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Toby Hodges

@tobyhodges.bsky.social

310 followers 300 following 160 posts

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

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Reposted by Toby Hodges

Endless Screaming @infinitescream.bsky.social · 6d

AAAAAAAAAAAAAHHHHHHH

Toby Hodges @tobyhodges.bsky.social · 7d

Gym? What's a gym? Oh, a _gym_!
www.youtube.com/watch?v=rFrP...

Reposted by Toby Hodges

Gareth Corn @garethcorn.bsky.social · 7d

It was the best of times, it was the BLURST of times?!

Willow @rockshrimp.bsky.social · 7d

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.

Reposted by Toby Hodges

Stephen Turner @stephenturner.us · 8d

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

Toby Hodges @tobyhodges.bsky.social · 8d

Put another way: in my experience it is still rare to find people sharing stories that are not (roughly) either "I tried this and it worked!" or "I tried this and it was useless!"

Toby Hodges @tobyhodges.bsky.social · 8d

Interesting read, thanks. It chimes with my own experience and with other examples that I have seen people share. I was particularly interested in your case because you described a situation where the result of your first attempt was messy and needed a lot of manual work to fix.

Toby Hodges @tobyhodges.bsky.social · 8d

That's my interest as well. Currently supporting Carpentries community members in the creation of a workshop teaching careful and effective use of genAI for (research) software development, and how to think about the risks/implications of that use. Case studies like yours are very informative.

Toby Hodges @tobyhodges.bsky.social · 8d

Super interesting, thanks.

Toby Hodges @tobyhodges.bsky.social · 8d

Right. Thanks for the detailed response. Since you mention that the model "guessed" what the input data would look like, could more context also have been helpful? E.g. what input will be and what output should be expected?

Toby Hodges @tobyhodges.bsky.social · 8d

Reflecting on this experience, what will you do next time? Take the same approach, on the grounds that you have improved your debugging skills now & you estimate that this still saved you time? Or is there something you would adjust about the way you prompted Claude? Would you avoid altogether?

Reposted by Toby Hodges

Jason Williams @jasonwilliamsny.bsky.social · 13d

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/

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

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Zamin Iqbal @zaminiqbal.bsky.social · 13d

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

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Zamin Iqbal @zaminiqbal.bsky.social · 13d

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

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

Toby Hodges @tobyhodges.bsky.social · 12d

Great thread, thanks for posting it. And congratulations on the paper.

Reposted by Toby Hodges

Tim Head @betatim.bsky.social · 13d

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?

Toby Hodges @tobyhodges.bsky.social · 13d

Error code: √-1

Reposted by Toby Hodges

Software Sustainability Institute @softwaresaved.bsky.social · 14d

📄 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...

Reposted by Toby Hodges

European Medicines Agency @ema.europa.eu · 15d

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-...

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

Reposted by Toby Hodges

The Carpentries @carpentries.carpentries.org · 15d

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 @carpentries.carpentries.org · 15d

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

Reposted by Toby Hodges

Michael Donnay @mjdonnay.bsky.social · 16d

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!

Society of RSE @society-rse.org · 16d

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

RSECon26 Call for Conference Committee Members - Society of Research Software Engineering

RSECon26 Committee call is now open.

society-rse.org

Reposted by Toby Hodges

Ming Tommy Tang @tommytang.bsky.social · 16d

1/ Bioinformatics moves fast.

If you rely only on recipes from books, you’ll soon find they’re obsolete.

Let me show you why. 🧵

Reposted by Toby Hodges

Philipp Bayer @philippbayer.bsky.social · 17d

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

UoM Research IT @uomresearchit.bsky.social · 20d

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!

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…

Reposted by Toby Hodges

Malte Elson @malte.the100.ci · 22d