im IPOL - Image Processing Online journal
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ENGLISH EDITION: Beyond Open Research is a project at Imperial College in London (UK), that tries to change research culture more open and transparent. I met with Dr Hamid Khan, who was leading the project and Prof Julie McCann, Vice-Dean for the Faculty of Engineering to find out more about exactly how they want to go "beyond" open research.
A few links
- https://www.imperial.ac.uk/research-and-innovation/support-for-staff/scholarly-communication/open-research/ one of the workshops at Imperial as part of the Beyond Open Research project
- https://www.ukrn.org The UK Reproducibility Network
- https://www.go-fair.org/fair-principles/ FAIR principles
- https://sfdora.org the San Francisco Declaration on Research Assessment (DORA)
- https://coara.eu the Coalition for Advancing Research Assessment
- https://royalsociety.org/news-resources/projects/research-culture/research-culture-conference/the-pitch/the-pitch-winner-dr-alexandra-freeman/
- https://profiles.imperial.ac.uk/hamid.khan Dr Hamid Khan
- https://profiles.imperial.ac.uk/j.mccann Prof Julie McCann
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ENGLISH EDITION: Welcome back to Season 8 of Code for Thought. Just before we dive into the new season, this trailer will tell you what lies ahead between September and December 2024.
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In May 2024, I attended a workshop/training course on Software Management Plans (SMP), held at the University Paris Gustav-Eiffel east of Paris, France.
In this episode I talk to the organisers and participants about why SMPs might be useful and under what circumstances.
- http://igm.univ-mlv.fr/~teresa/presoft/documents/2018/ModeleSMP_PRESOFTV3.1.pdf the PRESOFT template by Teresa Gomez-Diaz and Geneviève Romier
- http://igm.univ-mlv.fr/~teresa/presoft/2024FormationPlansGestionLogicielsRecherche/ The event schedule
- https://www.software.ac.uk/news/software-management-plans The SMP post by the Software Sustainability Institute in the UK
- https://siteigm.univ-mlv.fr/home/ The Laboratoire d'Informatique Gaspard-Monge
- https://www.cnrs.fr/fr the French national research centre CNRS
- https://www.inria.fr/fr the French national centre for digital research and technology
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Support the show on Patreon https://www.patreon.com/codeforthought
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My guest for this episode is Dr AJ Lauer. AJ has been working hard to make the HPC workplace a more open and welcoming environment. She was inclusivity chair at SC21 in St Louis, US and worked with other groups such as Women in HPC. Lately, in 2023, she created her organisation 'Thriving Ibis' to work with senior managers and leaders in the field.
- https://www.thrivingibis.com Thriving Ibis home page
- https://subscribepage.io/TC6R2f Subscribe to the Thriving Ibis newsletter
- http://www.linkedin.com/in/ajlauer contact AJ on LinkedIn
- https://sc21.supercomputing.org/attend/inclusivity/demographics/ A demographics overview of the attendees of the annual supercomputing conference in St Louis, Missouri, US in 2021
- https://womeninhpc.org Women in HPC home page
And some fun facts about the word 'Ibis':
- https://en.wiktionary.org/wiki/ibis#Etymology_2_2 its meaning in Latin - as a verb
- https://en.wikipedia.org/wiki/Ibis the species
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The Digital Research Academy - DRA - was created in 2023 to meet the increasing demand for training in open science and research. In this episode I talk to the two founders, Heidi Seibold and Joyce Kao, as well as members like Yeganeh Khazaei (Yegi) and Danny Garside.
- https://digital-research.academy the home page of the DRA
- https://digital-research.academy/train-the-trainer/ Train the Trainer programme
- https://events.digital-research.academy/event/41/ the next Train the Trainer program in summer 2024, Delft NL
- https://openscienceretreat.eu Open Science Retreat
- https://mastodon.social/@digiresacademy/ Mastodon
- mailto:hello@digiresacademy.org the email address
- https://www.linkedin.com/company/digital-research-academy/ on LinkedIn
- https://gitlab.com/digital-research-academy on GitLab
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In the second part episode on the Turing Way, I meet with contributors like Patricia Herterich and Sarah Gibson - who were part of the original team - as well as Malvika Sharan and Anne Steele who joined later.
Through these conversations I hope to show how the Turing Way transitioned from being an online guide for reproducibility and open science to a thriving community with members across the globe.
- https://book.the-turing-way.org/index.html the home page of the Turing Way
- https://edsbook.org/welcome.html The environmental data science book
- https://nasa.github.io/Transform-to-Open-Science/ NASA's Transform to Open Science project home page
- https://adriennemareebrown.net/book/emergent-strategy/ Emergent Strategy a book by Adrienne Brown
- https://www.jstor.org/stable/j.ctt5hhdf6 Understanding Knowledge as a Commons: From Theory to Practice
- https://www.jofreeman.com/joreen/tyranny.htm Jo Freeman's article on Tyranny of Structurelessness
- https://mybinder.org Binder project homepage
- https://jupyter.org Jupyter project homepage
- https://2i2c.org 2i2c homepage
I would like to thank the Turing Way and the Alan Turing Institute in the UK for their patience, time and kind support.
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CERN, the European Nuclear Research Centre, is celebrating its 70th birthday in 2024 and I want to give you a glimpse of the kind of work that happens there. Meet Spyridon Trigazis, who will take us through CERN's infrastructure and how they use OpenStack and Kubernetes to "keep the lights" on.
- https://home.cern/ CERN homepage
- https://www.openstack.org OpenStack
- https://kubernetes.io Kubernetes
- https://inspirehep.net/authors/1907786 A selection of the work Spyridon has been involved with
- https://alumni.cern The CERN alumni network
- https://home.cern/summer-student-programme the summer student programme. Applications for 2024 are closed now, but I am sure there will be another on in '25
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In this last ByteSized RSE episode of this season, we talk about an important subject for Python engineers: Packaging. With my guests Liam Pattinson from York University (UK) and Laszlo Sranger from Hypergolic, we go through the standard Python tools as well as package managers such as Poetry.
Links:
- https://packaging.python.org/en/latest/ Python packaging guide
- https://pypi.org The PyPI Index
- https://test.pypi.org Test PyPI - publish your package there first
- https://peps.python.org The site for Python Enhancement Proposals (PEP)
- https://python-poetry.org Poetry manager
- https://www.anaconda.com The home page for Anaconda
- https://toml.io/en/ What is a TOML file
- https://the-hitchhikers-guide-to-packaging.readthedocs.io/en/latest/history.html a bit of packaging history
- https://www.cpan.org
Thanks to the Universe-HPC program for supporting the ByteSized RSE series.
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In dieser letzten Folge vor den Sommerferien treffe ich mich mit Dr Iris Ehlert und Dr Hendryk Bockelmann, um mit ihnen über ihre Arbeit am natESM (nationale Erdmodellierungs Systeme) zu sprechen.
Hier ein paar Links
- https://www.nat-esm.de/ Home page vom natESM
- https://www.nat-esm.de/services/support-through-sprints Der Sprintprozess beim natESM Projekt
- https://www.dkrz.de/de das Deutsche Klimarechenzentrum (DKRZ)
- https://www.nat-esm.de/who-we-are/governance/white_paper_natesm_strategy_v2.pdf Das White Paper für die natESM Strategy
- https://www.nat-esm.de/news/newsection/240517_newsletter_-5.pdf Der Newsletter vom Max 2024
- https://www.fz-juelich.de/de das Forschungszentrum in Jülich das mit dem DKRZ an dem Projekt zusammen arbeitet.
Es geht dann im September mit einer neuen Serie am letzten Dienstag im Monat weiter. Euch ein paar schöne Ferien.
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The International Conference of Supercomputing, ISC, met in Hamburg (Germany) between 12-16 May 2024. For the first time, a workshop on Research Software Engineering was held there. And I talk to some of the organisers, Stefanie Reuter and Matt Archer and presenters, Eleanor Broadway and Samantha Wittke, how it all went.
- https://www.rse-hpc.org/program/ The program for the workshop
- https://www.isc-hpc.com The home page of ISC 2024
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What a fun day that was: the National Research Software Day in Hilversum on 23 April 2024. It was organised by the eScience Center in the Netherlands and in the course of this episode you will hear from one of the organisers, Lieke, a keynote speaker - Jenny Bryan, members of a panel discussions on research infrastructure.
But also from 4 artists - because the organisers added an art exhibition to the one day conference.
The sound samples you can hear in the episode are from one of the artists Christian Schwarz.
- https://www.esciencecenter.nl/national-research-software-day-2024/ The conference home page
- https://www.beeldengeluid.nl The home page of the Netherlands Institute for Sound and Vision
- https://jennybryan.org Jenny Bryan's home page - keynote speaker
- https://www.ru.nl/en/people/kievit-r-a Rogier Kievit - keynote speaker
- https://ilar.xyz Christian Schwarz - artist
- https://soundcloud.com/ilarxyz Christian on Soundcloud
- https://xingkuangyi.com Kuangyi Xing - artist
- https://www.eusebijucgla.com/collaborations/hyperview-barcelona Eusebio Jucgla - artist
- https://guidovanderkooij.nl Guido van der Kooij - artist
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In this session of ByteSized RSE we talk about the FAIR principles and research software. My guest helping me with that is Jamie Quinn, currently RSE at Imperial College London.
Here are a few links:
- https://www.nature.com/articles/sdata201618 The article on FAIR
- https://www.nature.com/articles/s41597-022-01710-x The article on FAIR research software
- https://research-and-innovation.ec.europa.eu/strategy/strategy-2020-2024/our-digital-future/open-science/open-science-monitor/facts-and-figures-open-research-data_en Data produced in research
- https://coderefinery.github.io/github-without-command-line/doi/ An article on the integration of GitHub and Zenodo
- https://citation-file-format.github.io the Citation File Format and GitHub - also see one of our previous ByteSized RSE episodes
- https://direct.mit.edu/dint/article/2/1-2/1/10016/The-FAIR-Principles-First-Generation here is another interesting article on FAIR principles
- https://en.wikipedia.org/wiki/Cold_fusion The Wikipedia entry on the "Cold Fusion" case from Fleischmann/Pons (1989)
- https://www.youtube.com/watch?v=LWFzPP8ZbdU The YouTube presentation on noise generators
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The Turing Way was created 5 years ago and during the Collaborations Workshop 2024 at the University of Warwick, UK, we had a big birthday party to celebrate the occasion.
In this episode, part 1 of 2 episodes on The Turing Way, I sit down with the founder of The Turing Way, Dr Kirstie Whitaker, who is also the Programme Director for Tools, Practices and Systems at the Turing Institute in the UK.
You also hear a moment when a new chapter was merged into The Turing Way during this recording, done by Sophia Batchelor.
- https://book.the-turing-way.org/ the Home page of The Turing Way
- https://github.com/the-turing-way/the-turing-way the GitHub repository of The Turing Way
- https://www.turing.ac.uk/people/researchers/kirstie-whitaker Profile page of Dr Kirstie Whitaker
- https://book.the-turing-way.org/community-handbook/translation/translation-workflow the part that deals with localising content
- https://github.com/the-turing-way/the-turing-way/pull/3638 the pull request for the chapter that was merged during the recording of this episode
- https://github.com/BrainonSilicon Sophia Batchelor's GitHub page
I would like to express my heartfelt thanks to the Alan Turing Institute for their support and for sponsoring this episode.
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Bastian Greshake Tzovaras arbeitet am Alan Turing Institute in London zum Thema Citizen Science, also Bürgerwissenschaften. Und dies ist auch das Thema unseres Gesprächs, denn Bastian arbeitet daran schon seit geraumer Zeit. Und er zeigt uns wie Wissenschaft durchaus von einer engeren Zusammenarbeit mit Bürgern profitieren kann.
Links
- https://tzovar.as/ Bastian's Homepage
- https://scholar.social/@gedankenstuecke Bastian's Mastodon Konto
- https://www.cambridge.org/core/journals/data-and-policy/article/how-to-cocreate-content-moderation-policies-the-case-of-the-autspaces-project/DF59760CB3F89901CB5634981C588B55 Ein Paper zum Thema Content Moderation Policies
- https://www.openhumans.org Die Open Humans Platform
- https://opensnp.org Eine Platform zur Veröffentlichung von genetischen Testdaten
- https://www.turing.ac.uk Das Alan Turing Institut in London
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In part two of this "mini-series" on diverse roles in data science teams, I speak with Dr Emma Karoune from the Alan Turing Institute https://www.turing.ac.uk/ and the deputy director of the Software Sustainability Institute of the UK, Simon Hettrick.
Emma and I explore the skills and policy landscape of modern data science roles. Emma is one of the awardees of the Skills Policy Award at the Alan Turing Institute.
Simon discusses how groups like the Research Software Engineering community and initiatives like the Hidden REF help to bring about real change.
- https://www.turing.ac.uk/skills-policy-awards-20232024 The home page for the Project Dr Emma Karoune is involved with at the Alan Turing Institute
- https://www.software.ac.uk The Software Sustainability Institute
- https://hidden-ref.org The "Hidden REF" initiative home page
Both Emma and Simon are Committee member of the Hidden REF (The hidden REF – Celebrating all research outputs (hidden-ref.org)), a campaign to recognise all research outputs and every role that makes research possible.
More information about Emma's project can be found on the project website - Professionalising traditional and infrastructure research roles in data science | The Alan Turing Institute.
Emma would like to thank her project team members Malvika Sharan and Alexandra Araujo Alvarez as well as all those at The Alan Turing Institute and other data science professionals who have contributed to this project through attending workshops and interviews.
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The Collaborations Workshop, run by the Software Sustainability Institute https://www.software.ac.uk/ is a long-running institution. I had the pleasure of going there in May 2024 for the first time. It was an exciting, but also exhausting, couple of days. The 3 themes focused on AI/ML in science, environmental sustainability and citizen science.
Here is a report on the workshop with a bunch of interviews:
- Arfon Smith from GitHub/Copilot
- Becky Osselton from Newcastle University
- Dave Horsfall from Newcastle University
- Kirstie Pringle from the Software Sustainability Institute
- Shoaib Sufi from Uni Manchester/Software Sustainability Institute
Many thanks for the organisers and sponsors of this event (Wellcome Trust, Alan Turing Institute)
https://www.software.ac.uk/workshop/collaborations-workshop-2024-cw24
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My guest in this episode is Greg Wilson, who co-founded the Carpentries in 1998 together with Brent Corda. Since then, the Carpentries have gone global teaching essential computing and data skills and training the next generation of teachers.
Greg stepped down from the Carpentries a while ago, but he still feels passionate about their mission and goals.
Links:
- https://carpentries.org/ The Home page about all things Carpentries
- https://third-bit.com Greg Wilson's homepage
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In dieser Folge geht es um die Frage, wie man Software in wissenschaftlichen Artikeln zitieren kann. Die Antwort: das Citation File Format (CFF) - an dem mein Gast Stephan Druskat maßgeblich mitgewirkt hat. Stephan und ich hatten uns auf der letzten UK RSE Konferenz in Swansea in einer der Pausen zu einem Schwätzchen getroffen.
Inzwischen wird das CFF von etlichen Organisationen wie z.B. GitHub, Zenodo und Zotero unterstützt und das eScience Center in den Niederlanden unterstützt das Projekt tatkräftig.
Hier ein paar Links
- https://citation-file-format.github.io Homepage vom Citation File Format
- https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files GitHub CFF Support und Hilfe Webseite
- https://www.esciencecenter.nl/news/code-citation-was-made-possible-by-research-software-engineers-in-germany-and-the-netherlands/ eScience Center in den Niederlanden und CFF
- https://codemeta.github.io Code Meta
- https://json-schema.org JSON Schema
- https://project.software-metadata.pub Hermes Projekt (Helmholtz)
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Property based testing can help you make your tests more effective and your code more robust. Together with my guests Duncan McGregor and Nicholas del Grosso we talk about what property based testing is and in particular go into one widely used implementation for Python - the Hypothesis library.
Here are a few links:
- https://increment.com/testing/in-praise-of-property-based-testing/ from David MacIver (creator of hypothesis) about the benefits of property based testing
- https://hypothesis.works/articles/what-is-property-based-testing/ explaining what property based testing is
- https://www.inspiredpython.com/course/testing-with-hypothesis/testing-your-python-code-with-hypothesis Testing your code with Hypothesis
- https://reiddraper.com/writing-simple-check/ Reid Draper (QuickCheck) on shrinking
- https://hackage.haskell.org/package/QuickCheck-1.0 the QuickCheck tool
- https://hypothesis.works/articles/how-many-tests/ How many tests is hypothesis running?
- https://hypothesis.works/articles/quickcheck-in-every-language/ property based testing in other languages (a bit outdated - it's from 2016)
- https://hypothesis.works/articles/integrated-shrinking/ David MacIver on how he implemented shrinking in Hypothesis
- https://hypothesis.works/articles/compositional-shrinking/ and more on shrinking
- https://jqwik.net the property based testing library for Java/Kotlin
- https://en.wikipedia.org/wiki/Functional_programming What is functional programming
- https://www.youtube.com/watch?v=xgDPvlgUSLE Duncan's YouTube episode on property based testing with jqwik (from his channel 'Refactoring to Kotlin')
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In this episode I talk about two different aspects of diversity in tech and in research software engineering in particular. First we hear from Jeremy Cohen, who has been running the DiveRSE seminar series since 2022 and is the co-author on a paper on the subject (link below). Then I talk to Michael McLeod, who is telling us about the role LGBTQ+ people play in tech.
Links
- https://diverse-rse.github.io the DiveRSE seminar series
- https://arxiv.org/abs/2104.01712 the paper Understanding Equity, Diversity and Inclusion Challenges Within the Research, 2021
- https://softwaresaved.github.io/international-survey-2018/ RSE International Survey from 2018
- https://zenodo.org/records/7015772 International RSE Survey 2022
- https://prideinstem.org Pride in STEM
- https://stemlgbtqyou.gay STEM and LGBTQ+ you
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How can we make computing environmentally more sustainable. Meet Loïc Lannelongue, who - together with Michael Inouye - created the Green Algorithms project. Amongst other things, it allows us to estimate the carbon footprint of our algorithms and computing jobs.
The project has been awarded the HDR UK Susannah Boddie Award for Impact of the Year in March 2024.
Links:
- https://www.green-algorithms.org the home page of Green Algorithms where you also find the link to their estimation tool
- https://github.com/GreenScheduler/cats the green task scheduler - an output from the Collaborations Workshop 2023
- https://www.hdruk.ac.uk/news/winners-announced-2024-hdr-uk-annual-prizes/ the HDR UK award page for 2024
- https://github.com/Llannelongue Loïc's GitHub
- https://www.lannelongue.eu his homepage
- https://www.inouyelab.org Michael Inouye his colleague
- https://greensoftware.foundation The Green Software Foundation
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Lecturers without Borders wants to bring scientists and school students together. It is an exciting project and for this episode I talked to Eugenia Covernton, who's leading the non-profit organisation.
So, if you are a travelling researcher or RSE, or even if you want to do it from the comfort of your home, LeWiBo give you an opportunity to share your work in schools.
https://www.lewibo.org
The web-site lists a number of partnering organisations like https://www.europlanet-society.org/european-planetary-science-congress/ .
You can also register your interest there directly.
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scikit-learn is a highly successful and popular Python library for data science and machine learning. It is open source and has a large contributor base.
I had the pleasure to meet with some of the scikit-learn team to talk about how they got involved and how it is possible to run an Open Source project of this size and scale.
If you like to get involved, here are a few links to their home page and GitHub repository.
- https://scikit-learn.org/stable/index.html scikit-learn homepage
- https://github.com/scikit-learn/scikit-learn GitHub repo
- https://blog.scikit-learn.org Blog post
Go to the community page of scikit-learn to get links to LinkedIn, Twitter and others
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In this episode I meet with Dr Emma Karoune and some of her colleagues from The Alan Turing Institute in London https://www.turing.ac.uk/ to talk about who and what skills we need to create and run modern data science teams. Emma is one of the awardees of the Skills and Policy award at the Turing.
- https://www.turing.ac.uk/skills-policy-awards-20232024 The Skills and Policy Award by The Alan Turing Institute
- https://iuk.ktn-uk.org/programme/bridgeai/ The UKRI Bridge AI programme
People interviewed in this episode
- Dr Emma Karoune, Senior Research Community Manager, Health & Tools, Practices & Systems https://www.turing.ac.uk/people/research-associates/emma-karoune
- Dr Aida Mehonic, TPS Senior Researcher - Research Applications. Research Application management webpage - Research Application Management | The Alan Turing Institute
- Vicky Hellon, Research Community Manager. Open Research Community Management Team - Open Research Community Management | The Alan Turing Institute
- Luis Santos, Senior Data Wrangler. Data for research Team - Data for Research (Data Wrangling) | The Alan Turing Institute
- Katriona Goldman and Jonathan Yong, Research Data Scientists. Research Engineering Group - Research Engineering Group | The Alan Turing Institute
Dr Emma Karoune's *work is supported by the Ecosystem Leadership Award under the EPSRC Grant EP/X03870X/1 and The Alan Turing Institute.
Turing data science case study will be published at: https://www.turing.ac.uk/research/research-projects/professionalising-traditional-and-infrastructure-research-roles-data*
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This ByteSized RSE episode talks about the Citation File Format (CFF) https://citation-file-format.github.io/ , created in 2017 to promote the inclusion of software in scientific papers. My guest is Jason Maassen from the eScience Center in the Netherlands.
For answers to the quiz questions, email: mailto:code4thought@proton.me
Background:
- Early scientific Journals: https://en.wikipedia.org/wiki/Journal_des_sçavans and https://en.wikipedia.org/wiki/Philosophical_Transactions_of_the_Royal_Society
- The "Garfield" Index (impact factors) original paper: https://garfield.library.upenn.edu/papers/science1955.pdf
- overview of impact factors: https://en.wikipedia.org/wiki/Impact_factor
CFF/Software Citations
- https://doi.org/10.7717/peerj-cs.86 the Force11 paper on principles of software citation
- https://www.software.ac.uk/publication/how-cite-and-describe-software a blog post from the Software Sustainability Institute
- https://citation-file-format.github.io/ The CFF project on GitHub
- https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files GitHub documentation on CFF
- https://zenodo.org/records/10650644 Stephan Druskat's paper on CFF
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Die diesjährige Konferenz des deRSE Vereins in Deutschland fand in Würzburg zwischen dem 5.März und 7.März statt.
Es gab, wie auch schon letztes Jahr viele interessante Schwerpunktthemen, wie z.B. Continuous Integration oder Teaching RSE.
In dieser Folge hört Ihr von verschiedenen TeilnehmerInnen der Konferenz:
- John Arnold RWTH Aachen - 3min06s
- Jan Küster Universität Bremen - 7min7s
- Uwe Schmitt und Franziska Oschmann - 15min12s
- Guido Juckeland - 21min30s
- Heidi Seibold - 27min38s
- Florian Goth und Jan Phillip Thiele - 33min10s
Ein paar Links
- https://events.hifis.net/event/994/overview die Homepage von der Konferenz, auf der Ihr alle Vorträge (mit Präsentationen) finden könnt
- Zum Thema Teaching
- https://github.com/DE-RSE/learn-and-teach die GitHub page
- https://arxiv.org/pdf/2311.11457.pdf das Paper zum Thema RSE Kompetenzen etc
- https://lists.uni-wuerzburg.de/mailman/listinfo/teachingrse die Mailing Liste
- https://digital-research.academy die Digital Research Academy
- https://rse.ethz.ch Die ETH Zürich RSE Gruppe
- https://westai.de WestAI der RWTH Aachen
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Yanina Saibene is well known in the R community and from her work e.g. in the Software Carpentries. In this episode we talk about what it takes to localise and translate training programs and indeed software applications and packages.
- https://yabellini.netlify.app/about/ a bit about Yanina from her home page
- https://carpentries.org/ the Carpentries home page
- https://rladies.org R Ladies
- https://latin-r.com Latin R
- https://ropensci.org rOpenSci
- https://fosstodon.org/@yabellini Yanina on Mastodon
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I had the pleasure of meeting with Janan Arslan in Paris in 2023. Janan has a fascinating career path that involved not only forensics but also various roles in AI in medicine, which is what she now does at the Brain Institute in Paris.
- https://www.inria.fr/fr/aramis The Aramis Lab in Paris
- https://melbourne-cshe.unimelb.edu.au/events/3mt/video-archive/2020-grand-final Janan has been a finalist in the 3 minute Thesis challenge
- https://www.researchgate.net/profile/Janan-Arslan Her profile on Research Gate
- https://www.webofscience.com/wos/author/record/2454976 Web of Science
- https://www.linkedin.com/in/janan-arslan/ LinkedIn profile
- https://twitter.com/JananArslan Twitter/X
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In this session we talk about the importance of user experience and user experience design.
My guest is Meag Doherty, who works for the National Institutes of Health in the USA and is a Fellow of the Software Sustainability Institute (SSI).
- https://www.software.ac.uk/fellowship-programme/meag-doherty Meag’s Fellow profile at the SSI. Check out the link to her contributions on the same page.
- https://www.youtube.com/watch?v=rmM0kRf8Dbk The YouTube page to the full clip from Donald Norman, the author of 'The Design of Everyday Things'
- https://designmuseum.org/discover-design/all-stories/what-is-good-design-a-quick-look-at-dieter-rams-ten-principles Dieter Rams, the influential industrial designer and his 10-point thesis on what makes a good design
- https://en.wikipedia.org/wiki/A_Pattern_Language The book by Christopher Alexander on design principles and the importance on finding a common (pattern) language
- https://www.uxdesigninstitute.com/blog/history-of-ux/ A bit of history on User Experience (UX)
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In dieser Folge hören wir Beiträge vom Vorstand des Vereins zur Forschungssoftwareentwicklung deRSE e.V., Anna-Lena Lamprecht und der RSE Arbeitsgruppe in der Gesellschaft für Informatik und Bernd Flemisch und Martin Hammitzsch über deren Arbeit im NFDI.
Denn, es tut sich so einiges im Bezug auf Forschungssoftware im deutschsprachigen Raum.
- Interview mit dem deRSE e.V. Vorstand 1'46"
- Interview mit Anna-Lena Lamprecht (Gesellschaft für Informatik) 22'12"
- Interview mit Bernd Flemisch und Martin Hammitzsch (NFDI) 39'23"
- https://fg-rse.gi.de Fachgruppe RSE in der Gesellschaft für Informatik
- https://www.nfdi.de/section-infra/ NFDI Common Infrastructure Sektionen - und da findet Ihr auch den Eintrag für RSE
- https://zenodo.org/records/6483449 Konzeptpapier der Arbeitsgruppe
- https://de-rse.org/de/ der deRSE e.V.
- https://events.hifis.net/event/994/overview die Konferenz Webseite für deRSE Konferenz in Würzburg 5. - 7. März 2024
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In this episode I talk to Chris Holdgraf, executive director of https://2i2c.org about what it takes to manage and run open source organisations.
Open source projects come with unique challenges (and opportunities) and I think Chris brings important insights from his experience at 2i2c.
Some links:
- https://chrisholdgraf.com Chris' home page
- https://press.stripe.com/working-in-public 'Working in Public' by Nadia Eghbal, mentioned in this episode
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People are talking about the "Reproducibility Crisis" in science. Good to see, that there are researchers that do something about it. Meet Rima-Maria Rahal and Peter Steinbach from the German Reprodicibility Network.
I met Rima and Peter in 2023 to talk about why reproducibility is important, what we as researchers can do to make our work more reproducible and what the network is doing in Germany
- https://reproducibilitynetwork.de The German Reproducibility Network homepage
- https://www.ukrn.org The UK Reproducibility Network
- https://reproducibilitynetwork.nl The network in the Netherlands
- https://www.ukrn.org/global-networks/ and a list of other networks around the globe (from the UK network site)
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If you want to co-host an episode on Code for Thought get in touch.
- per email on mailto:code4thought@proton.me
- RSE Slack channels in the UK (@code4thought or @piddie) or the US (@Peter Schmidt)
- Mastodon https://fosstodon.org/@code4thought
It's great fun, as my co-host Selina tells us in the short interview.
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With her online course 'Learning How to Learn' (and companion book 'A Mind for Numbers'), Barbara Oakley, distinguished professor in engineering, reached many of us who - like myself - wanted to improve the way we learn, adopt new technologies or get into complex subject areas.
Many researchers, PhD students, post-docs teach themselves how to program while trying to get their thesis or work done. But how do you go about it.
I hope this interview gives some food for thought on how to get better with learning (and teaching).
- https://barbaraoakley.com Barbara Oakley's homepage
- https://www.coursera.org/learn/learning-how-to-learn The course Learning How to Learn on Coursera
- https://blog.innerdrive.co.uk/interleaving-your-teaching Interleaving
- https://en.wikipedia.org/wiki/Pomodoro_Technique the Pomodoro Technique
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Softwareentwicklung, auch im Forschungsbereich ist immer noch eine Männerdomäne. Aber es gibt inzwischen viele Bestrebungen den Zugang zu Stellen und Berufsaussichten für Frauen und andere unterrepräsentierte Gruppen zu öffnen.
In dieser Folge hören wir von zwei Vertreterinnen: Bernadette Fritzsch vom Alfred Wegener Institut in Bremerhaven und Ruth Schöbel vom Forschungszentrum in Jülich.
- https://womeninhpc.org Women in HPC
- https://womeninhpc.org/membership/chapters-and-affiliates/chapters Chapters der Women in HPC da ist auch der Link zum FZ-J
- https://www.awi.de Alfred Wegener Institut für Polar- und Meeresforschung
- https://www.fz-juelich.de/de Forschungszentrum Jülich
Zum Schluss noch ein Hinweis auf die deRSE Konferenz in Würzburg vom 5.März bis zum 7.März: Anmeldeschluss ist der 1. Februar. Wie ihr dem Kurzinterview mit Florian Goth am Ende der Folge entnehmen könnt.
https://derse24.physik.uni-wuerzburg.de/
Diese Folge ist vom Forschungszentrum Jülich gefördert.
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It's time for a ByteSized RSE episode - and this time on the subject of 'easybuild' a tool to help you build and install software on high performance computers (HPC).
My guest to help me with presenting easybuild is Jörg Saßmannshausen from Imperial College in London, UK.
NOTE: this is an entry level discussion.
And there is a QUIZ as well. If you know the answer to the two following questions email them to code4thought@proton.me :
- What is the main reason to use a tool like EasyBuild rather than installing software manually?
- Why is reproducible software installation important?
And we have some links for you as well:
- https://easybuild.io easybuild homepage
- http://tutorial.easybuild.io tutorials for easybuild
- https://github.com/easybuilders/easybuild easybuild GitHub
- https://www.eessi.io European Environment for Scientific Software Installation (EESSI - pronounced "easy")
- https://www.eessi.io/docs/ the docs for EESSI
- https://github.com/spack Spack GitHub
- https://www.archer2.ac.uk/training/courses/200617-spack-easybuild/ a discussion on Spack and Easybuild by the Archer team
- https://github.com/hpc-uk HPC-UK
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My guest in this episode is Veronika Cheplygina, Associate Professor at the IT University of Copenhagen in Denmark.
We talk about machine learning and AI in medicine and Veronika brings a badly needed realism to the discussions. In the latter part of our conversation we also focus on the difficult and sometimes frustrating aspects of academic life.
I enjoyed my discussion with Veronika and I hope you will, too.
- https://veronikach.com Veronika's home page
- https://dasya.itu.dk The Data-Intensive Systems and Applications institute in Denmark DASYA
- https://purrlab.github.io Patterns Revisited Lab, part of DASYA
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Welcome back to a new season of Code for Thought. The subject of this episode is energy consumption in computing. My guests are Wim Vanderbauwhede (University of Glasgow, UK) and John Wernvik (Eco Datacentre, Sweden). This is a big subject area and there will be more on this later this season - so watch out.
Links:
- https://www.dcs.gla.ac.uk/~wim/ Wim's page at Uni Glasgow
- https://www.science.org/doi/10.1126/science.aam9744 There is room at the top - paper
- https://arxiv.org/abs/2303.06642 Wim's paper on Frugal computing
- https://wimvanderbauwhede.codeberg.page/articles/frugal-computing-developer/ developer perspective on frugal computing
- https://wimvanderbauwhede.codeberg.page/articles/frugal-computing-consumer/ consumer perspective
- https://wimvanderbauwhede.codeberg.page/articles/climate-cost-of-ai-revolution/ an article on the climate costs of AI
- https://en.wikipedia.org/wiki/Moore%27s_law Moore's "Law" summary
- https://en.wikipedia.org/wiki/Koomey%27s_law Koomey's "Law" summary
- https://en.wikipedia.org/wiki/Landauer%27s_principle Landauer's principle
- https://ecodatacenter.tech Eco Datacentre in Sweden - homepage
- https://www.datacenterdynamics.com/en/news/ai-data-centers-could-use-more-electricity-than-the-netherlands-by-2027/ John mentioned an article estimating the future energy used with increase of AI/ML
- https://www.sciencedirect.com/science/article/pii/S2542435123003653?dgcid=author another article on energy consumption and AI
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So, das ist jetzt die letzte Folge der 6. Serie von Code for Thought und diesmal geht es um Open Science. Mein Gesprächspartner ist Konrad Förstner von der TH Köln, den einige von Euch vielleicht vom Open Science Radio her kennen, das er mit Matthias Fromm schon seit längerer Zeit betreibt.
Euch Allen ein paar schöne und hoffentlich erholsame Tage. Ich mache eine kleine Pause und es geht dann im Januar 2024 mit der 7. Folge des Podcasts weiter.
Hier noch ein paar Links zu dieser Folge:
- https://konrad.foerstner.org Konrad's Webseite
- https://www.openscienceradio.org Open Science Radio - das Podcast
- https://sci-hub.st Sci-Hub
- https://royalsociety.org/about-us/history/ "Nullius in verbia" das Motto der Royal Society das Konrad anspricht. Will soviel heissen wie: traut nicht den Aussagen von anderen (und implizit - traut Euren Daten).
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In this last (English) episode of Season 6, I'll be talking to Sara Petti and Evgeny Karev from the Open Knowledge Foundation. Sara and Evgeny work on a project called Frictionless Data, which aims to make working with (open) data easier and more seamless.
Like many organisations around open source and open data they invite contributions from engineers.
Some links for the Open Knowledge Foundation and others mentioned in this episode:
- https://okfn.org Open Knowledge Foundation home page
- https://github.com/okfn GitHub of Open Knowledge Foundation
- https://frictionlessdata.io Homepage of the Frictionless Data project
- https://en.wikipedia.org/wiki/CKAN the CKAN project
- https://csvw.org CSV on the Web
- https://datadryad.org/stash Data Dryad
- https://zenodo.org Zenodo
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I met Ghislain Vaillant for our interview at the Brain Institute at the Pitié Salpetrière Hospital in Paris. Ghislain has an interesting career path that took him from an RSE role in the UK to the private sector and back to academia (in France) again.
Our conversation touches on differences in RSE roles between countries (e.g. UK/France) and how big events shape our careers.
Some links:
- https://institutducerveau-icm.org/en/ The Brain Institute
- https://institutducerveau-icm.org/en/team/team-colliot-durrleman/ The team Ghislain has been part of
- https://www.inria.fr/en/aramis The Aramis project
- https://www.linkedin.com/in/ghisvail/ Ghislain's LinkedIn profile
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In this episode of ByteSized RSE I talk about Django, a Python based web development framework that was developed in the mid 2000s.
My guests are Tom Couch from the University College London and Max Albert from Southampton University.
Links:
- https://www.djangoproject.com the entry point for Django with tutorials and references
- https://www.dj4e.com Django for you tutorial site
- https://www.feldroy.com/books/two-scoops-of-django-3-x the Book Two Scoops of Django by David Greenfeld
- https://pydanny.blogspot.com and here is his blog
- https://2024.djangocon.eu If you want to go to a Django conference - here is one...
- https://django-crispy-forms.readthedocs.io/en/latest/ Crispy forms in Django
- https://cookiecutter-django.readthedocs.io/en/latest/ Cookie Cutter Django
- https://medium.com/@devsumitg/how-to-connect-reactjs-django-framework-c5ba268cb8be an article how to connect ReactJS with Django
Trivia
- https://www.holovaty.com Adrian Holovaty gave Django the name - apart from an engineer he is also a talented musician
- https://www.quora.com/What-is-the-history-of-the-Django-web-framework-Why-has-it-been-described-as-developed-in-a-newsroom/answer/Simon-Willison an interview with Simon Willison on how Django got created
- https://simonwillison.net Simon is co-creator of Django
- https://web.archive.org/web/20140716123229/https://docs.djangoproject.com/en/dev/internals/committers/ a brief history of the first Django committers
- https://archive.org/details/django-reinhardt/107-django_reinhardt-djangos_blues.mp3 The MP3 file of the music played in the episode. 1947, Django Blues by Django Reinhardt
Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
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In the second part of the diversity in the RSE community series, I am talking to Mariann Hardey. Mariann is an associate professor at Advanced Research Computing of the University of Durham, UK. She also published a book called 'The Culture of Women in Tech' in 2020. In our conversation we don't only talk about the barriers women and other underrepresented groups in tech still face, but also what is and can be done about it.
This episode is sponsored by the Forschungszentrum Jülich in Germany (Research Centre Jülich) https://www.fz-juelich.de/en
- https://www.mariannhardey.com Mariann's home page
- The Culture of Women in Tech, Mariann Hardey, Emerald Publishing, 2020: ISBN 978-1-78973-426-3 (print), ISBN 978-1-78973-425-6 (Epub)
- https://arxiv.org/abs/2104.01712 Understanding Equity, Diversity and Inclusion Challenges within the Research Software Community, paper Neil Chue Hong, Jeremy Cohen and Caroline Jay
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Was alt und gebraucht ist muss nicht immer schlecht sein. So Markus Harrer von der Firma InnoQ. Markus erklärt uns wie man Legacy Software erhalten kann und warum "Boring Software" eigentlich ganz gut ist. Und wenn man schon erneuern muss, sollte man sich über die Vor- und Nachzüge im Klaren sein.
Markus zieht durch die Lande mit Vorträgen und Seminaren. Unten eine kleine Auswahl von Links.
- Markus Handle auf Mastodon und Twitter is @feststelltaste. Seine Webseite ist https://markusharrer.de
- https://tqdev.com/2018-the-boring-software-manifesto The Boring Software Manifesto - mit Links zum z.B. Agile Manifesto
- https://leanpub.com/strategische-spielzuege Ein Buch von Markus (im Entstehen)
- https://www.innoq.com/de/staff/markus-harrer/ Markus bei InnoQ
- https://www.feststelltaste.de/ Blog
- https://www.feststelltaste.de/top5-legacysystems/ Markus' Top 5 legacy Systeme
- https://github.com/feststelltaste/awesome-legacy-systems Ein Link zu guten Legacy Systemen
- https://softwareanalytics.de/ Eine Webseite zum Thema Software Analytics
- https://scholar.google.de/citations?user=OND5wuAAAAAJ Markus auf Google Scholar
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I met with Nathan Cassereau and Hatim Bourfoune from IDRIS, a national computing centre for the CNRS (the national research centre in France). Nathan and Hatim work on the Bloom project, an open source large language model, which was created using the Jean-Zay supercomputer.
Thanks to Nathan and Hatim I had the chance to take a look at the machine after our interview.
LLMs and AI/ML in general have created a lot of excitement. Hatim said he got into AI/ML himself, and he highlighted a Coursera course run by Andrew Ng.
Here are a few links:
- https://arxiv.org/abs/2211.05100 a paper on BLOOM on ArXiv
- https://github.com/ncassereau-idris/lm-evaluation-harness Evaluation of LM
- https://github.com/dptrsa-300/start_with_bloom Getting started with BLOOM on GitHub
- https://huggingface.co/bigscience/bloom Summary on BLOOM from Huggingface
- https://www.technologyreview.com/2022/07/12/1055817/inside-a-radical-new-project-to-democratize-ai/ a technology review on BLOOM by MIT
- https://towardsdatascience.com/run-bloom-the-largest-open-access-ai-model-on-your-desktop-computer-f48e1e2a9a32 another BLOOM article
- https://www.youtube.com/@CNRS-FIDLE YouTube channel by CNRS
- https://github.com/NVIDIA/Megatron-LM Megatron LM library used in the project
- https://github.com/microsoft/DeepSpeed DeepSpeed library used in the project
- https://pytorch.org PyTorch library
- https://www.genci.fr/en a national infrastructure to provide access to HPC (Grand Equipement National de Calcul Intensif) in France
- https://en.wikipedia.org/wiki/Jean_Zay brief summary of Jean Zay's life
- http://www.idris.fr/eng/jean-zay/jean-zay-presentation-eng.html The Jean Zay supercomputer at IDRIS/Paris-Saclay
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Finally! After a failed attempt in 2022, I managed to visit Simon Pinches and Olivier Hoenen at ITER this time. ITER is the international thermonuclear energy reactor - and its aim is to build a nuclear fusion reactor that produces a surplus of energy in a sustainable manner. And can be used as a blueprint for future power stations.
Simon and Olivier gave me the grand tour before we sat down and discussed their work. It was a truly impressive tour - in every way. No less impressive is the work that Simon and Olivier are doing on the software side to help put it all together.
Links
- https://www.iter.org the main portal for ITER.
- https://www.iter.org/mach more details about the ITER tokamak
- https://www.iter.org/jobs/IPA ITER project associates scheme - as mentioned in the interview
- https://ccfe.ukaea.uk/fusion-energy-record-demonstrates-powerplant-future/ the record breaking JET tokamak in Oxford, UK
- https://en.wikipedia.org/wiki/Tokamak a good Wikipedia summary of tokamaks
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Welcome back to Season 2 of ByteSized RSE, a program supported by Universe-HPC http://www.universe-hpc.ac.uk .
The subject for this session is: Software Estimation and some ideas on how to approach it.
Things mentioned in this episode:
- The Mythical Man Month, Frederick Brooks, 1975,
- Software Estimation, Steve McConnell, https://www.google.co.uk/books/edition/Software_Estimation/U5VCAwAAQBAJ?hl=en&gbpv=0
- https://rclayton.silvrback.com/software-estimation-is-a-losing-game a critical view on software estimation by Richard Clayton
- https://www.stepsize.com/blog/the-best-software-estimation-techniques an overview of some estimation techniques
- https://en.wikipedia.org/wiki/Planning_poker The Planning Poker
- https://en.wikipedia.org/wiki/Three-point_estimation 3-point estimation
Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/
ByteSized RSE link to Imperial College
Audio clips:
- Frying sound: https://www.fesliyanstudios.com/royalty-free-sound-effects-download/frying-cooking-food-34
- "Golden Girls" S6E15: one of the many YouTube videos with Bea Arthur's (aka Dorothy Zbornak) best lines.
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This episode takes us to Chicago, the host for the first ever conference of Research Software Engineering (RSE) in the US https://us-rse.org/usrse23/ . The conference was organised by the US RSE association https://us-rse.org and was sold out. In this report I'll talk to a number of participants, presenters and organisers.
In order of appearance:
- Mary Anne Leung Founder and President of the Sustainable Horizon's Institute https://shinstitute.org
- Joseph Tuccillo from Oak Ridge National Laboratory https://www.ornl.gov
- Geoffrey Lentner from Purdue University https://www.purdue.edu
- Leah Wasser founder and director of pyOpenSci https://www.pyopensci.org
- Daniel S. Katz US RSE association co-founder and board member https://danielskatz.org
- Ian Cosden US RSE association co-founder and board member https://researchcomputing.princeton.edu/about/people-directory/ian-cosden
- Sandra Gesing executive director http://sandra-gesing.com of the US RSE assoc. and Julia Damerow, member of the steering committee
Other links
- https://www.software.ac.uk Software Sustainability Institute, its director Neil Chue Hong gave the second keynote at the conference
- https://data.agu.org/notebooks-now/ Notebooks Now! initiative by the American Geophysical Union (AGU) https://www.agu.org
- Music excerpts from the Chris Green Quartet, Chicago Jazz Festival 2016 - with kind permission https://chrisgreenequartet.bandcamp.com
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Die Nationale Forschungsdateninfrastruktur - NFDI - hat die grosse Aufgabe Forschungsprojekte, deren Daten und Anwendungen miteinander zu vernetzen. Der Verein wird geleitet von Prof. Dr. York Sure-Vetter, mit dem ich über die Aufgaben und Herausforderungen des NFDI spreche.
Links
- https://www.nfdi.de/ Das Hauptportal des NFDI
- https://www.nfdi.de/cordi-2023 Die erste Konferenz - CoRDI 2023 - ausgetragen im September 2023
- Auf Mastodon: @NFDI@nfdi.social
- https://twitter.com/NFDI_de Auf Twitter (Verzeihung X) gibt es sie auch
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My guests for this episode are Marie Piraud and Peter Steinbach from the Helmholtz Association in Germany. Helmholtz is the largest research association in Germany and has created a unit around all things AI and machine learning recently. Marie and Peter talk about their contributions and how AI/ML can help in research and science.
Links
- https://www.helmholtz.ai Helmholtz AI
- https://www.helmholtz-munich.de/en/computational-health-center Helmholtz Centre in Munich (Marie)
- https://www.hzdr.de/ Helmholtz Centre Dresden-Rossendorf (Peter)
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In this first episode on the theme of diversity in tech I talk to Cristin Merritt and Elsa Gonsiorowski from Women in HPC.
The aim is to raise awareness and give a voice and visibility to women and other underrepresented groups in high performance computing, as Cristin and Elsa explain during our conversation.
Links:
- https://womeninhpc.org The main website for Women in HPC
- https://n8cir.org.uk/news/diversity-checklist/ A proposed checklist for recruitment re diversity and inclusion from N8 (UK)
- https://sc23.supercomputing.org Women in HPC will be at SC23 the supercomputing conference in Denver/US in Nov '23
- Follow Women in HPC on
- https://twitter.com/women_in_hpc
- https://www.linkedin.com/company/women-in-hpc/
- Women in HPC have a jobs board on
- https://womeninhpc.org/community/jobs
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In dieser Sonderausgabe berichte ich von der Unkonferenz des deutschen RSE Vereins, die zwischen dem 26. und 28. September in Jena stattfand.
Ca 60 Teilnehmer*innen trafen sich, um über Themen zu diskutieren, die sie in ihrem Alltag bewegen. Im Rahmen dieser Veranstaltung traf ich mich mit mehreren Organisatoren und Teilnehmern um über ihre Eindrücke und Beiträge zu sprechen.
- https://un-derse23.sciencesconf.org Der link zur Veranstaltung
- https://theconversation.com/re-designing-the-conference-46894 Ein Artikel aus dem Jahr 2015 zum Thema Unkonferenz (Englisch)
- https://link.springer.com/book/10.1007/978-3-319-05155-0 Das Buch das in der Folge erwähnt wurde: Agile the good, the hype and the ugly von Bertrand Meyer.
- https://project.software-metadata.pub/index.html Helmholtz Hermes Projekt
- https://the-turing-way.netlify.app/index.html The Turing Way - vom Alan Turing Institut in London, UK
- https://www.dfg.de Webseite der deutschen Forschungsgemeinschaft
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In this second report on research software archives and directories I am talking to Jason Maassen from the eScience Centre in the Netherlands and Christian Meessen from the Helmholtz Association in Germany.
The eScience Centre developed the Research Software Directory (RSD) to show the impact software has on research. Researchers who code can register their software with the directory from all over the work.
Helmholtz has adopted the RSD platform to produce a Helmholtz specific version and use that to monitor and track development from within the various research centres within Helmholtz.
Here some links:
- https://research-software-directory.org/ The portal to the RSD from the eScience Centre in NL
- https://www.esciencecenter.nl The eScience Centre
- https://helmholtz.software The RSD Helmholtz site
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The HiddenRef https://hidden-ref.org in the UK is an initiative to push for considering a wider range of research outputs than publications, e.g. software and data. The members of the initiative organised an event on 21 September 2023 to bring together academic institutions, funders and publishers. The aim is to increase the amount of non-publication output for the next research assessment in the UK in 2028.
- https://hidden-ref.org/festival-of-hidden-ref/ The HiddenREF festival page
In this episode I spoke to a number of participants and presenters. In order of appearance;
- James Baker, director of digital humanities at Southampton University
- Steven Hill, director of research at Research England
- Guillaume Wright, publisher at https://f1000.com F1000
- Tony Roche HiddenRef committee member and director at https://www.emeraldgrouppublishing.com Emerald publishing
- Emma Karoume, community manager at the https://www.turing.ac.uk Alan Turing Institute in London
- Simon Hettrick, chair of the https://hidden-ref.org HiddenRef and deputy directory of the Software Sustainability Institute https://www.software.ac.uk
This episode is sponsored by F1000.
F1000, part of Taylor & Francis Group, is an scholarly open research publisher offering a unique publication model designed to ensure all research outputs are as accessible, usable and reusable as possible, thus accelerating the impact of that research. F1000 works in partnership with many research funders, institutions and societies across the globe, including the European Commission, Wellcome, the Bill & Melinda Gates Foundation and the American Nuclear Society, to develop bespoke publishing solutions to help them to achieve their open research ambitions. F1000 also has its own portfolio of open research publishing venues available to researchers from across all disciplines who wish to publish all research outputs openly, including F1000Research, Routledge Open Research, Open Research Africa and Health Open Research. Find out more at https://f1000.com.
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Julian arbeitet an der Universität Swansea in Wales in Grossbritannien. Zusammen mit Kollegen bemüht er sich darum, Ergebnisse von Simulationen und Berechnungen reproduzierbar zu machen. Erstaunlicherweise, sind wenige der Papers und Ergebnisse auch heute noch reproduzierbar und Julian und das Team bemühen sich darum das zu ändern.
In unserem Gespräch geht es auch ein wenig um den Physik Zusammenhang - der sogenannten Quantenchromodynamik (QCD).
Dazu ein paar Einführungslinks
- https://de.wikipedia.org/wiki/Quantenchromodynamik Quantenchromodynamik (QCD)
- https://de.wikipedia.org/wiki/Gittereichtheorie Gittereichtheorie
- https://de.wikipedia.org/wiki/Quantenfeldtheorie Quantenfeldtheorie
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And it's this time of the year again, when the RSE communities meet for their annual gathering. The UK RSE Society held its annual conference in the Welsh city of Swansea this year. And in this episode you'll hear from a range of different participants and presenters. Here they are in the following order
- Jamie Quinn (University College London and trustee of the Society until this year) https://www.ucl.ac.uk/advanced-research-computing/advanced-research-computing-centre
- Gael Varoquaux from Inria and Scikit-learn in France https://scikit-learn.org/stable/
- Neil Chue Hong from the Software Sustainability Institute https://www.software.ac.uk
- Sarah Gibson from https://2i2c.org
- Hannah Williams from the UK Health Security Agency https://ukhsa.blog.gov.uk
- Rich Pitts from Oracle Research https://www.oracle.com/uk/research/
- Milo Thurnston from https://fairsharing.org
- Becky Smith from the organising committee https://rsecon23.society-rse.org/conference-committee/
Presentations have been streamed and should be accessible soon.
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I had the great pleasure to meet with Morane Gruenpeter and Benoît Chauvet from Software Heritage in Paris in 2023. Software Heritage aims to help preserve and archive software, not only for research but also for the private sector.
Unlike research software directories (from whom we will hear later this season), Software Heritage archives the actual code. Morane and Benoit take us through what's involved in that.
Links:
- https://www.softwareheritage.org/ the main Software Heritage portal
- https://archive.softwareheritage.org/ Link to the actual archive
- https://archive.softwareheritage.org/save/ Save code now feature
- https://archive.softwareheritage.org/add-forge/request/create/ Add forge now feature
- https://www.softwareheritage.org/2023/08/08/swh-technical-roadmap-priorities/ Presentation of the 2023 technical roadmap
- https://archive.softwareheritage.org/?guided_tour=0&guided_tour_next=https://archive.softwareheritage.org/add-forge/request/create/ Interactive guided tour
- https://www.softwareheritage.org/howto-archive-and-reference-your-code/ How to archive and reference Research Software
- https://docs.softwareheritage.org/ Documentation
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Despite the fact that Fortran has been around since the 1950s, it remains a very relevant programming language today and has an active community of keen engineers. In this episode I'll take a sweep from the origins of Fortran, how to deal with legacy (Fortran 77), how the language evolved to modern day use cases of Fortran. In the course of the episode you'll hear from Thomas Clune (NASA, US), Wim Vanderbauwhede (Uni. Glasgow, UK), Milan Curcic (Uni. of Miami, US) and Ondrej Certik (GSI Technologies, US).
- Fortran-lang website: https://fortran-lang.org
- Fortran-lang GitHub: https://github.com/fortran-lang
- LFortran website: https://lfortran.org
- LFortran GitHub: https://github.com/lfortran/lfortran
- Milan's book: https://www.manning.com/books/modern-fortran
- Neural-Fortran: https://github.com/modern-fortran/neural-fortran
- FastGPT: https://github.com/certik/fastgpt
- US Fortran Standard Committee: https://j3-fortran.org/
- Ondrej's website: https://ondrejcertik.com/
- Milan's website: https://milancurcic.com/
- Tom Clune's site at NASA: https://sciences.gsfc.nasa.gov/sed/bio/thomas.l.clune
- Wim Vanderbauwhede's site at Uni Glasgow https://www.dcs.gla.ac.uk/~wim/
- pFUnit testing framework https://github.com/Goddard-Fortran-Ecosystem/pFUnit
- gFTL template library: https://software.nasa.gov/software/GSC-17742-1
- Wim's paper (Journal of Supercomputing 2021): Making legacy Fortran code type safe through automated program transformation https://link.springer.com/article/10.1007/s11227-021-03839-9
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Let me interrupt your well-earned summer break for a brief episode and teaser: the first ever US RSE conference will be upon us between 16-18 October in Chicago, USA.
I met with Sandra Gesing from the organising committee to talk about how the preparations are going and what you can expect from the conference.
- https://us-rse.org/usrse23/ - here the official US RSE Conference web-site
- http://sandra-gesing.com Sandra's web-site
- https://twitter.com/us_rse US RSE Twitter (yes, I won't call it X)
- https://fosstodon.org/@us_rse US_RSE in Mastodonia
Talking of conferences. There is a lot happening this autumn, including
- the UK RSE Conference in Swansea 5-8 Sep https://rsecon23.society-rse.org
- the Hidden Ref Festival in Bristol 21 Sep https://hidden-ref.org/festival-of-hidden-ref/
- the German RSE Un-conference in Jena 26-28 Sep https://un-derse23.sciencesconf.org
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Dr Uwe Konrad von der Helmholtz Forschungsgemeinschaft stellt den neuen Preis für Softwareentwicklung vor. Obwohl der Preis im Moment nur für Helmholtzprojekte (oder solche mit hauptsächlicher Beteiligung von Helmholtz) zur Verfügung steht, hofft Dr Konrad dass der Preis Schule macht. Denn schliesslich wird es endlich Zeit, dass Software (und deren EntwicklerInnen) ernst genommen wird und als gleichwertiger Beitrag von Forschungsprojekten anerkannt wird.
Die Frist für Bewerbungen ist der 30. September. Die einzelnen Helmholtzinstitute haben interne Fristen auf die im Gespräch nochmal hingewiesen wird.
Der Link für den Preis ist hier
- https://os.helmholtz.de/en/newsroom/news/article/helmholtz-incubator-software-award/
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Peter Steinbach leitet eine Gruppe von Consultants am Helmholtz Institut in Dresden-Rossendorf. Die Gruppe ist Teil der Helmholtz AI Initiative und beratet WissenschafterInnen bzgl KI, Machine Learning usw.
Neben Fragen über KI in der Wissenschaft hat mich auch interessiert wie Datenwissenschaft mit Software Entwicklung zusammenhängt. Schliesslich sind mehr und mehr Research Software Engineers mit KI und ML Themen beschäftigt.
Links:
- https://www.helmholtz.ai Helmholtz AI Home Page
- mailto:consultant-helmholtz.ai@hzdr.de die Kontaktadresse für Helmholtz AI
- https://twitter.com/helmholtz_ai Helmholtz AI auf Twitter (oder X wie es sich jetzt nennt)
- https://fosstodon.org/@helmholtz@helmholtz.social Mastodon Konto von Helmholtz
- https://twitter.com/psteinb_ Peter Steinbach´s Twitter Konto
- https://fosstodon.org/@psteinb_@beta.birdsite.live Peter´s Mastodon Konto
Konferenzen im Herbst 2023
- https://rsecon23.society-rse.org UK RSE Conference in Swansea, UK, 5-8 September with satellite events
- https://hidden-ref.org/festival-of-hidden-ref/ Hidden Ref Festival in Bristol, UK, 21 September
- https://un-derse23.sciencesconf.org German Unconference in Jena, Germany, 26-28 September
- https://us-rse.org/usrse23/ First ever US RSE Conference in Chicago, USA, 16-18 October
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The guest for this episode is Teresa Gomez-Diaz from Université Paris Gustav-Eiffel, east of Paris, France. For a long time Teresa has been promoting Open Science and last year she talked on this show about the need for licences in research software.
Teresa and her collaborator, Tomas Recio from the University Antonio de Nebrija, Madrid published two papers about Research Data and how to ensure they adhere to Open Science and in particular FAIR principles.
We start with a discussion of the so-called Borgman conundrum, or why it is hard to share research data before going into what we can do about it.
A couple of clarifying notes: Teresa speaks of F mille, which refers to F1000. Also, when "users" of research data are being mentioned, it refers to authors and contributors.
Links:
- https://f1000research.com/articles/11-118/v2 Research Software vs. Research Data I: Towards a Research Data definition in the Open Science context
- https://f1000research.com/articles/11-117/v2 Research Software vs. Research Data II: Protocols for Research Data dissemination and evaluation in the Open Science context - introduces CDUR protocol
- Borgman's Conundrum
- https://onlinelibrary.wiley.com/doi/abs/10.1002/asi.22634
- https://www.researchgate.net/publication/228295710_The_Conundrum_of_Sharing_Research_Data
- https://coara.eu Coalition for Advancing Research Assessment
Upcoming conferences:
- https://rsecon23.society-rse.org UK RSE Conference in Swansea, UK, 5-8 September with satellite events
- https://hidden-ref.org/festival-of-hidden-ref/ Hidden Ref Festival in Bristol, UK, 21 September
- https://un-derse23.sciencesconf.org German Unconference in Jena, Germany, 26-28 September
- https://us-rse.org/usrse23/ First ever US RSE Conference in Chicago, USA, 16-18 October
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Nick Radcliffe, data scientist and entrepreneur, talks to us about the importance of test your data. As software engineers we are familiar with test driven development. Test driven data analysis puts the same emphasis on validating and testing data for your AI app. We also dive into the Python library of the same name tdda.
Links:
- https://linkedin.com/in/njradcliffe LinkedIn profile Nick Radcliffe
- http://www.tdda.info Test Driven Data Analysis Blog
- https://tdda.readthedocs.io/en/latest/ tdda library documentation
- https://github.com/tdda/tdda TDDA GitHub repo
- https://smartdatafoundry.com/ Smart Data Foundry
- https://stochasticsolutions.com Stochastic Solutions - also contains links to papers and publications by Nick Radcliffe
Other libraries mentioned:
- https://www.evidentlyai.com Evidently AI
- https://greatexpectations.io Great Expectations
Don't forget the upcoming RSE conferences and the Hidden Ref event
- https://rsecon23.society-rse.org UK RSE Conference in Swansea 5-8 September 2023
- https://hidden-ref.org/festival-of-hidden-ref/ The Hidden Ref Festival, Bristol 21 September
- https://un-derse23.sciencesconf.org deRSE Unconference in Jena, Germany, 26 - 28 September
- https://us-rse.org/usrse23/ US RSE Conference in Chicago, USA, 16-18 October
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With Sam Mangham and Ed Bennett from the Uk RSE Conference organising committee.
In this episode I want to take a look behind the scenes and find out what it takes to organise and run a conference. And how we participants can contribute to the success of this UK RSE Conference and future events!
The conference takes place on the campus of Swansea University, UK and runs from 5-7 September. There are satellite events on Monday 4 Sep and Friday 8 Sep.
The main link for the conference is below.
https://rsecon23.society-rse.org
Note: the committee negotiated accommodation with Swansea Uni. The deadline for getting a room there is end of July 2023. Details can be found here
https://rsecon23.society-rse.org/about-swansea/#accommodation
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Fredo Erxleben vom Helmholtz Institut in Dresden erzählt uns, wie er und seine KollegInnen WissenschaftlerInnen, DoktorantInnen und Postdocs Programmieren beibringt. Der Bedarf an Training ist riesig. Der Bedarf an Ausbildern auch.
In dieser Folge schauen wir ein wenig hinter die Kulissen und Fredo erzählt welche Herausforderungen es bei den Trainingsprogrammen gibt.
Hier ein paar links:
- https://hifis.net HIFIS Platform (Helmholtz Federated IT Services)
- https://hifis.net/services/overall/learning-materials Lehrmaterialien
- https://www.helmholtz-hida.de/en/ HIDA (Helmholtz Information and Data Science Academy)
- https://www.helmholtz-hida.de/course-catalog/en/ HIDA Kurskatalog (beinhaltet auch die Kurse von Fredo)
- https://software-carpentry.org/ Software Carpentries
- https://www.gather.town/ Gathertown - die App die Fredo und das Team in den online Kursen benutzen
- https://www.helmholtz.de/en/research/challenges/information-data-science/helmholtz-incubator/ Helmholtz Inkubator
- https://hifis.net/services/software/consulting.html Helmholtz Consulting
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JupyterCon 2023, the conference on all things Jupyter was held in Paris between 10-12 May 2023, followed by 2 days of hands-on "sprints".
Jupyter is a very popular open source platform with tools such as Jupyter notebook/lab and driven by a very active community. There were a number of excellent talks from a range of different subjects. I had the pleasure to meet and talk to a number of people, see the interview list below.
Order of Interviews:
- Leah Silen and Arliss Collins from Numfocus 02:04
- Franklin Koch (MyST) from Curvenote 04:59
- Nicolas Thiery (Paris-Saclay) 09:13
- Sarah Gibson (2i2c) 13:19
- Ana Ruvolcaba (Jupyter executive council) 18:57
- Fernando Perez (Jupyter executive council) 23:48
- Raniere de Silva (Gesis) 29:56
Links:
- https://jupyter.org Jupyter project
- https://jupyter.org/enhancement-proposals/79-notebook-v7/notebook-v7.html# Release notes for the new Jupyter Notebook v7
- https://jupyterlab.readthedocs.io/en/latest/getting_started/changelog.html#v4-0 Release notes for JupyterLab v4.0 (further incremental updates of v4 are available)
- https://www.youtube.com/@JupyterCon YouTube channel for JupyterCon 2023
- https://cfp.jupytercon.com/2023/schedule/ JupyterCon 2023 schedule
- https://www.outreachy.org Outreachy project
- https://numfocus.org Numfocus project
- https://data.agu.org/notebooks-now/ Notebooks Now initiative
- https://myst-tools.org MyST tool for scientific and technical communication
Upcoming RSE conferences:
- https://rsecon23.society-rse.org UK RSE conference in Swansea 5-8 Sep 2023
- https://hidden-ref.org/festival-of-hidden-ref/ Hidden Ref in Bristol, UK, 21 Sep 2023
- https://un-derse23.sciencesconf.org Unconference of the German RSE society deRSE in Jena 26-28 Sep
- https://us-rse.org/usrse23/ 1st face to face US RSE Conference in Chicago 16-18 Oct 2023
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And in this last episode of our first ByteSized RSE season, we talk about the README file. My guest in this episode is Julian Lenz from the University in Swansea, UK who will take us through the importance of READMEs, what should go into them and at what stage should you create one (spoiler alert: a.s.a.p.).
Here are a few links you might find useful.
Example READMEs and templates
- https://github.com/matiassingers/awesome-readme a list of example READMEs
- https://dev.to/documatic/awesome-readme-examples-for-writing-better-readmes-3eh3 a guide for writing better READMEs
- https://github.com/matiassingers/awesome-readme#articles more articles on how to write READMEs
- https://github.com/othneildrew/Best-README-Template templates for READMEs
- https://github.com/Louis3797/awesome-readme-template another README template
Background
- https://www.gnu.org/prep/standards/ GNU Coding standards. READMEs are mentioned in chapter 7.3
- https://medium.com/@NSomar/readme-md-history-and-components-a365aff07f10 a history of READMEs
- https://daringfireball.net/projects/markdown/ the MARKDOWN format
Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/
ByteSized RSE link to Imperial College
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This episode is about Quantum Computing and trying to look behind the hype around it. Helping me with that is Oliver Brown from the Edinburgh Parallel Computer Centre (EPCC), where he leads a quantum applications group.
There is plenty of material on the subject out there. Here are some links, also mentioned in the episode:
- Quantum Computation and Quantum Information
Textbook by Isaac Chuang and Michael Nielsen
ISBN: 978-1-107-00217-3 - https://qiskit.org An open source toolkit and resource for Quantum Computing including tutorials etc
- https://learn.qiskit.org/course/ch-algorithms/quantum-fourier-transform Quantum Fourier Transform
- https://en.wikipedia.org/wiki/Quantum_logic_gate Gates in Quantum Computing
- https://en.wikipedia.org/wiki/Transmission_gate "Classical" gates
- https://en.wikipedia.org/wiki/Phase_qubit Qubits and phases
- https://en.wikipedia.org/wiki/No-cloning_theorem The no-cloning theorem
- Shor's algorithm
- https://quantum-computing.ibm.com/composer/docs/iqx/guide/shors-algorithm an article on Shor's algorithm by IBM
- https://en.wikipedia.org/wiki/Shor%27s_algorithm summary of Shor's algorithm
- https://en.wikipedia.org/wiki/Variational_quantum_eigensolver Variational Eigensolver in quantum computing
- https://ai.googleblog.com/2022/06/quantum-advantage-in-learning-from.html Quantum advantage
- https://arxiv.org/abs/2111.05176 a paper on the subject
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Mit Kristine Schima-Voigt und Kay Liewald von der Niedersächsischen Staats- und Universitätsbibliothek in Göttingen.
In dieser Folge berichten Kristine und Kay von ihren Erfahrungen über die Einführung von Agilen Software Methoden, insbesondere Scrum, in ihrem Bereich der Softwareentwicklung. Agile Methoden wie Scrum, Kanban und andere finden eine immer weitere Verbreitung. Um so wichtiger ist es von praktizierenden Gruppen wie dem Team aus Göttingen zu hören. Und zum Abschluss geben Kay und Kristine Tipps für die Einführung von Scrum.
Links:
- https://zenodo.org/record/7727988 Kristine's Vortrag bei der deRSE Konferenz 2023 über RSE an der Bibliothek in Göttingen
- https://zenodo.org/record/7715041 Kay's Vortrag bei der deRSE Konferenz 2023 über Scrum
- https://www.sub.uni-goettingen.de/kontakt/abteilungen-a-z/abteilungs-und-gruppendetails/abteilunggruppe/software-und-service-entwicklung/ Die Webseite für die RSE Arbeitsgruppe in Göttingen
- https://lab.sub.uni-goettingen.de Der Blog von der RSE Arbeitsgruppe
- https://www.agile-bibliothek.org Eine Gemeinschafts-webseite für Agile Softwaremethoden in Bibliotheken
- https://www.liberatingstructures.com Eine Zusammenfassung der Liberating Structures
- http://agilemanifesto.org Das Agile Manifesto (in Englisch)
- https://scrumguides.org Hinweise für Scrum (in Englisch)
Und dann gibt es noch die "Klassiker", d.h. Bücher, über Scrum von Jeff Sutherland und Ken Schwaber.
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Research Software Engineering is a global movement. In this episode, I had the pleasure of talking to Saranjeet Kaur and Jyoti Boghal from India, how they built the RSE Asia network from scratch. In this conversation they take us through the journey of building a RSE community.
Here are some links:
- https://rse-asia.github.io/RSE_Asia/ The homepage for RSE Asia
- https://twitter.com/RSE_Asia Twitter RSE_Asia
- https://github.com/rse-asia RSE GitHub
- https://openlifesci.org Open Life Sciences network
- https://www.rladies.org R Ladies
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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 patterns and features such as stash and cherrypick.
Here are a few links:
- https://git-scm.com a great resource of documentation including GIT references and a book you can freely download
- https://git.kernel.org/pub/scm/git/git.git/ the repo for GIT itself. Try and find the first release 0.99 from 2005 by Linus Torvalds!
- https://www.gesis.org/en/institute the Gesis Institute
Linus wrote that about the name of GIT in the README of version 0.99:
"git" can mean anything, depending on your mood.
- random three-letter combination that is pronounceable, and not actually used by any common UNIX command. The fact that it is a mispronunciation of "get" may or may not be relevant.
- stupid. contemptible and despicable. simple. Take your pick from the dictionary of slang.
- "global information tracker": you're in a good mood, and it actually works for you. Angels sing, and a light suddenly fills the room.
- "goddamn idiotic truckload of sht": when it breaks*
Enjoy working with GIT
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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 conversation we discuss his thesis and questions such as: is RSE actually a distinct role/discipline and what the future might hold.
Talking of conferences:
- UK RSE Conference https://rsecon23.society-rse.org Swansea, UK, between 5-6 September 2023.
- NOTE: submissions of abstract deadline extended to 3 May 2023!
- Keydates: https://rsecon23.society-rse.org/key-dates/
- US RSE Conference (the first!) https://us-rse.org/usrse23/ Chicago, IL, USA, 16-18 October 2023
- deRSE Unconference https://un-derse23.sciencesconf.org/index Jena, Germany, 26-28 September 2023.
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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 gespielte Partitur zu verändern.
Lynn von Kurnatowksi von der DLR erzählt uns in dieser 2. deutschsprachigen Folge wie das ganze Experiment zwischen Kunst, Wissenschaft und Software Engineering verlaufen ist.
Links:
- https://wiki.theater.digital/projects:theunansweredquestion:start Projektbeschreibung
- https://vimeo.com/712835935 Video auf Vimeo
- https://www.dlr.de/sc/en/desktopdefault.aspx/tabid-1192/1635_read-34048/sortby-lastname/ Lynn von Kurnatowski von der DLR
- https://twitter.com/LYNX_V Twitter Konto
- https://www.martinhennecke.com Martin Hennecke's Webseite
- https://theater.digital Akademie für Theater und Digitalität
- https://www.mdc-berlin.de Das Max Selbrück Zentrum in Berlin (Aufnahme der MRI Daten des Schauspielers)
- https://www.helmholtz-hida.de/en/hida-news/when-data-becomes-sound
- https://www.dlr.de/content/en/institutes/institute-for-software-technology.html DLR Institute for Software Technology
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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 declaration that came out of it.
Links:
- https://future-of-research-software.org the workshop page
- https://zenodo.org/record/7330542#.ZCHG7C8w3uc the draft declaration
- https://www.researchsoft.org ReSA the research software alliance
- https://www.esciencecenter.nl/ the eScience Centre in the Netherlands
- https://www.esciencecenter.nl/news/global-support-for-funding-sustainable-research-software-in-amsterdam/ the workshop
Other links mentioned
- https://eosc-portal.eu European Open Science Cloud
- https://wellcome.org Wellcome Trust
- https://chanzuckerberg.com The Chan-Zuckerberg Initiative
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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 (Mac only for now).
Here a links to some editors etc.:
- https://code.visualstudio.com Visual Studio Code by Microsoft - also used in the interactive ByteSized RSE sessions
- https://github.com/microsoft/vscode VSCode GitHub
- https://www.youtube.com/watch?v=W--_EOzdTHk example of how to set up VSCode for Python
- https://analyticsindiamag.com/is-microsofts-vs-code-really-open-source/ is VSCode open source?
- https://www.jetbrains.com/pycharm/ PyCharm - there is a free Community edition
- https://neovim.io Neovim - a Vim based IDE
- https://www.pydev.org PyDev as part of the Eclipse IDE
- https://github.com/spyder-ide/spyder Spyder
- https://zed.dev - seems a new kid on the block (beta version), for now it's Mac only
Some older stuff
- https://www.gnu.org/software/emacs/download.html - good ol' Emacs
- https://github.com/jorgenschaefer/elpy Python for Emacs
Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/
ByteSized RSE link to Imperial College
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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 programs, but here are the links for those mentioned in the panel discussion:
- https://software-carpentry.org Software Carpentry
- https://coderefinery.org Code Refinery
- http://www.hpc-carpentry.org HPC Carpentry
- https://excalibur.ac.uk/projects/universe-hpc/ UK Universe-HPC programme
- https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/ ByteSized RSE programme (and this podcast) as part of Universe-HPC
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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 Einblick geben was so an den Konferenztagen passiert ist, inklusive Interviews mit einigen der TeilnehmerInnen und VeranstalterInnen.
- https://zenodo.org/communities/derse23/ die Vortrags PDFs gibts hier
- https://de-rse23.sciencesconf.org Konferenz Homepage
- https://de-rse.org/de/index.html Homepage des deRSE Vereins
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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 podcast show, which is being published as a separate episode.
- https://zenodo.org/communities/derse23 papers for the conference can be found here
- https://de-rse23.sciencesconf.org the conference home page for deRSE23
- https://de-rse.org/de/index.html the home page for the German RSE association
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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.html
- black https://black.readthedocs.io/en/stable/index.html
- pre-commit https://pre-commit.com
- pre-commit hooks https://pre-commit.com/hooks.html
Other links you may find interesting and have been mentioned in the episode
- PEP8 https://peps.python.org/pep-0008/
- Google Python Style Guide https://google.github.io/styleguide/pyguide.html
- YAML file format https://yaml.org
- Stephen C. Johnson's paper on lint https://web.archive.org/web/20220123141016/https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.56.1841&rep=rep1&type=pdf
- Definition of spaghetti code (yes there is one) https://en.wikipedia.org/wiki/Spaghetti_code
Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/
ByteSized RSE link to Imperial College
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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, London, UK) who signed up for the pilot project as mentor and mentee, to find out how it all went for them.
Here is the link to the Pilot program.
https://society-rse.org/events/pilot-mentoring-programme/
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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 can view the presentations following the links on the conference website
https://www.fosdem.org/2023/
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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 has become of it and where (we hope) it will go.
Here a few links you might look up:
- https://www.budapestopenaccessinitiative.org The site of the Budapest Open Access Initiative - which includes the declaration
- https://en.wikipedia.org/wiki/Jean-Claude_Guédon Jean-Claude's bio on Wikipedia
- https://www.frontiersin.org/articles/10.3389/frma.2018.00008/full a history on the Garfield scientific indexing
- https://www.michaeleisen.org/blog/?p=1580 Michael Eisen another co-author of the Budapest declaration. This article is from 2014 where he talks about why he forsake open access
- https://en.wikipedia.org/wiki/Stevan_Hanard Stevan Hanard is another signatory of the Budapest declaration
- A History of Scientific Journals: publishing at the Royal Society 1665 - 2015, UCL Press A Fyfe, N Moxham, J McDougall-Waters, C Moerk Roestvik, 2022
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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 as well as the code review pyramid links.
After a brief introduction to the topic, I will be talking to Sarah Gibson from 2i2c. Sarah and I talked about JupyterHub in an episode last year. In this episode she talks about how important Continuous Integration and Deployment are in her daily work
Tools (not an exhaustive list - there is more):
- https://github.com/features/actions GitHub actions.
- https://about.gitlab.com/features/continuous-integration/ CI with GitLab
- https://www.jenkins.io/ Jenkins
- https://www.travis-ci.com/ Travis
Blogs and other links:
- https://martinfowler.com/articles/continuousIntegration.html Martin Fowler's blog on Continuous Integration
- https://www.morling.dev/blog/the-code-review-pyramid/ Code Review Pyramid by Gunnar Morling
- https://github.com/sgibson91 - Sarah Gibson's web-site
- https://2i2c.org/ International Interactive Computing Collaboration, the company helping you built your Jupyter Hub infrastructure.
Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/ ByteSized RSE link to Imperial College
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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 software engineers to train people up in computing in the future.
Here a few links, mentioned in the episode:
- https://nicolas.thiery.name/ Nicolas' homepage
- https://nicolas.thiery.name/CandyceProposal/ the proposal for Candyce (in French)
- https://www.maplesoft.com/ Maple products
- https://quantstack.net/ Quantstack cloud solutions provider
Thank you for listening and your ongoing support. It means the world to us!
You can also support our efforts by leaving a rating or review.
Follow or contact us on
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This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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 extra.
- https://docs.python.org/3/library/unittest.html the built in unit testing framework of Python
- https://docs.python.org/3/library/unittest.mock.html mock testing in the unittest framework
- https://docs.python.org/3/library/unittest.html#class-and-module-fixtures fixtures for classes and modules
- https://docs.pytest.org/en/7.2.x/ the popular PyTest framework
- Mocking can be done with monkeypatch in PyTest https://docs.pytest.org/en/7.1.x/how-to/monkeypatch.html#
- Fixtures in PyTest: https://docs.pytest.org/en/7.2.x/reference/fixtures.html
Books mentioned
- Working effectively with legacy code, Michael Feathers, ISBN: 9780131177055, Pearson's, 2004
- Refactoring: Improving the Design of Existing Code, Martin Fowler, ISBN: 9780134757681, 2nd edition, Addison-Wesley Professional
Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/ ByteSized RSE link to Imperial College
Thank you for listening and your ongoing support. It means the world to us!
You can also support our efforts by leaving a rating or review.
Follow or contact us on
- Email mailto:code4thought@proton.me
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This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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 assay in his studies. SMURF, as it turns flies blue as they near their end.
Michael is also very passionate about Open Science, and he is quoting Jon Tennant, who once said: 'Open Science is just Good Science'.
Links:
- https://www.sciencedirect.com/science/article/pii/S0092867413006454 The Hallmarks of ageing by Carlos Lopez-Otin - 2013
- https://crowdid.hypotheses.org/548 A transcript of Jon Tennant's talk on Open Science
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812435/ How to catch a SMURF, Michael Rera et al. 2018
Michael can be found on Mastodon at
@Michael__Rera@drosophila.social
Thank you for listening and your ongoing support. It means the world to us!
You can also support our efforts by leaving a rating or review.
Follow or contact us on
- Email mailto:code4thought@proton.me
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- LinkedIn: https://www.linkedin.com/in/pweschmidt/
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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 how he manages to bring and keep it all together.
Here a few links
- https://www.iter.org ITER
- https://www.euro-fusion.org/ European Fusion Consortium
- https://conferences.iaea.org/event/251/contributions/20713/attachments/11191/16492/IMAS%20Tutorial%20-%20Pinches.pdf Introduction to the Integrated Modelling & Analysis Suite (IMAS)
- https://indico.euro-fusion.org/event/1246/sessions/728/attachments/1988/3798/IMAS_introduction_ACH_20210920.pdf The IMAS Data Dictionary: an introduction
- https://www.sciencedirect.com/science/article/abs/pii/S0010465597001070 IMAS Integrated Modeling and Analysis System for the solution of optimal control problems
- https://ui.adsabs.harvard.edu/abs/2020APS..DPPJ10009M/abstract
OMAS: A Python Library to Interface with the ITER Integrated Modeling and Analysis Suite (IMAS) - https://arxiv.org/abs/2006.09198 The initial step towards JOREK integration in IMAS
Thank you for listening. You can find us on Twitter @Code_4_Thought, on Slack (RSE) and lately on Mastodon as @code4thought (fosstodon.org server)
For the music cognoscenti amongst you: the music is taken from Gymnopedie No 1 by Eric Satie and covered by the licence mentioned below.
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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.
Thank you for listening. You can find us on Twitter @Code_4_Thought, on Slack (RSE) and lately on Mastodon as @code4thought (fosstodon.org server)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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.
Thank you for listening. You can find us on Twitter @Code_4_Thought, on Slack (RSE) and lately on Mastodon as @code4thought (fosstodon.org server)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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.
Thank you for listening. You can find us on Twitter @Code_4_Thought, on Slack (RSE) and lately on Mastodon as @code4thought (fosstodon.org server)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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 mechanism of 'pull requests' to start a conversation and review with your colleagues.
In my conversation with Thibault Lestang from Imperial, we discuss what to look out for when doing a code review with your colleagues. And the fact that reviews are still useful, even if you are not using Github.
Links
- https://ieeexplore.ieee.org/document/5388086 Michael Fagan's paper on code inspections
- https://git-scm.com/ The GIT versioning system book. Has a chapter on branching
- https://github.com/features/code-review GitHub pages on code reviews
Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
Thank you for listening. You can find us on Twitter @Code_4_Thought, on Slack (RSE) and lately on Mastodon as @code4thought (fosstodon.org server)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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://academic.oup.com/gigascience/article/8/6/giz076/5523201 Journal article on open humans platform
Thank you for listening. You can find us on Twitter @Code_4_Thought, on Slack (RSE) and lately on Mastodon as @code4thought (fosstodon.org server)
This podcast is licensed under the Creative Commons Licence: https://creativecommons.org/licenses/by-sa/4.0/
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 your event project and closing down. The guide can be tailored to your needs, giving hints and tips on varied subjects such as venue, catering, budget, agenda, publicity and more.
- Read the Event Organisation Guide on Read the Docs.
- If you’d like to raise any issues, offer suggestions or get involved, you can use the GitHub project associated with the guide.
- Read how SSI Communications Manager Selina Aragon used the guide to plan the first Research Software Camp in this blog post and find out more about our upcoming Research Software Camp on supporting mental health in research.
- Read Shoaib’s blog post on Behind the scenes: SSI Event Organisation Guide which explores the how and why of the guide.
- Find out more about Collaborations Workshop 2023 (CW23).
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 at info@software.ac.uk.
This first episode of “Code for Thought Bye-sized” 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 UNIVERS-HPC project.
Disclaimer: The presenters and content producers for this podcast are not lawyers and do not have any legal background. The material in this podcast is not legal advice and must not be considered as such. There may be errors and we accept no responsibility or liability for actions you take based on this material. The podcast is intended to provide some high-level general background on open source software licensing and to raise awareness of the area. The content is based on our understanding and experience as research software engineers but this may not be correct in all cases. If you have questions or are unsure about any legal aspects relating to licensing of software that you are making available to others, talk to a legal professional.
Some useful links
- GNU General Public License v3.0: https://www.gnu.org/licenses/gpl-3.0.en.html
- BSD-3-Clause Licence: https://opensource.org/licenses/BSD-3-Clause
- MIT Licence: https://opensource.org/licenses/MIT
- The Unilicense: https://unlicense.org/
- Creative Commons License: https://creativecommons.org/
- Links to specific Creative Commons Licenses:
- CC-BY:https://creativecommons.org/licenses/by/4.0/
- CC-BY-SA: https://creativecommons.org/licenses/by-sa/4.0/
- CC-BY-NC: https://creativecommons.org/licenses/by-nc/4.0/
- CC0: https://creativecommons.org/publicdomain/zero/1.0/
- Full details on Creative Commons licenses can be found at https://creativecommons.org/about/cclicenses/
- GitHub information on licensing a repository (GitHub documentation): https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/licensing-a-repository
- Adding a licence to a GitHub repository (GitHub documentation): https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-license-to-a-repository
- The Software Sustainability Institute guide to choosing an open source licence: https://software.ac.uk/resources/guides/choosing-open-source-licence
- UNIVERS-HPC project: https://excalibur.ac.uk/projects/universe-hpc/
After 3 years, the RSE Conference returned to an in-person event, this time held at the Frederick Douglas Centre in Newcastle, UK.
Apart from meeting people that I only met online so far, it was also the first RSE conference for me personally and the first time I recorded with a live audience.
The subject of the event was: RSE the next 10 years. Now that we passed the 10th anniversary of the birth of research software engineering as we know - what will the next 10 years bring.
With me on the panel were
- Idil Ozdemir (University College London)
- Simon Hettrick (Software Sustainability Institute)
- Jennifer Richards (University of Newcastle)
- Anika Cawthorn (University College London)
-
Michael James (EPSRC - UKRI)
-
https://rsecon2022.society-rse.org RSE Conference 2022 site with links to the program
- https://www.software.ac.uk Software Sustainability Institute
- https://society-rse.org Society for Research Software Engineering in the UK
For this episode I am very excited to talk to Ben Goldacre. Ben has an outstanding career in medicine, science and science communication and is the author of many articles and books, like e.g. "Bad Science". Today is he running the Bennett Institute for Applied Data Science in Oxford, UK.
I met with Ben Goldacre earlier this year (2022) to discuss his report on 'Better, Broader, Safer: Using Health Data for Research and Analysis'. This report, published in April 2022 and commissioned by the UK government, is based on more than 300 individual interviews and many more with key stakeholder groups.
One of the key findings and recommendations is the need for proper software engineering. Needless to say that RSEs play an important part in this.
In fact, Ben has been a strong supporter and promoter for Research Software Engineering as well as open science and software.
Here a few links
- https://www.phc.ox.ac.uk/team/ben-goldacre Ben Goldacre's web-site
- https://twitter.com/bengoldacre Ben on Twitter
- https://www.gov.uk/government/publications/better-broader-safer-using-health-data-for-research-and-analysis - 'Better, Broader, Safer: Using Health Data for Research and Analysis' report, April 2022
- https://www.bennett.ox.ac.uk Bennett Institute
Licence: https://creativecommons.org/licenses/by-sa/4.0/
2022 Software Sustainability Institute (SSI) Fellow Sophia Batchelor speaks to SSI Communications Officer Jacalyn Laird about her Fellowship plans.
Find out more about the Turing Way and their online Collaboration Cafe.
Follow Sophia on Twitter: https://twitter.com/brainonsilicon
Welcome back to another season of Code for Thought. And I'd like to kick it off with an interview with Bastien Guerry. Working for the French government, Bastien promotes the use, creation and distribution of Free Software. And in our conversation we discuss the four freedoms as defined by the Free Software Foundation.
Bastien is also an active member of the Emacs community and a contributor to one of the modes: Org mode - a note taking facility. Having used Emacs for a long time it's good to see that it is alive and well.
- https://bzg.fr/en/libreplanet2022-notes/ Bastien's blog and intro
- https://www.fsf.org The Free Software Foundation
- https://www.gnu.org/licenses/gpl-3.0.en.html GPL licence
- https://fosdem.org/2022/schedule/event/open_research_french_ecosystem/ Bastien's presentation on open software at FOSDEM early 2022
- https://www.gnu.org/software/emacs/ - YES, it's EMACS
- https://orgmode.org Emac's Org mode for note taking etc
Licence: https://creativecommons.org/licenses/by-sa/4.0/
The way that the Research Excellence Framework (REF) exercise is conducted overlooks many of the people who are vital to the success of research. In this episode we hear from Gemma Derrick, part of the organising committee for the Hidden REF, which recognises all research outputs and every role that makes research possible.
Publications rarely name all of the people who make research possible, yet these were the basis for 97% of the outputs submitted to REF 2014. This is not the fault of the REF itself: the guidelines allow submission into a wide range of categories, from software to musical compositions. But with so much funding reliant on the results, universities are highly risk-averse in what they will submit. Publications are well understood in academia, so they are almost the only output submitted to REF – and this means the work of many people goes unrecognised. The goal of the Hidden REF is to celebrate all research outputs and the people who make them possible.
Visit the Hidden REF website: https://hidden-ref.org/.
Open Science is a broad term. While in Paris in 2022 I had the pleasure of meeting Teresa Gomez-Diaz from the Université Gustave Eiffel for my very first face to face interview. In it we discuss what the term Open Science entails and how free/open software fit into it.
For some years, Teresa Gomez-Diaz has been working with others to arrive at a common understanding of the term. Together with her collaborators they provided a definition that rests on three pillars: Open Access (publication), Free/Open Software, Open Data.
As for research software, Teresa stresses the importance of software licensing. And in the course we touch on different strategies how that can be accomplished with GNU GPL licence (strong copyleft) and other Free/Open Source Software licences.
Here are some references for this episode, with papers by Teresa Gomez-Diaz and co-authors. The Twitter link below is with respect to the "mushroom" of Open Science we discuss during the episode.
- https://f1000research.com/articles/8-1353/v2 On the evaluation of research software: the CDUR procedure
- https://zenodo.org/record/4577066#.Ys0lfi8w1k4 Towards an Open Science definition as a political and legal framework: on the sharing and dissemination of research outputs
- https://zenodo.org/record/6433533#.Ys0l4C8w1k4 The future of Open Science asks for a common understanding
- https://twitter.com/evamen/status/844158610225664000
- http://igm.univ-mlv.fr/~teresa/logicielsLIGM/documents/CoursLL/2022avril_RS_UGE_TGD.pdf course material (in French) for the course on research software (including licences,
Open Science definition etc.) by Teresa Gomez-Diaz
The Unesco recommendation on Open Science can be found on
- https://unesdoc.unesco.org/ark:/48223/pf0000379949
A definition of 'copyleft'
- https://www.gnu.org/licenses/copyleft.en.html
Licence: https://creativecommons.org/licenses/by-sa/4.0/
2022 Software Sustainability Institute (SSI) Fellow Jesper Dramsch speaks to SSI Communications Officer Jacalyn Laird about their fellowship plans and experience of applying.
Jesper's SSI Application video: https://www.youtube.com/watch?v=wxMZxbui4Bg
Newsletter: https://dramsch.net/newsletter
Linkedin: https://dramsch.net/linkedin
Twitter: https://dramsch.net/twitter
Espanso text-expander: https://espanso.org/
Tweet your comments or questions @SoftwareSaved using #CodeForThought!
Meet Isla Myers-Smith from the University of Edinburgh, who describes herself as a global change ecologist. Her work focuses on tundra ecosystems.
To measure changes in plants - shrubs in this case - the team collects data on the ground as well as from drones and satellite data. That involves quite a lot of effort and requires technical skills. Skills that Uni courses in ecology (and other fields) typically don't prepare you for.
Being largely self-taught, Isla made it her mission to help other early career researchers ramp up skills they will need in their future career.
Today, Isla is a Software Sustainability Institute Fellow and she and her colleagues manage a drone network called HiLDEN.
Here are a few links:
- https://www.software.ac.uk/about/fellows/isla-myers-smith A SSI blog post about Isla's work
- https://arcticdrones.org the HiLDEN network site
- https://teamshrub.com/lab-blog/ the lab website
Follow Isla and Team Shrubs on Twitter
- https://twitter.com/IslaHMS Isla's Twitter
- https://twitter.com/TeamShrub Team Shrub's Twitter
Licence: https://creativecommons.org/licenses/by-sa/4.0/
Over the past year or two nuclear fusion made its way into the headlines not least in early 2022, when researchers at the JET (Joint European Torus) experiment reported a breakthrough in terms of generating energy.
Finding new and sustainable energy sources is more important than ever. And what better way than to harness energy like our very own sun does.
Enter Dr Adam Stephen, director of innovation at the UK Atomic Energy Authority’s lab in Culham. Adam and his team and collaborators are working hard to overcome the engineering challenges and help make nuclear fusion a safe and sustainable way of producing energy. Amongst the work they do are building and designing real time systems and in my conversation we talk about some of the challenges they face.
Links to follow up on the conversation
- https://ccfe.ukaea.uk UK Atomic Energy Authority Fusion site
- https://ccfe.ukaea.uk/research/mast-upgrade/ UKAEA Mast: plasma exhaust system
- https://rt.wiki.kernel.org/index.php/ real time Linux
- https://vcis.f4e.europa.eu/marte2-docs/master/html/ MARTe2 documentation
- https://github.com/aneto0/MARTe2 MARTe2 GitHub repo
- https://en.wikipedia.org/wiki/Digital_twin Digital twin technology
Selection of general announcements from 2022
- https://www.theguardian.com/environment/2022/feb/09/nuclear-fusion-heat-record-a-huge-step-in-quest-for-new-energy-source Guardian UK on breakthrough in JET experiment Feb 2022
- https://www.whitehouse.gov/ostp/news-updates/2022/03/15/fact-sheet-developing-a-bold-vision-for-commercial-fusion-energy/ White House (US) summit on nuclear fusion announcement
Jupyter is a well known tool in the education and research sector (and in the private sector, too). Jupiter can also be used in a collaborative environment, be that for teaching purposes or work within a research/product team. With Jupyter Hubs, you can run Jupyter in a variety of different environments and cloud services.
Meet Dr Sarah Gibson, who works at the International Interactive Computing Collaboration - or 2i2c for short. She is also involved in the myBinder project as well as being a Fellow at the Software Sustainability Institute.
At 2i2c, Sarah and her team help design, develop and manage Jupyter Hubs, so that researchers, developers and teachers can focus on their projects.
Sarah takes us through the challenges of managing open source projects and the benefits of Jupyter Hubs.
- https://2i2c.org/author/sarah-gibson/
- https://2i2c.org
- https://mybinder.org
2022 Software Sustainability Institute (SSI) Fellows James Byrne and Tom Russell speak to SSI Communications Officer Jacalyn Laird about their fellowship plans.
Find out more about James' work at the British Antarctic Survey (BAS) Artificial Intelligence Group and see the BAS blog.
Find out more about Tom's work on the Colouring Cities GitHub.
Tweet your comments or questions @SoftwareSaved using #CodeForThought!
The Victoria and Albert Museum in London is the museum for art and design. It spans nearly 5000 years of human history and has well over 1 million objects.
The Victoria and Albert museum was also one of the first to be accessible on the internet. Which is, why it gives me great pleasure to talk to Kati Price who leads the digital media and publishing team at the V&A.
The V&A catalogue is accessed not only by the occasional visitors, hobbyists but also by scientists and researchers. Keeping the digital estate up to date and compelling for users is a challenge and Kati Price takes us through how she and her team approach this in their work.
Think of "user centred".
If you have a chance to check out the vast offerings of the V&A check out the links below.
The V&A also has APIs and GitHub repos which people can access.
Having said this, I would encourage you to go and visit the V&A in person if you can.
- https://www.vam.ac.uk The V&A main site
- https://developers.vam.ac.uk/guide/v2/welcome.html Site for developers
- https://www.vam.ac.uk/blog/ V&A Blogs
- https://github.com/vanda V&A GitHub repo
- https://iiif.io International Image Interoperability website.
Meet Software Sustainability Institute (SSI) 2022 Fellow Connah Kendrick as he tells SSI Communications Officer Jacalyn Laird about his plans for his fellowship relating to digitising museum artefacts.
You can contact Connah by email Connah.kendrick@mmu.ac.uk and follow him on Twitter @connahkendrick.
Tweet your comments or questions @SoftwareSaved using #CodeForThought!
(Apologies for the audio quality issues at the beginning).
Meet James Baker, newly appointed director of Digital Humanities at the University of Southampton in the UK. Digital Humanities covers a wide area of different disciplines and James has his work cut out for him to help and bring it all together.
By creating "collaborative spaces" we can bring experts together from different disciplines. An opportunity to innovate and create. But facilitating this is hard and in our conversation we touch on some of the challenges.
- http://digitalhumanities.soton.ac.uk The Digital Humanities at the University of Southampton, UK
- https://twitter.com/sotonDH Follow Digital Humanities tweets
- https://twitter.com/j_w_baker James Baker on Twitter
The term research software engineering is celebrating its 10th anniversary today. It was coined during a Collaborations workshop on 21 March 2012. I was privileged to meet with 7 of the participants who took part in this workshop and together we talk how it all came about.
My guests are:
- Neil Chue Hong MPhys FBCS, Director, Software Sustainability Institute and Senior
- Prof. Simon Hettrick, Deputy Director, The Software Sustainability Institute
- Robert Haines, Head of Research IT, Uni Manchester
- Dirk Gorissen, Product Manager
- Rob Baxter, Director of Data Services, EPCC, University of Edinburgh
- Ilian Todorov, STFC UKRI
- James Hetherington FBCS, Director, Advanced Research Computing Centre, University College London
But it's not just walking down memory lane. Even though, RSEs are now found in a number of research centres and universities across different countries, there is still lots to do. The challenges ahead range from creating attractive and sustainable career paths, securing funding, improving on diversity and others.
- https://software.ac.uk/cw22 Collaborations workshop of the Software Sustainability Institute in the UK for 2022 (April)
- https://software.ac.uk The Software Sustainability Institute UK
- https://society-rse.org The Society for Research Software Engineering in the UK
And finally, after 2 years of pandemic, it is great to see the announcement for an in-person RSE conference again. And this year, it will be in Newcastle, UK.
- https://rsecon2022.society-rse.org
Yo Yehudi, Executive Director at Open Life Science, joins Selina Aragon, Software Sustainability Institute Communications Lead and host of the series, as the first guest of Software Horror Stories.
Yo talks through one of the scariest moments of her life as an RSE, how she fixed it, and her tips to overcome your very own horror stories.
Based on the Coding Confessions project, Software Horror Stories shares people’s unintended oversights when coding and how this impacted their research. The aim is to help normalise mistakes and emphasise how they’re a necessary evil of the learning journey in developing software for research. Look out for new episodes each month!
Tweet your comments or questions @SoftwareSaved using #CodeForThought!
Would you like to share your very own horror story? Get in touch at s.aragon@software.ac.uk
Agile software development practices and methodologies have been around for a while and have indeed become mainstream. In particular Scrum and its many variants. In this episode I talk to Raj Heda, who helps organisations roll out agile methodologies. I was interested to find out, why "Agile" has become so successful, and what it is organisations need to look out for when they roll it out.
I also wrote a brief blog post on Medium on the subject: https://medium.com/@pweschmidt/is-agile-still-agile-a13b20230bc
There is plenty of material on agile methodologies out there. But here are a few pointers, some of which were also mentioned in the interview
- Agile Manifesto https://agilemanifesto.org
- Scrum https://www.scrum.org
- Scaled Agile Framework (SAFe) https://www.scaledagileframework.com
- Kanban https://kanbanize.com/kanban-resources/getting-started/what-is-kanban
- What is Lean? https://theleanway.net/what-is-lean
- Toyota Just in Time manufacturing https://www.rcbi.org/updates/lean-manufacturing-made-toyota-the-success-story-it-is-today/
- John Kotter: 8 steps to lead change https://www.kotterinc.com/8-step-process-for-leading-change/
- Simon Sinek: empathy and perspective https://github.com/dwyl/leadership/issues/4
- Business Agility Institute: https://businessagility.institute
- Digital AI (publisher of the State of Agile annual survey): https://digital.ai (go to Resources in the nav bar and select State of Agile)
Code for Thought is one year old! (Did I hear anyone say - Hurrah?)
Time to think what we can do for you in the coming weeks, months and beyond. In this short trailer, Selina and Jacalyn from the Software Sustainability Institute (SSI) https://www.software.ac.uk
and I talk about some of the new content that will be heading your way.
In future we will be ca 10min episodes as well as longer ones, the latter ca every 3 weeks:
- meet the new/existing SSI fellows
- hear some truly gruesome horror stories (albeit about software)
- get some news
- and also get more in depth and longer interviews and coverages
If you have a story you would like to share, or you want to contribute and host an episode, do not hesitate to get in touch with one of us
Selina s.aragon@epcc.ed.ac.uk
Jacalyn J.Laird@epcc.ed.ac.uk
Peter peter.schmidt@ucl.ac.uk
In this episode we take a trip into the exciting world of insects - mantises to be precise. Prof Jenny Read and her colleague Dr Vivek Nityananda from Newcastle University in the UK have been conducting some exciting research into 3D vision of these iconic animals.
I have come across their research through an article in the New York Times and was hooked.
3D vision in insects? Yes, dear listeners, you read that right. Mantises have stereoscopic vision as well but not quite like humans.
Given the fact that mantises are so much smaller and still capable of 3D vision - is there something we can learn from them with regards to practical applications and robotics?
Here some links you might want to check out:
- https://www.nytimes.com/2017/09/22/science/praying-mantis-eating-birds.html the New York Times article
- http://www.jennyreadresearch.com/research/m3/media/ some cool videos including how we can trace what's going on in a mantis brain
- https://pubmed.ncbi.nlm.nih.gov/26740144/ the paper of the research
Welcome to Season 3 of Code for Thought!
In this episode, I met with 7 of the new EPSRC fellows in the UK. EPSRC stands for Engineering and Physical Sciences Research Council. The EPSRC fellowship has been pivotal in putting research software engineering (RSE) firmly on the map in universities and research centres. RSE has become a recognised role not only in the UK, but also in an increasing number of countries around the globe.
I had the pleasure and privilege to meet with some of the new fellows last autumn.
As you will hear from my discussion with Eilis, Heather, Carlin, Tom, Jamie, Peter and Ed - they bring a lot of interesting and different hopes, ideas and aspirations to their fellowship.
- https://www.ukri.org/councils/epsrc/
Mental health in the workplace is often ignored or sidelined. Not to mention that it is difficult to talk about it in the first place.
And yet, pressures in our work environment has been rising, not least because of the pandemic. How we can look out for ourselves and others is a question I'll be discussing with Graham McCartney and Dave Horsfall. Dave and Graham are leading the UK charity Jonathan's Voice, which was born under tragic circumstances.
As Graham says in the podcast: if you have difficulties in coping, don't struggle alone. Reach out!
Your employer may provide services such as mental health aiders or services provided by your HR department.
In addition to that most if not all countries provide helplines and advice on mental health. In the UK e.g. there are the
- Samaritans https://www.samaritans.org
- Mind https://www.mind.org.uk
Here are a few links you might find useful
- https://jonathansvoice.org.uk Jonathan's Voice Charity - speaking out for mental health
- https://mhfaengland.org Mental Health First Aiders England
- https://www.gov.uk/government/publications/thriving-at-work-a-review-of-mental-health-and-employers Thriving at Work: UK government's Stevenson Farmer report from 2017 on Mental Health
- https://medium.com/newcastle-university-research-software-engineering/mental-health-for-research-software-engineers-in-academia-2a5f0274f16e Dave's article on mental health in Academia in Medium
- https://www.mentimeter.com MentiMeter a tool to gauge how your audience, team etc are doing
Reproducibility efforts are community efforts, as this episode's guest Grigori Fursin makes very clear. But you also need the tools.
For some time, Grigori worked on the Collective Knowledge (CK) Framework to help researchers and machine learning practitioners get the best out of their solutions.
In this episode we talk about the challenges you face when trying to evaluate machine learning applications and taking them to production. And how tools like CK Framework and others can help.
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https://cknowledge.org - Collective Knowledge (CK) Framework web site
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https://mlcommons.org/en/ - ML Commons, a non-profit organisation & community for tools around machine learning applications: in particular ML Perf for performance testing
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https://github.com/mlcommons/ck - CK framework GitHub repository
Four researchers, from various career stages and research areas, took their first steps into coding in R and Python throughout September and October 2021, as part of the Learning to Code mentorship programme. The programme was an initiative brought by the Software Sustainability Institute's (SSI) Research Software Camp: Beyond the Spreadsheet.
In this episode, we (Selina Aragon, SSI Communications Lead, and Jacalyn Laird, SSI Communications Officer) spoke to the four researchers who volunteered to take part in the mentorship programme. Emma, Amirah, Yenn and Rebecca talk us through their experience over the last two months, what they learnt, and how having a mentor impacted on their journey. Listen as they share their reasons to join the programme and the tips they have for other beginner coders.
As part of the Research Software Camp, we've signposted to resources for people learning to code. It's likely that we'll be running this mentorship programme again, so if you're interested, sign up to receive updates.
About Research Software Camps
The Software Sustainability Institute runs free online Research Software Camps twice a year over the course of two weeks. Each Camp focusses on introducing and exploring a topic around research software, thus starting discussions among various research communities.
Our latest Research Software Camp: Beyond the Spreadsheet took place from 1 to 12 November 2021.
This episode is all about music and the role software and technologies such as AI and machine learning play in creative processes.
Meet Emily Howard, David De Roure and Chris Melen from the Centre for Practice & Research in Science and Music (PRiSM) at the Royal Northern College of Music. They talk about how they use AI in their creative processes.
One of the key tools the team has developed and uses for experimenting and composing music is an open source tool called PRiSM SampleRNN - and you will be able to listen to some of the audio samples.
Occasionally, you hear concerns about AI replacing humans - or in this case - composers and performers. But that's not the case as David, Emily and Chris reassure us. Rather, it is a new tool that can enhance and augment our creativity.
And furthermore:
“If society is going to have AI so pervasively embedded then we really have to understand what it means to be a creative human being in the context of AI”
Links
- https://github.com/rncm-prism/prism-samplernn PRiSM SampleRNN open Source
- https://www.rncm.ac.uk/research/research-centres-rncm/prism/ PRiSM main web site
- https://www.rncm.ac.uk/whats-on/events/ Events at the Royal Northern College of Music/PRiSM
- https://www.turing.ac.uk/research/interest-groups/ai-arts The Alan Turing Institute AI & Arts Special Interest Group
Sometime in early 2021 there was a bit of excitement on the Research Software Engineering Slack channel. It was all about a blog post called: "Research Software code is likely to remain a tangled mess". The author, Derek Jones, is quite critical of what we are doing with software in research. I accept that not everybody is a fan of Research Software Engineering and I reached out to Derek, who kindly agreed to talk to me for this episode.
In our discussion we touch on a number of subjects, from sustainability, best practices to testing.
Links:
http://shape-of-code.coding-guidelines.com/2021/02/21/research-software-code-is-likely-to-remain-a-tangled-mess/
Derek's book on Evidence Based Software Engineering
http://www.knosof.co.uk/ESEUR/
Leprechauns of Software Engineering (mentioned in the discussion)
https://leanpub.com/leprechauns
Graph Theory has been around for a long time. Its use in computing has found a number of applications, most prominently social networks. In this episode I will be talking with Ben Steer and Gabor Szarnyas about their experiences in working with graphs. In particular: how to assess the performance of graphs, their use in science and research, the state of graph query languages and more.
Here are a few links you might find useful:
- https://www.routledgehandbooks.com/doi/10.1201/b16132-3 Handbook of Graphs, a nice overview.
- https://arxiv.org/abs/2012.06171 The Future is Big Graphs! An overview of graph processing systems - for which Gabor is co-author
- https://github.com/GraphBLAS/LAGraph LAGraph is a draft library plus a test harness for collecting algorithms that use the GraphBLAS
- https://www.tigergraph.com Tiger Graph database
- https://neo4j.com Neo4j a popular graph DB
- https://opencypher.org Open Cypher - the open source graph query language
- http://ldbcouncil.org Linked DB Benchmark Council
- https://graphblas.github.io GraphBLAS
- https://szarnyasg.github.io/posts/graph-query-languages/ Gabor's post on graph query languages
- https://raphtory.github.io Raphtory, a temporal graph tool developed by Ben and others
Here is the final SeptembRSE special episode. And this time I'll be talking to Apeksha, James and Natalia from Amazon Web Services (AWS). We touch on a variety of subjects: e.g. how to come to grips with the ever increasing complexity of what cloud services like AWS offer today (hint: start simple & experiment). Natalia talks about her internship with AWS and I like James' soundbite, likening the role of RSEs to the 'Colossus of Rhodes'.
Meet Brad Tipp from Microsoft. Brad thinks that research software engineering has a crucial role to close the ever growing skills gap. The gap between demand for more research and research results and the ever increasing technical landscape that helps make it happen. This is not just a question of using cloud services but also a question of changing the mindset in training the next generation of scientists and facilitating roles that keep up with the technological landscape.
This year's annual conference on Research Software Engineering (see link below) is upon us at the moment. And this year, SeptembRSE is running online only.
On this occasion, Code for Thought is throwing some light on some of the sponsors of the SeptembRSE, without whom none of this would happen. In the first of these extra episode I have the pleasure of talking to Richard Pitts, Alison Derbenwick Miller and Kevin Jorissen. Alison, Kevin and Richard are at Oracle for Research and they talk us through the work they do and how this links to research software engineering.
-
SeptembRSE: https://septembrse.github.io/#/timetable/all
-
Oracle for Research: https://www.oracle.com/oracle-for-research/
-
Oracle Blog posts: https://blogs.oracle.com/documents
-
Open Nebula: https://opennebula.io
Welcome back to Season 2 of Code for Thought!
Reproducibility is hard and no one knows this better than Heidi Seibold. In this episode Heidi and I talk about the new reproducibility network she helped building in Germany and the many challenges we all face when trying to reproduce scientific output and papers.
Find the German reproducibility network on
https://reproducibilitynetwork.de
Or find them on Twitter
https://twitter.com/germanrepro
Have you thought about turning your PhD and research into a business? You are not alone. It can be a daunting task. But there is help at hand in form of support programmes and organisations. Of course, not all of them will end up being successful. But as I hope you will hear in this episode you may want to give it a try because, after all, nothing ventured, nothing gained.
In the first part of this episode I'll be talking to a team of researchers, Ben, Haaroon and Alhamza about why they created a startup and the challenges they face. For the second part, we'll be hearing from Riam Kanso - CEO of ConceptionX. ConceptionX is a programme designed to aid researchers turn into venture scientists.
Finally:
It's the beginning of summer here in the Northern Hemisphere and I'll be taking a break. Season 2 of Code for Thought will start again on 6 September.
Links
- https://conceptionx.org
- https://raphtory.github.io
This episode is about mobile apps in research software engineering. Not surprisingly, there is an increasing demand for mobile apps by researchers. In this SORSE event from February 2021 I am talking to Adrian Harwood, Patricia Barnby and Mark Turner how their teams at the University of Manchester and the University of Newcastle deal with this.
We also talk about a subject that will sound very familiar to engineers developing mobile apps: native iOS, Android development or cross platform solutions such as React Native or Xamarin.
- The RSE Team at Uni. Manchester, UK https://www.itservices.manchester.ac.uk/research/
- The RSE Team at Uni. Newcastle, UK https://rse.ncldata.dev
-
SORSE events 2020/2021 https://sorse.github.io
-
Developing mobile apps with Xamarin https://dotnet.microsoft.com/apps/xamarin
-
Developing mobile apps with ReactNative https://reactnative.dev
And of course native Android and iOS development:
- Android https://developer.android.com
- iOS https://developer.apple.com
Whereas the last episode focused on architecture at enterprise scale, this episode is looking at architecture for software solutions.
I was fortunate enough to meet with 3 solutions architects from Amazon Web Services in the US: Akash Gheewala, Ro Mullier and John Majarwitz.
As we discuss in this episode, the path to become an architect varies: whether it is moving into the role straight away or gradually after years in software engineering.
Architecture can be an attractive choice for engineers who want to develop their career but don't want to leave the technical field. However, as you move into the role of architect you will need to develop more than technical skills, be that business acumen or stakeholder management.
Research software engineering is a relatively young discipline. But it is rapidly expanding and I think there is an opportunity for us to learn from our colleagues in the private sector: whether it is for developing career paths or software solutions for complex engineering tasks.
Architecture at large scale, such as in enterprises and organisations with complex infrastructure, puts very different demands on the role than being a software engineer or even solutions architect. For sure, you will need solid technical skills. But the ability to convince and drive solutions become more and more important.
In this episode I talk to three ex-colleagues of mine from Elsevier - who have been working as enterprise architects for some time. And we touch on the challenges of the role and how they deal with it.
Links you may want to follow up on:
-
Lean Software Architecture http://www.leansoftwarearchitecture.com
-
Melvin Conway's paper: "How do committees invent?" http://www.melconway.com/Home/Committees_Paper.html
-
Conway's Law: http://www.melconway.com/Home/Conways_Law.html
This is the first part on software architecture. Meet James Smithies from Kings College in London (UK), Steve Crouch from the Software Sustainability Institute/Southampton (UK) and Keith Gutfreund from Elsevier, Boston (USA).
Together we explore, what architecture means in software development, both in the private sector and in research; how - and if - architecture fits in with research software engineering.
Links:
- Digital Lab, King's College London https://kdl.kcl.ac.uk
-
Software Sustainability Institute https://www.software.ac.uk
-
Martin Fowler's take on architecture https://martinfowler.com/architecture/
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Is architecture overrated? https://blog.pragmaticengineer.com/software-architecture-is-overrated/
In this episode we continue our journey into the Julia programming language and dive a little deeper into some aspects of Julia. For that reason I met with 2 engineers: Jarvis Frost from Imperial College and Lyndon White from InveniaLabs. Both wrote a lot of Julia code and we discuss some of the projects they have worked on.
The projects in question:
Jarvis' project example: Polaron Mobility
- https://github.com/jarvist/PolaronMobility.jl
Differentiation with Julia
- https://github.com/JuliaDiff
- https://discourse.julialang.org/t/state-of-automatic-differentiation-in-julia/43083
Lyndon's project: NamedDims
- https://github.com/invenia/NamedDims.jl
Named Tensor post (mentioned in episode) by Alexander Rush http://nlp.seas.harvard.edu/NamedTensor
Other links you might find interesting
Composing code with Julia
https://www.oxinabox.net/2020/02/09/whycompositionaljulia.html
Multiple Dispatch comparison
https://medium.com/swlh/how-julia-uses-multiple-dispatch-to-beat-python-8fab888bb4d8
Flux Julia package
https://fluxml.ai/Flux.jl/stable/
Linear Algebra/Julia
https://docs.julialang.org/en/v1/stdlib/LinearAlgebra/
In 2009 a group of engineers Jeff Bezanson, Stefan Karpinski, Viral Shah and Alan Edelman set out to develop a new language that is open source, easy to use but also highly performant. They called this language "Julia" and it appeared ca 2012.
Since then the community of Julia developers has grown year on year, with some exciting projects happening at e.g. Nasa but also commercial products.
In this first part of episodes on Julia I want to get a flavour of the Julia language, what it is used for and how the community of developers is developing. I am talking to Logan Kilpatrick (Community Manager of Julia) and then with Mayeul d'Avazac and Mose Giordano, both practitioners and contributors.
Here are a few links you might be interested in:
- https://julialang.org the main go site for the Julia programming language. If you want to learn Julia, go to https://julialang.org/learning/
- https://julialang.org/blog/2012/02/why-we-created-julia/ the Blog post explaining why Julia
- https://www.youtube.com/c/TheJuliaLanguage/videos there is a great set of videos on Julia on YouTube
- https://github.com/JuliaLang/julia checkout the repo and see what's currently going on with Julia
- https://discourse.julialang.org/t/tiobe-index-rank-23-as-of-jan-2021/42730/5 how does Julia fare in the world of computing. Look at the ranking
- https://juliacomputing.com/blog/2021/01/newsletter-january/ Julia adoption
The Nordic RSE network held a 3 day workshop in December 2020 and I was delighted to record a panel discussion on the subject of 'Research Software Engineering careers and their position in academia'.
Despite the fact that some countries established roles for research software engineers (e.g. the UK, US and France), in many places aspiring RSEs face obstacles and hurdles to turn their passion into a career. Samantha Wittke from Aalto University in Finland chaired the discussion.
Interesting links:
- Declaration of Research Assessment (DORA) https://sfdora.org
- Nordic RSE organisation https://nordic-rse.org
Some of them universities participants were joining from
- https://www.ntnu.no (Home to Digital Lab, Norway)
- https://www.helsinki.fi/en (University of Helsinki, Finland)
- https://www.kth.se (Royal Institute of Technology, Sweden)
- https://www.aalto.fi/fi (Aalto University, Finland)
- https://www.imperial.ac.uk/admin-services/ict/self-service/research-support/rcs/research-software-engineering/ (RSEs at Imperial College, London, UK)
Talking about sociology in software development is rare. But that is exactly what happened at a meet-up I went to in Paris in 2019. Fabien Lamarque, software craftsman from Bordeaux, gave a presentation on what sociology can teach us in terms of team dynamics and team structure. Specifically, the work of Pierre Bourdieu, a leading French philosopher and sociologist.
In this episode we talk about a number of important aspects facing today's software developers: team structure, flat teams and hierarchy and how télétravail - remote working - has impacted all of that during the pandemic.
Here is a list of books and links mentioned in this episode:
- https://fabien-lamarque.eu/Bourdieu-and-sociology-in-software-development/ - Fabien's Blog post in English on Pierre Bourdieu
- and here in French https://fabien-lamarque.eu/les-impacts-de-Bourdieu-sur-les-coding-dojo/
- Jo Freeman's position paper on 'The tyranny of structurelessness' https://www.jofreeman.com/joreen/tyranny.htm
- Culture and Power: The sociology of Pierre Bourdieu, an introductory book by David Swartz
- Pierre Bourdieu: vie oeuvres concepts (French) Patrice Bonnewitz
- Mutual Aid: A Factor in Evolution, by Pëtr Kropotkin
- Extreme Programming Explained, by Kent Beck
It's publish or perish for researchers and scientists. In addition to that many researchers and scientists from African countries struggle to get their work published and recognised. The team around https://info.africarxiv.org AfricarXiV work hard to address that.
Here are a few links mentioned in this episode you may want to check:
- https://www.stm-assoc.org The International Association of science, technology and medical publishing
- https://www.tcc-africa.org the Training Centre in Communication in Africa
- https://peerreviewweek.wordpress.com Peer Review Weekly and annual event for networking of partners in the publishing and peer review sector
- https://www.sspnet.org The Society for Scholarly Publishing
- http://openaccessweek.org Open Access Week
Most of today's research depends on software. So, reproducing science and research results is ever more important. For this episode I have been following a 'ReproHack' event held at the University College of London in late 2020. This event was the first of its kind held at UCL. In particular, since - due to the coronavirus pandemic - it was run entirely online.
Listen to find out more about this event and what ReproHacks are from organisers, participants and presenters.
- ReproHack web page https://reprohack.github.io/reprohack-hq/ and Twitter account https://twitter.com/reprohack
- ReproHacks are happening all over the globe. Here a selection
- Latin R community ReproHack https://latin-r.com/blog/reprohack-en
- ReproHack in Belgium https://www.elixir-belgium.org/training/reprohack-hackathon-reproducible-data-analysis
- ReproHack Leiden 2019 (there will be one in 2021 as well) https://www.library.universiteitleiden.nl/events/2019/11/reprohack
In this episode I speak with Richard Gunn and Sarah King from the Engineering and Physical Sciences Research Council (EPSRC).
Recognising the work research software engineers do is one thing. But funding and supporting career paths in it quite another.
In the UK, the EPSRC together with the Science and Technology Facilities Council (STFC) have provided fellowship programmes to help getting roles and career paths off the ground.
Some links:
- EPSRC https://epsrc.ukri.org
- Hidden Ref and their work to recognise software contributions in scientific output https://hidden-ref.org
- REF (Research Excellence Framework) in the UK https://www.ref.ac.uk
Welcome to Code for Thought. The new podcast about software, engineering, research and anything in between.
In this episode I want to give you some background of research software engineering (RSE) and a taster for things to come.
If you want to find out more about RSEs and what we do look up the following links
- the Software Sustainability Institute https://www.software.ac.uk
- the (UK) Society for Research Software Engineering https://society-rse.org
And, of course, our other podcast show RSE Stories at https://us-rse.org/rse-stories/ where you can meet our colleagues from around the globe.