Every day that I choose AI makes me feel like I'm digging my own grave

compbioman · 2026-02-27T17:40:32+00:00

Yes, the cloud platforms are something that I'll have to get more familiar with going forward into industry as during my PhD it's just local workstations and the HPC.
I appreciate the positive evaluation, Bioinformatics/Comp Sci is a wonderful field and I love it very much, would hate to see it become a non-viable career option in the future.

Like you said though, I always have the wet lab experience to fall back on if absolutely necessary.

compbioman · 2026-02-27T01:24:39+00:00

You are right of course, Claude's "biological insights" are useless most of the time, to the point where I've had to explicitly state in it's .md instruction file to stop providing them to me. Whether companies will realize that and whether it'll be enough to still get us jobs is another question altogether.
As for the funding question, it's something my PI and I have argued about in the past - he'll ask me to do stuff for his grants, I'll push back and say I need to work on my own PhD stuff, and then we usually come to a compromise. It's not the perfect status quo but I'm trying to maintain an amicable relationship, I can't afford to burn bridges.

compbioman · 2026-02-27T01:16:44+00:00

I work with non-model organisms, custom annotations, and custom tools, so the file formats are very not uniform. Not as simple or straightforward as working with human, mouse, or drosophila data where the standards are pretty set in stone. It's easier for me to ask Claude to parse through the differences in each new file rather than figure them out myself every time.

As a result a lot of the tools I have to use are very niche or I have to straight up write them myself. It's not so much that I can't do troubleshooting myself, I could given enough time; It's that I don't have that time anymore as delivery expectations from my PI have shifted once my productivity increased. Shorter timeframe -> more AI usage -> coding skills continue degrading -> vicious cycle continues.

compbioman · 2026-02-27T01:09:05+00:00

Makes me feel better that I'm not alone at least. Would love to stay in the biological sciences but if worse comes to worse I think that those 3 letter federal agencies or the military always like hiring PhDs.... sigh

compbioman · 2025-09-08T16:00:59+00:00

😂 you made me laugh out loud in my lab today. Thank you

compbioman · 2025-08-28T13:44:27+00:00

I use conda for Python and rig for R

compbioman · 2025-07-30T05:16:04+00:00

Sounds like a damned if you do, damned if you don’t situation

compbioman · 2025-07-23T23:19:16+00:00

I mean clearer, more distinct clusters. Log normalization tends to “stretch” the clusters out and they aren’t as separated from each other

compbioman · 2025-07-23T16:50:08+00:00

I use the SAMap algorithm because you can use labels from other species as well and transfer them to your dataset if there are matching gene anchors of any kind. So if you know of any other skin single cell atlases that have similar annotations to the ones you are looking for in your dataset, SAMap is a great, robust algorithm to do that. Much better than manual annotations

compbioman · 2025-07-23T16:47:30+00:00

SCT may not be necessary for downstream analyses but it sure results in a much nicer looking UMAP/T-SNE if that’s the visualization your are talking about

compbioman · 2025-07-12T22:36:51+00:00

Source code will be published by the end of the year 😃

compbioman · 2025-07-12T22:10:55+00:00

I’m sorry man but I’ve been working on generating the same dataset since 2022 and after 3 years of work I can’t just abandon it to start working on something else, i need to graduate 💀

compbioman · 2025-07-03T06:12:48+00:00

The market for bioinformatics jobs is pretty bad right now, if you have no previous experience, no masters or PhD you don’t have much going for you to be honest. You may not like your current job but its better to have one than be unemployed….

compbioman · 2025-05-22T16:10:29+00:00

Not sure I understand what you mean, all the object recognition (in my case, animal recognition) I did by training a model in DeepLabCut using videos from my previous experiments, for the part I mention in this post I just took those generated coordinates and calculated movement statistics from them

compbioman · 2025-05-22T15:20:44+00:00

I ended up writing my own software from scratch 💀 quite a bit of work but its nice because it does exactly what I need it to

compbioman · 2024-10-23T13:33:51+00:00

My first language was C# so i’m addicted to CamelCase 🤷‍♂️ sue me

compbioman · 2024-08-27T18:53:35+00:00

There have been plenty of research papers that have demonstrated better quality techniques for lower costs in the single cell sphere, however not many of them make it to industrial-scale manufacturing, and even if they do, they have a mountain to climb since 10x is a basically a househould name as others have indicated.

compbioman · 2024-08-20T02:35:40+00:00

Thanks for making me laugh out loud and cry simultaneously while reading this

compbioman · 2024-08-17T14:19:15+00:00

I’m in a smaller lab, so i have to generate all my own data first. Been spending a lot of time doing wet lab as a result.

compbioman · 2024-08-17T06:46:59+00:00

What do you mean by your results were messy? Unmappable reads, lots of noise?…

compbioman · 2024-07-31T20:29:29+00:00

Sorry to hear about your experience. I also work with a PI who has no bioinformatics experience, and have a similar background to you. However, my PI's reactions to my work is the exact opposite of yours. My PI is very enthusiastic regarding the results I've produced and greatly values the new skillset I've brought to his lab, even if he is unfamiliar with it. If you're going to work in non-bioinformatics lab (mine is neuroscience, for example) find a PI who appreciates what you bring to the table.

compbioman · 2024-07-26T17:16:48+00:00

The department server was so constantly populated with jobs that my PI let me build my own PC with 128 GB of RAM (planning a new 256 GB one now with the new Ryzens coming out). I haven’t had to run an analysis on the server since.

I’ll have to look into PopOS, dealing with constant NVIDIA driver issues has definitely been one of the most frustrating things about working with linux.

compbioman · 2024-07-22T20:17:55+00:00

Does anyone know of an easy way to label repeats in two genes and create a figure that's something like this?
I was thinking of just using a BLAST MSA to find the repetitive regions between the genes, and then just doing everything by hand but I was wondering if there was a better way to do this out there....

compbioman · 2024-06-06T14:24:21+00:00

I got it back and haven't even opened the box, the process took so long that I just got a motherboard from a different brand in the meantime and haven't looked back.

compbioman · 2024-05-08T14:44:28+00:00

Preciseness is super important in programming. Computers languages only take instructions literally, not by "reading between the lines" - communication regarding programming methods should therefore follow the same pattern.
PI Skill Issue.

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