Hi,

I'm currently doing a PhD in bioinformatics algorithms development. One big issue of my sub-field is, that there aren't any good extendable benchmarking packages out there, so its always the same 5 methods + the proposed one being compared in any new article.

The existing benchmark suites are either extremely old or can not be extended by your own method easily, because their code was never ment to be extended by others (I guess nobody wants to include a method, that outperforms their own method; all of the benchmarking tools are made by groups that develop their own algorithms).

As I worked as a software engineer before starting my PhD, I have some experience with designing larger projects from scratch. Therefor I wrote like a 20 page description of all the modules, design question, data flow etc, I would like to have in such a tool. However, my supervisor told me, that this would be to big to run as a side project (and I agree) and this also isn't anything to be given to a bachelor or master student.

Today we received an email from the department, that PhD students can apply for Claude Code licenses, if they have some science related usage for it. That's why I thought about maybe letting Claude do the real coding using my project description and then put it on GitHub under MIT license, give it a DOI, use it for my own benchmarks in my next articles and let people - if they want to - just add their own methods (the design is pretty simple, one would in theory just need to add a script, that forwards the data to the corresponding method and formats the output in the correct way).

However, that doesn't really feel right, as this is of course a vibe coding project and I'm not really sure, whether vibe coding projects should be deployed in science. Thus I would really appreciate your thoughts on how you handle such things. (I'm usually keeping GenAI out of all my algorithm related work, except for plotting functions)

Hi everyone!

I'm currently learning step by step bulk RNA analysis with no affiliation to any lab, and throughout my learning journey I discover that I must have an HPC to access rna data which non of them are free.

Can anyone suggest an alternative for accessing data to at least to work on Shell.

Thank you

What makes or breaks a startup of this type? It feels like a gold rush with everyone using agentic AI workflows to try and innovate in some way, most fail obviously.

Firsthand experiences greatly appreciated.

Say I have two clusters of cells, healthy and diseased, which are contributed to by highly phenotypically similar cells, with patients contributing cells to each cluster, and with the diseased cluster having higher % mt genes.

After conducting differential expression on the psuedobulks, is it valid to interpret an increase in metabolic genes in the mitochondria as a real effect (but nuclear encoded), given this could be due to an increase in mitochondrial number rather than mitochondrial activity, meaning that in theory these metabolic genes that are upregulated may not be suitable targets, as they would be equally abundant in the healthy cells. Ie, equally as abundant per mitochondria. I hope what I'm saying makes sense, let me know your thoughts or any clarifications I can give!

Hello,

I'm looking into foundation models for scRNA-seq data, including spatial. A lot of the papers I've found cluster around 2022 and 2023, riding the LLM wave and the newer work seems to be different, leaning toward benchmarks, spatial models, and a virtual cell framing.

I understand that these models have been benchmarked as performing below comparative, traditional methods, so perhaps the pursuit of better performing models was not desirable.

Could it also be resource or time constraints, with the next big model still being trained? Or has the interest shifted toward virtual cell and perturbation prediction models? And if so, is that work mostly happening in companies and well-funded institutes because of the cost?

Please point out if I've missed something or if you have an opinion on this! I'm curious.

Undergrad here, just wanted to ask if anyone is going for ISCB-LATAM 2026 conference. If yes, let's connect.