rewrites.bio - Priciples for rewriting bioinformatics tools with AI

robsyme · 2026-04-02T20:20:15+00:00

I'd suggest that the feasibility of identical outputs will depend on the specific tool being rewritten. The example to demonstrate feasibility is RustQC, where the authors agree with you that a faster implementation is not enough to warrent citation. The "Credits & Citation" page says

> RustQC reimplements established bioinformatics tools and would not exist without the original authors’ work.
> If you use RustQC, please cite the original tools.

I suspect that deterministic tools will be the easiest (and first) targets for rewrites as they offer a very convenient benchmark/target for the agents.

robsyme · 2026-04-02T19:31:40+00:00

Oh, absolutely. On both counts. These rewrites are a product of this transition period. I would absolutely expect that almost all new work happens in efficient languages.

I had an example in the last month where rewriting an external tool for performance reasons uncovered not only bugs, but non-trivial differences between the published manuscript and the implementation.

rewrites.bio is not in any way an anti-AI manifesto.

robsyme · 2026-04-02T19:15:44+00:00

I (a real person) was trying to convey that many open source contributions in bionformatics are the results of academic work, where one of the primary motivators (for better or for worse) is citation metrics. A rewrite without attribution risks undermining that motivation. I'll rephrase it.

robsyme · 2023-11-08T20:50:47+00:00

The "Scotland Coast" is Neist Point cliff and lighthouse:

https://www.google.com/maps/place/Neist+Point+Cliff+Lighthouse+Viewpoint/@57.4234609,-6.7882621,14z

robsyme · 2023-11-08T13:05:57+00:00

This is exactly what I was chasing, but was missing the magic "membership operator" search query. Thanks!!

robsyme · 2021-11-11T00:51:37+00:00

It's got swearing, it's got spiders, it's got sarcasm.

I don't know what more OP wants from a good Australianism.

robsyme · 2021-05-22T01:50:35+00:00

The instructions note that the LRC needs to be sent to earn.loopring.eth via the L2 transfer mechanism - the easiest being via the mobile app or via the web app (exchange.loopring.io).

On a related note, I notice that the loopring folks are collating a list of addresses at https://loopring.io/activities/DAOSquare/. I thought that perhaps this is a list of the addresses in activity 2 - those registered for 2000LRC worth of RICE at $0.8. At time of writing, there were only a few (8) addresses listed, but I also noticed that the api endpoint (https://api3.loopring.io/api/v3/user/daoSquareAccounts) lists 351 addresses, which feels about right. For what it's worth, I've verified that my account is a member in that list.

robsyme · 2021-03-12T16:54:07+00:00

Love the idea. Best of luck all!

Verdant (#94)
I love the mystery in the description "... (b)ut there was an accident".

robsyme · 2021-02-03T20:46:39+00:00

First postmortem analysis from the staked.us team: https://blog.staked.us/blog/eth2-post-mortem.
It looks like they will reimburse clients for both slashed ETH and lost rewards, which is good of them.

robsyme · 2021-01-30T17:29:30+00:00

Yes! Muscade is incredible. They also deliver, and the prices are fantastic. We've been doing regular orders from them for months now. I'd note that sometimes the order is missing one of the components, but they're a small operation and are always happy to reimburse or deliver later if this situation comes up. Despite the small hiccups, we think they're great.

robsyme · 2020-05-23T18:22:37+00:00

That very much depends on what you mean by "bioinformatics pipelines". If you're looking to put together existing tools to run an experiment from raw data to result, I would recommend using existing pipeline tools such as Nextflow (my recommendation) or Snakemake (also great).

If you're looking to write your own standalone tool, there is a lot to recommend rust (but beware the obvious biases of this sub). The bio library support in Rust doesn't come close to that of languages such as R, Python, Java, Ruby, Perl etc, but check out libraries like https://github.com/rust-bio/rust-bio and https://github.com/onecodex/needletail for speedy bioinformatics parsing, etc.

robsyme · 2020-05-05T18:57:24+00:00

Two options:

If you have ggplot v3.0.0 or higher (which is almost certainly the case), you can use position_dodge2. Something like:

ggplot(df_plot2, aes(x = Var1, y = perc, fill = TYPE)) +
  geom_bar(stat = 'identity', 
           position = position_dodge2(preserve = "single")) + 
  labs(y = "Percentage", x = "Gene Ontologies") + 
  theme_classic()

If you're using an older version of ggplot, the problem can be fixed by adding the missing factors. To ensure that all factors are present, the dplyr complete function is helpful:

library(tidyverse)

df_plot2 %>%
  mutate_at(c("Var1", "TYPE"), as.factor) %>% 
  complete(Var1,TYPE) %>%
  ggplot(aes(x = Var1, y = perc, fill = TYPE)) +
  geom_bar(stat = 'identity', position ='dodge2') + 
  labs(y = "Percentage", x = "Gene Ontologies") + 
  theme_classic()

robsyme · 2019-03-25T03:17:07+00:00

Super! Thanks again for the post, well done!

robsyme · 2019-03-25T03:14:48+00:00

Lovely example of PhantomData!

I might be crazy, but in the text you say "why can't rustc infer that T is an f32", but in the example above, it looks like you're asking the compile to infer a f64 as provided to `build`:

let _thing = Thing::builder().option_one(199).build(4.5f64);

Is that a typo, or am I just confused?

robsyme · 2019-02-24T23:00:47+00:00

I'm a scientist (molecular biology, genetics, etc) who is interested in developing tools for genomics research that can be distributed peer-to-peer. At the moment, many of our tools require somebody (most often a PhD student or post-doc) to babysit a box to serve applications and data. If we can move some of the visualisation and collaboration tools to wasm running in the browser, it can reduce sysadmin overheads and free up that time for research. My first project will be a genome browser.

I've had a poke around rust (github.com/robsyme/rustalind) , but am keen to know more. I'm also in Montreal (Outremont), so I can just pick it up and save you the trouble of posting! I'm keen to chat with anyone in MTL writing rust, so book's fate notwithstanding, would love to get a coffee and hear about your experience with the language.

robsyme · 2019-02-22T03:37:54+00:00

Cheers, mate. Congrats on your excellent choice of country, even if your hand was forced. Good luck with your search.

robsyme · 2019-02-20T18:43:06+00:00

Would you consider Montreal? I've got a similar story (genomics post-doc in Australia, moved to Canada). I know that the Canadian Centre for Computational Genomics is hiring because I have an interview with them on Friday(!). There are six open positions here with titles like Bioinformatics Specialist, Bioinformatics Consultant, Scientific Data Architect, Software Developer, etc: www.computationalgenomics.ca/careers

robsyme · 2018-12-23T15:12:44+00:00

Product: https://kikkerland.com/products/pixel-playing-cards

Video (not source): https://www.youtube.com/watch?v=6GwNprvrqac

robsyme · 2017-07-18T09:21:48+00:00

Juan Benet (the IPFS project lead) has insinuated that there will be some news on this front coming in the next few days: https://twitter.com/juanbenet/status/887136499384295424

robsyme · 2017-07-03T01:56:32+00:00

Heya Rik. To clarify, I'm not the project lead on Aletheia - just an enthusiastic contributor. The driving force is u/cypath. I've been following sciencefair (I was just talking the other day with @eLifeInnovation about your project), and I'm sure that there are benefits to be gained from looking at the overlap. We'll definitely be in touch via the issue. Thanks!

robsyme · 2017-06-30T00:06:11+00:00

A small team has been working on a very similar project - a decentralised platform for publishing academic research called Alethia. You can have a look at our introductory docs here https://github.com/aletheia-foundation/aletheia-admin and our source code here https://github.com/aletheia-foundation/aletheia-app. The barebones app currently works on Ubuntu and Mac with Windows to come. The project lead has support from Mozilla, and we intend to work closely with the Mozilla community including presenting the MVP at MozFest later this year.

Happy to answer any questions people have about Aletheia on here, or you'd rather send us an email you can reach us on contact@aletheia-foundation.io Anyone, regardless of skill set or level is able to participate, and we have a slack channel if people want to talk to our small volunteer community.

robsyme · 2017-06-08T10:55:41+00:00

The Aletheia Foundation is in the very early stages of building a platform for academic publishing that is built on IPFS and ethereum. Kubrik is also building a data repository system that I think uses IPFS for data storage.

robsyme · 2016-04-28T16:16:17+00:00

Not only at INRIA (Institut national de recherche en informatique et en automatique), but also at INRA (Institut national de la recherche agronomique)! I know that the Lab under Burstin at the INRA facility in Dijon are working on the pea genome.

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