rewrites.bio - A manifesto for bioinformatics Principles for responsible AI-assisted rewriting of bioinformatics tools.

The true purpose of rewrites.bio is as a guide for backporting all of the current bioinformatics stack into Perl

With the heavy discounting on the first year of .bio domains right now, how can we not? It is decidedly not well-considered, but I will accept debate only in the form of a pull request

compbiovs.bio

That took longer than I thought to put into words!

I'll end by saying that the more I think in this, the less sure I am, but wonder if replacing "rewrite" with "fork of original code" helps in thinking about what to do - and what not to.

If an LLM can help add a new functionality in the rewrite language, it could probably do the same for the original language, and it might be nice to submit a PR to the original open source repo to maintain parity.

For the preprint threshold question, I guess my main query is what to do with novel contributions - a 5.6 or an extension to 5.5 "Contribute upstream responsibly" in the manifesto. Should (and will) extensions to the original make it upstream? and is this one criteria to meet for a preprint?

The recent JOSS update on what needs to be done to reach their publication benchmark was interesting I thought, blog.joss.theoj.org/2026/01/prep... and I really appreciate rewrites.bio for starting this conversation as well.

I totally agree there needs to be space for the careful human-driven rewrite, but worry along the lines of @katholt.bsky.social that there will be flood of inhuman ones that drown them out. The journal level will be important to filter genuine contributions, but preprints are a different beast.

Sorry, I guess that is what I meant - is there line for a rewrite to get to, to justify a preprint? I don't have any answers, and it gets murkier if it is a rewrite+, with the + being some new (and hopefully non-trivial) features that maintain backwards compatibility.

One thing I keep asking myself is where preprints of the rewrites sit. Easier to produce and get out there, and how they'll sit in the ecosystem?

The almost best thing about this is that Bioinformatics Twitter is back!

"Introducing AI in RStudio" on top of the You Were The Chosen One meme from Star Wars

Irrespective of the validity of any of the arguments in this announcement (posit.co/blog/introdu...), this is how it *feels*

🚨Two weeks to get your abstracts in! 🚨

cancerbioinformatics.au/abstracts

Remembering Phil Bourne Personal reflections on a legendary scientist, leader, builder, and mentor

Remembering Phil Bourne. Personal reflections on a legendary scientist, leader, builder, and mentor. blog.stephenturner.us/p/rememberin...

The community was enriched for his legacy, and is lessened by his passing. Vale Phil. 8/8

And while it was true at the time that statistically speaking it helped to be PEB to publish a 10SR, I think the mark he has left on the community is that you no longer need to be him. He taught everyone how to do things and the attitude to have. 7/8

We passed a few drafts back and forth and that was it!

I have no doubt that Phil's involvement helped the publication in its journey, but read the article - Phil's commentary elevates that paper. I find those insights invaluable and with no false modesty, they are the best bits of the paper. 6/8

- I inject comments about what you have written highlighted in italics
- We all review the result and if we agree it gets submitted for consideration by another editor (who may of course reject it)"

Phil noted that "not only is the article unorthodox so is the process - I love that!". 5/8

"I cant recall ever laughing out loud at a PLOS submission but now I have. But laughter in a positive way - I agree this is a celebration of the series and I suggest the following.
- I become an author (why deny the stats)
- I make a few changes to the article and comments for you to consider 4/8

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article

We'd just read a lot of them in our journal club. It could have very easily been desk rejected and not ever seen the light of day. Instead, it was received in the best way. Phil's email response to our  inquiry directly aligns with the opening line of the paper: journals.plos.org/ploscompbiol... 3/8

In 2014 a couple of rag tag PhD students from Melbourne, Australia, submitted a Presubmission Inquiry to PLOS Comp Bio - "Ten Simple Rules for a PLOS Ten Simple Rules". This was unsolicited. We hadn't written a 10SR, had no position of authority on a 10SR to speak from. 2/8

Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and @hdashnow.bsky.social and I think had in indelible mark on our careers. 1/8

[Slams the Inception button]

We’re proud to celebrate Dr Aparna Rao, Dr Deborah Meyran and Associate Professor Safeera Hussainy, who have been awarded the 2026 Lea Medals.

Read more: www.petermac.org/about-us/new...

Join the local Melbourne #illumina Field Apps team to specialise in #Bioinformatics. It's a great team, you get to play with #DRAGEN and help customers get the best data for analysis. #genomics #multiomics #singlecell #spatial #transcriptome #epigenetics bit.ly/46o4sRj
I can refer the right folks.

2026 Winner of the Lorne Genome Julian Wells Medal: Christine Wells (no relation!) @stemcellsystems.bsky.social congratulations, well deserved!!

Almost literally too late, but here is a feed for BlueSky to collate #LorneGenome posts that blends mentions of Lorne + Genome along with posts from @lornegenome.bsky.social

Should still work next year though!

bsky.app/profile/did:...

Emotional rollercoaster at #LorneGenome today:

- adipose tissue remembers being overweight in the transcriptome, nudging you back to weight gain after a loss

- Meerkats reproductive success correlates with higher body mass

I’m sure there is a lesson in there somewhere

Can only tag @antobeck.bsky.social here on BlueSky to say that the #Illumina coffee cart is once again the quiet hero of #LorneGenome

We’re hiring: Research Group Leader in computational biology.

Are you generating more research ideas than you can explore? Lead cutting-edge AI & biology research at EMBL-EBI.

Apply by 11 April 2026: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

#ScienceCareers @ewaldlab.org @embl.org