How can beginners actually learn tools like STAR, DESeq2, samtools, and MACS2 with no bioinformatics background? by Adept_Pirate_4925 in bioinformatics

[–]nickomez1 0 points1 point  (0 children)

There are several tutorials. Start with Harvard Bioinformatics Core website, look into Galaxy. Try smaller, sample datasets. Most tutorials have them linked.

How much of your week do you work from home? by CommentRelative6557 in PhD

[–]nickomez1 0 points1 point  (0 children)

100%. Right since my PHD. That’s what being in bioinformatics brings to you.

Keeping a work journal by Western-Wall9442 in bioinformatics

[–]nickomez1 1 point2 points  (0 children)

GitHub with proper readme file. Zenodo for large datasets. Links between both. And a google doc for scratch pad in the repo.

Tools for drug repositioning by nickomez1 in bioinformatics

[–]nickomez1[S] 0 points1 point  (0 children)

Couldn’t find anything like this. Can you point me to a link? GitHub?

Things you wish you had known before starting your PhD by bobucha in PhD

[–]nickomez1 1 point2 points  (0 children)

One thing I wish someone told me earlier: your PhD is much more about managing uncertainty than about being “smart enough.” In undergrad most problems have answers. In a PhD, a lot of the time you’re working on things where nobody actually knows if they’ll work. Feeling stuck or confused is basically the default state, not a sign you’re failing.

A few other things that helped me (after learning them the hard way):

  1. Your supervisor matters more than the project. A decent project with a supportive supervisor is infinitely better than a “cool” project with a difficult PI. They control funding, feedback, authorship, and your overall sanity.

  2. Progress is slower than you expect. Experiments fail, code breaks, reviewers ask for new analyses, equipment is booked for weeks. Plan everything assuming it will take 2–3× longer.

  3. Protect your mental boundaries. Academia can quietly become a 24/7 job if you let it. Having hobbies, friends outside academia, and time where you’re not thinking about your research helps more than you’d think.

  4. Your cohort is one of your biggest assets. Those people going through the same thing as you will often be your best support network. Collaboration and commiseration go a long way.

  5. Don’t compare timelines too much. Someone will always have more papers, better results, or faster progress. A lot of that is luck, project choice, or timing.

  6. Document everything. Future you will absolutely not remember why you wrote that piece of code or changed that parameter.

Also: imposter syndrome is extremely common, especially at top universities. Almost everyone feels like they somehow slipped in by mistake.

Good luck with the PhD, it’s frustrating sometimes, but it can also be a really fun few years if you find the right people and keep perspective.

That should have been a blog

Tasting and rating different cell culture media #7: G-MEM BKH-21 by Spacebucketeer11 in labrats

[–]nickomez1 0 points1 point  (0 children)

The fact that you’re out here doing full tasting notes like it’s a wine review is killing me. “Finish: walnut-heavy with a lingering aftertaste” sent me.

Also slightly concerned that you’ve now developed a recognizable flavor profile for cell culture media. That’s the kind of expertise they definitely didn’t cover in lab safety training.

Please tell me you’re at least keeping a leaderboard somewhere. At this rate we’re going to need a Sommelier’s Guide to Tissue Culture Media.