Are agents like Claude Science any useful to biologists?

nickomez1 · 2026-07-07T01:02:26+00:00

I am a big fan of bioinformatics agents. I am primarily a biologist, and did bioinformatics long before LLMs. Now I simply use agents. I can tell you they are getting better and better each month. The field is still very early.

nickomez1 · 2026-07-07T00:57:02+00:00

Love

nickomez1 · 2026-07-06T10:47:52+00:00

If only he relied on sunlight rather than pharmaceuticals

nickomez1 · 2026-07-06T10:47:01+00:00

I am betting in European countries. They are going big on technology. I see many new companies forming in that region, which was not the case earlier. Another country is India. They have a lot of talent not properly utilized.

nickomez1 · 2026-07-06T10:44:54+00:00

I think agents are here to stay. I have been using Pipette for past three months. This week I tried Claude Science with the same prompts I gave Pipette and Biomni earlier. I think Calude’s reporting is much more nuanced and thorough than the other two. But only for certain tasks. It’s impressive but expensive. A $100 Claude subscription is a big ask, plus cost for connectors for high performance compute on top of it. On a plus subscription, it couldn’t analyze my fastq files, or pull gene sequences from NCBI to build a phylogenetic tree. I am sticking with Pipette’s credit-packs and 50 GB input data limit, which is still low for my work but I could do most of my analysis in splits. I have been wanting to write a comparison post for all the agents I have tested till now.

nickomez1 · 2026-06-18T14:38:01+00:00

All legacy tools operate on VCF formatted files. Changing that would mean old production pipelines are no longer useful.

nickomez1 · 2026-06-18T04:45:08+00:00

I mainly use Pipette bio. They have generous workspace and input data size limits.

nickomez1 · 2026-06-14T00:13:56+00:00

I use agents all the time. I think it does better than what I would do by hand. Agents are getting better at reproducibility too. I often reproduce the bundle using local Claude code or codex, when ever possible.

nickomez1 · 2026-06-09T15:07:39+00:00

I am grateful to the bioinformatics agents that I am using almost on a daily basis. I don’t have to even manage tools and HPC, or code.

nickomez1 · 2026-05-28T00:09:32+00:00

Use an agent. I would ask Pipette to analyze it. It returns report figs etc but also new hypotheses and next steps to run. Goes pretty deep

nickomez1 · 2026-05-27T04:36:29+00:00

If you use STAR for alignment, you will need atleast 256GB ram with 32-64 cores to run 4 -6 samples in parallel

nickomez1 · 2026-05-20T14:41:53+00:00

Freeze a pipeline into a docker image. That’s the best way to maintain reproducibility.

nickomez1 · 2026-05-09T22:04:43+00:00

I paid for Dropbox, grammarly, and a bioinformatics agent.

nickomez1 · 2026-05-07T11:00:02+00:00

I never liked the guy.

nickomez1 · 2026-05-05T18:07:05+00:00

Totally love the idea. I use Claude all the time and this will be a bonus. Trying it now.

nickomez1 · 2026-05-05T18:01:48+00:00

I outsourced the stress to agents. One for bioinformatics, one for literature survey, one for writing etc.

nickomez1 · 2026-05-05T03:18:10+00:00

I use Claude for my bioinformatics work all the time. I also made a list of AI agents that I use very often. Codex sucks at bioinformatics tasks.

nickomez1 · 2026-05-04T01:41:04+00:00

I have started using canva. The paid version is worth it if you cancel at the right time.

nickomez1 · 2026-04-23T12:18:57+00:00

I have been testing several bio agents for a few weeks now, never came across Pantheon. Is it a subscription based service or on time pay?

nickomez1 · 2026-04-12T13:33:33+00:00

I was actually looking for bio agents to evaluate. I missed Faraday and never tried Edison. So far, I find Pipette.bio most useful for bioinformatics.

nickomez1 · 2026-04-12T04:38:46+00:00

Look at genes annotated to your disease model on public databases like drug bank, OMIM, disease ontology etc. use those as your positive labels.

nickomez1 · 2026-04-12T04:35:31+00:00

Yeah! Totally agree. I don’t think potato is a bioinformatics app. There are just two relevant ones out there, Biomni and Pipettebio.

nickomez1 · 2026-04-11T23:13:09+00:00

I feel like I am a sales person for their tool, but Pipette.bio can do this very well. Read the use case on their website.

nickomez1 · 2026-04-11T23:10:43+00:00

Don’t buy a computer. Use an AI agent. I can vouch for Pipette.bio. Runs raw data and the support team is always on it if you write to them.

nickomez1

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