Toby Hodges
@tobyhodges.carpentries.org
he/him
Director of Curriculum at The Carpentries. Views my own. Sorry I haven't replied to your email.
"I only know that hearts made of stone will rarely sail far and may never reach home" - Chuck Ragan
Director of Curriculum at The Carpentries. Views my own. Sorry I haven't replied to your email.
"I only know that hearts made of stone will rarely sail far and may never reach home" - Chuck Ragan
Reposted by Toby Hodges
The support the Python community has shown to PSF for its decision has given us hope in the sustainability of open science communities. Please consider extending your generosity to our organisation’s fundraising efforts, and help us to reach others aligned to our mission: carpentries.org/support/
Support The Carpentries
We are grateful to the individuals and organisations who provide financial support to The Carpentries. If you are interested in supporting our work, you can learn more about becoming a Member Organisa...
carpentries.org
November 7, 2025 at 3:52 PM
The support the Python community has shown to PSF for its decision has given us hope in the sustainability of open science communities. Please consider extending your generosity to our organisation’s fundraising efforts, and help us to reach others aligned to our mission: carpentries.org/support/
Reposted by Toby Hodges
We are thrilled with the renewed attention that The Carpentries has received for deciding to withdraw a $1.5 million proposal to the National Science Foundation (NSF), thanks to a recent similar decision made by the @python.org (PSF) and the generous shout-out they gave us when they announced it. 🙏
November 7, 2025 at 3:52 PM
We are thrilled with the renewed attention that The Carpentries has received for deciding to withdraw a $1.5 million proposal to the National Science Foundation (NSF), thanks to a recent similar decision made by the @python.org (PSF) and the generous shout-out they gave us when they announced it. 🙏
Reposted by Toby Hodges
"Crucially, students will need to develop sufficient expertise to identify when AI systems produce plausible but incorrect outputs — which poses a dilemma because this requires the very skills that AI is starting to replace."
www.nature.com/articles/d41...
www.nature.com/articles/d41...
PhD training needs a reboot in an AI world
As machines get better at data analysis and writing tasks, doctoral training must evolve to make the most of artificial-intelligence outputs.
www.nature.com
November 6, 2025 at 9:22 AM
"Crucially, students will need to develop sufficient expertise to identify when AI systems produce plausible but incorrect outputs — which poses a dilemma because this requires the very skills that AI is starting to replace."
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Toby Hodges
Between @python.org and @carpentries.carpentries.org, the open-source ecosystem is rejecting the administration's inquisition against DEI. If you can support them with a donation please do. I just did!
Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
🧵
The official home of the Python Programming Language
www.python.org
October 27, 2025 at 5:47 PM
Between @python.org and @carpentries.carpentries.org, the open-source ecosystem is rejecting the administration's inquisition against DEI. If you can support them with a donation please do. I just did!
Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
Reposted by Toby Hodges
I'd also like to shout out @carpentries.carpentries.org for leading the way on this, having made a similar decision earlier this year.
October 27, 2025 at 3:47 PM
I'd also like to shout out @carpentries.carpentries.org for leading the way on this, having made a similar decision earlier this year.
Reposted by Toby Hodges
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
🧵
The official home of the Python Programming Language
www.python.org
October 27, 2025 at 2:47 PM
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
🧵
Reposted by Toby Hodges
📢 The Netherlands eScience Center is looking for a Programme Officer
• with the drive to help improve research software & impact on sciences
• who is creative and communicative
• enjoys tackling challenges in project management
• has passion in developing funding calls
Apply now! buff.ly/FU2JBVU
• with the drive to help improve research software & impact on sciences
• who is creative and communicative
• enjoys tackling challenges in project management
• has passion in developing funding calls
Apply now! buff.ly/FU2JBVU
October 14, 2025 at 10:15 AM
📢 The Netherlands eScience Center is looking for a Programme Officer
• with the drive to help improve research software & impact on sciences
• who is creative and communicative
• enjoys tackling challenges in project management
• has passion in developing funding calls
Apply now! buff.ly/FU2JBVU
• with the drive to help improve research software & impact on sciences
• who is creative and communicative
• enjoys tackling challenges in project management
• has passion in developing funding calls
Apply now! buff.ly/FU2JBVU
Reposted by Toby Hodges
AAAAAAAAAAAAAHHHHHHH
October 2, 2025 at 4:31 PM
AAAAAAAAAAAAAHHHHHHH
Gym? What's a gym? Oh, a _gym_!
www.youtube.com/watch?v=rFrP...
www.youtube.com/watch?v=rFrP...
October 1, 2025 at 7:56 PM
Gym? What's a gym? Oh, a _gym_!
www.youtube.com/watch?v=rFrP...
www.youtube.com/watch?v=rFrP...
Reposted by Toby Hodges
It was the best of times, it was the BLURST of times?!
what's the stupidest/randomest Simpsons quote that lives in your head rent free? Mine is the urge to say "you said go to bread" every time I am about to head to bed.
October 1, 2025 at 7:26 PM
It was the best of times, it was the BLURST of times?!
Reposted by Toby Hodges
Cory Doctorow (not on Bluesky) published IMHO one of the most compelling pieces about AI being a bubble pluralistic.net/2025/09/27/e...
Pluralistic: The real (economic) AI apocalypse is nigh (27 Sep 2025) – Pluralistic: Daily links from Cory Doctorow
pluralistic.net
September 30, 2025 at 2:10 PM
Cory Doctorow (not on Bluesky) published IMHO one of the most compelling pieces about AI being a bubble pluralistic.net/2025/09/27/e...
Reposted by Toby Hodges
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
jasonjwilliamsny.github.io
September 25, 2025 at 10:09 PM
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP
jasonjwilliamsny.github.io/grfp2025/
Reposted by Toby Hodges
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Toby Hodges
Finally, I should cite some related papers
1. From @baym.lol , a beautiful paper looking at genomes going back to the 1880s, showing how chromosomes gained AMR, with a very nice analysis of how AMR genes were mobilised and embedded in MGEs
www.microbiologyresearch.org/content/jour...
19/n
1. From @baym.lol , a beautiful paper looking at genomes going back to the 1880s, showing how chromosomes gained AMR, with a very nice analysis of how AMR genes were mobilised and embedded in MGEs
www.microbiologyresearch.org/content/jour...
19/n
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...
www.microbiologyresearch.org
September 25, 2025 at 9:41 PM
Finally, I should cite some related papers
1. From @baym.lol , a beautiful paper looking at genomes going back to the 1880s, showing how chromosomes gained AMR, with a very nice analysis of how AMR genes were mobilised and embedded in MGEs
www.microbiologyresearch.org/content/jour...
19/n
1. From @baym.lol , a beautiful paper looking at genomes going back to the 1880s, showing how chromosomes gained AMR, with a very nice analysis of how AMR genes were mobilised and embedded in MGEs
www.microbiologyresearch.org/content/jour...
19/n
Reposted by Toby Hodges
In the age of AI, LLMs and code assistants what does it mean to be an open-source project that is welcoming to newcomers? As a newcomer, is it enough to use AI to solve a good first issue and submit it as a PR? As a maintainer, what should you do with PRs like that?
September 25, 2025 at 9:51 AM
In the age of AI, LLMs and code assistants what does it mean to be an open-source project that is welcoming to newcomers? As a newcomer, is it enough to use AI to solve a good first issue and submit it as a PR? As a maintainer, what should you do with PRs like that?
Reposted by Toby Hodges
📄 A reminder that we are seeking writers (£600) and reviewers (£210) to support the development of new guides on:
- AI in research software
- Green Computing
- EDI in research software
Application deadline: Friday 3 October 2025
Find out more at www.software.ac.uk/news/writers...
- AI in research software
- Green Computing
- EDI in research software
Application deadline: Friday 3 October 2025
Find out more at www.software.ac.uk/news/writers...
September 24, 2025 at 8:10 AM
📄 A reminder that we are seeking writers (£600) and reviewers (£210) to support the development of new guides on:
- AI in research software
- Green Computing
- EDI in research software
Application deadline: Friday 3 October 2025
Find out more at www.software.ac.uk/news/writers...
- AI in research software
- Green Computing
- EDI in research software
Application deadline: Friday 3 October 2025
Find out more at www.software.ac.uk/news/writers...
Reposted by Toby Hodges
Paracetamol remains an important option to treat pain or fever in pregnant women.
Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.
Read more 👉 www.ema.europa.eu/en/news/use-...
Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.
Read more 👉 www.ema.europa.eu/en/news/use-...
Use of paracetamol during pregnancy unchanged in the EU | European Medicines Agency (EMA)
Paracetamol medicines can be used in pregnancy, in accordance with official recommendations
www.ema.europa.eu
September 23, 2025 at 10:28 AM
Paracetamol remains an important option to treat pain or fever in pregnant women.
Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.
Read more 👉 www.ema.europa.eu/en/news/use-...
Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.
Read more 👉 www.ema.europa.eu/en/news/use-...
Reposted by Toby Hodges
As our Executive team @drkariljordan.bsky.social @erinstellabecker.bsky.social states, our decision to withdraw was grounded in our commitment to The Carpentries' core values, which explicitly promote diversity, equity and inclusion in programming. "[DEI programming is] baked into everything we do.”
September 23, 2025 at 8:05 AM
As our Executive team @drkariljordan.bsky.social @erinstellabecker.bsky.social states, our decision to withdraw was grounded in our commitment to The Carpentries' core values, which explicitly promote diversity, equity and inclusion in programming. "[DEI programming is] baked into everything we do.”
Reposted by Toby Hodges
The Carpentries is again in the news, this time in @science.org. Our decision to withdraw from the National Science Foundation's POSE grant funding is discussed in this article criticising how Trump directives are undermining the NSF's 75-year history of independence: www.science.org/content/arti...
Under Trump, NSF faces worst crisis in its 75-year history
Political directives have undermined agency's independence and record of supporting the best basic research
www.science.org
September 23, 2025 at 8:05 AM
The Carpentries is again in the news, this time in @science.org. Our decision to withdraw from the National Science Foundation's POSE grant funding is discussed in this article criticising how Trump directives are undermining the NSF's 75-year history of independence: www.science.org/content/arti...
Reposted by Toby Hodges
Come join me on the organising committee for next year's #RSECon. It's a great way to give back and get to know the community, plus we'll cover the cost of your registration at the conference!
Have you enjoyed RSECon either this year or in the past?
Would you like to be involved in organising RSECon26 which is taking place 9-11th Sep 2026?
We have a call out for Committee Members, for details and application see
society-rse.org/rsecon26-com...
(Call closes 10th Oct 2025)
#rsecon26
Would you like to be involved in organising RSECon26 which is taking place 9-11th Sep 2026?
We have a call out for Committee Members, for details and application see
society-rse.org/rsecon26-com...
(Call closes 10th Oct 2025)
#rsecon26
RSECon26 Call for Conference Committee Members - Society of Research Software Engineering
RSECon26 Committee call is now open.
society-rse.org
September 22, 2025 at 1:22 PM
Come join me on the organising committee for next year's #RSECon. It's a great way to give back and get to know the community, plus we'll cover the cost of your registration at the conference!
Reposted by Toby Hodges
1/ Bioinformatics moves fast.
If you rely only on recipes from books, you’ll soon find they’re obsolete.
Let me show you why. 🧵
If you rely only on recipes from books, you’ll soon find they’re obsolete.
Let me show you why. 🧵
September 22, 2025 at 1:45 PM
1/ Bioinformatics moves fast.
If you rely only on recipes from books, you’ll soon find they’re obsolete.
Let me show you why. 🧵
If you rely only on recipes from books, you’ll soon find they’re obsolete.
Let me show you why. 🧵
Reposted by Toby Hodges
Just asked Claude to code me some simple Entrez stuff that pulls down taxonomy IDs for NCBI mitochondrial accessions - the code works and returns a table of taxonomy IDs from the API in a nice table, *but the taxonomy IDs are all wrong*. I hadn't that before: normally AI-written code just crashes
September 22, 2025 at 4:43 AM
Just asked Claude to code me some simple Entrez stuff that pulls down taxonomy IDs for NCBI mitochondrial accessions - the code works and returns a table of taxonomy IDs from the API in a nice table, *but the taxonomy IDs are all wrong*. I hadn't that before: normally AI-written code just crashes
Reposted by Toby Hodges
If you write software as part of your research then the RSE Society want to hear from you!
They want to hear from members and especially non-members about why they joined the Society (or not!). Closing date is the 26th Sept!
They want to hear from members and especially non-members about why they joined the Society (or not!). Closing date is the 26th Sept!
Society of RSE Community Survey 2025 - Society of Research Software Engineering
As part of our ongoing review of Society activities, we are pleased to announce that our 2025 Community Survey is now live. We’re inviting everyone in this fantastic community to share their thoughts…
buff.ly
September 18, 2025 at 8:21 AM
If you write software as part of your research then the RSE Society want to hear from you!
They want to hear from members and especially non-members about why they joined the Society (or not!). Closing date is the 26th Sept!
They want to hear from members and especially non-members about why they joined the Society (or not!). Closing date is the 26th Sept!
Reposted by Toby Hodges
Reposted by Toby Hodges
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned