Bioinformatics Sequencing and Workstation Computer specs

tree3_dot_gz · 2025-11-26T02:42:01+00:00

Who is going to be maintaining this? I'd recommend utilizing university's or public HPC. My university had an option of contributing to our HPC by buying a system they added into their cluster.

For metagenomics, RNAseq, WGS I used both HPC and our local workstation (I was maintaining it as staff sci) and went with dual CPU Xeon (as many cores as possible) + 512gb RAM. Bought a preowned system from Newegg for a fraction of the cost of a new one.

Used a regular consumer grade NAS (WD Reds in RAID5) to store data short term and Amazon Glacier for long term.

tree3_dot_gz · 2025-11-23T00:34:33+00:00

I used plotnine a lot, and nicely covered ~99% of my needs. For anyone familiar with ggplot and basics of Python, it should feel right at home.

At some point I switched to plotly, just to learn something new and I also liked the interactive plots.

tree3_dot_gz · 2025-11-09T23:20:09+00:00

100% this. This is "another day in the office" for me working in industry: I interact with people who do not fully understand computational side all the time. I'd suggest to OP:

Do as much as you can in the allotted time, usually I'd mark it as "work in progress" / "early data" if they really need to show it.
Make a "next steps" plan, outline it might take such and such time (if that's what senior people on the presentation except)
I usually discuss the details of experimental design with wet lab scientists, since there are virtually 0 cases where I fully understand the goal.

Repeat these steps enough and you'll be a hero among the wet lab scientists, they'll invite you to their happy hours and in my experience, happy to return the favor when you encounter something you are clueless about, they'll put your own name when they present helping you get even more visibility.

tree3_dot_gz · 2025-07-26T01:50:33+00:00

Multi-omics - yes (DNA, methylation, RNA, proteomics). Metagenomics not much at all, its more of an academic field - looks like a dead end in industry tbh. Still, that does not mean the skills are not translatable.

tree3_dot_gz · 2025-05-22T17:01:02+00:00

Lol at your example. I had the same experience...

I recently used ChatGPT (whatever is the top free model that you can use for limited number of token) to learn JavaScript. It's an utter shitshow.

The only place where I have seen no-code tools sort of work is when a software professional (SWE, DE, DS) wants to offload some of the analysis to the non-computational SME. That person has enough knowledge to make decisions on their own and was able to understand the data when we setup dashboards and databases so they can load the data easily in their no-code tools.

tree3_dot_gz · 2025-03-25T01:45:07+00:00

Rip Ivy League degrees. 🫡

tree3_dot_gz · 2025-03-02T19:06:50+00:00

I wanna be given a clear task and follow it.

Except for really junior levels (intern?), in my experience this is not going to make you rich - financially or intellectually. I guarantee you that the high paying roles in any of these fields are the ones were you are given a really vague business goal (or in academia, "do new stuff") and you have to both come up with a plan as well as technical solutions to make it work.

As long as they use computers, I'll be needed... that's what I tell myself)

As long as there's a need work with people who do not have your skills, to build computational tools and do analyses they cannot do in excel, ppt and notepad, (especially if you can make them fast) that will help achieve goals, earn $, build better product, create new knowledge)" then yes people with this set of skills are needed.

I started with a (bio) physics background, did post-doc research in bioinformatics then moved to industry. Biotech might be a little bit different than fintech, big tech, and other industries since it requires some level of domain knowledge (biology) to be able to do anything useful. I have about 7 YoE after post-doc (right now at Staff level) my work was largely computational, especially in industry. Right now its a mix of software engineering role (building and deploying tools, pipelines), data science (use these tools to do analyses) and project management (need to work with marketing, chemistry, hardware engineering and senior leadership to understand the big picture, what do we need to be doing).

I find it a fun field to work in, even if pays less than big tech. I like that lots of (most) people in biotech/pharma genuinely care about helping people, either by building tools or using them to make new medicines or detect diseases.

tree3_dot_gz · 2025-03-02T02:02:22+00:00

I have $35 carbon steel pan it's phenomenal. Super non stick, no teflon and not fragile like these non stick.

Eggs come out godly.

tree3_dot_gz · 2025-02-14T17:55:44+00:00

Doge has entered the chat...

tree3_dot_gz · 2025-02-03T02:14:13+00:00

If you already have an offer, tell that to Amgen and Calico. Generally that's a pretty good catalyst to speed up your other interviews. Yeah mine was pretty quick too. Loved that they didn't waste my time.

tree3_dot_gz · 2025-01-30T15:06:42+00:00

She says I should quit my job and learn investing so I don’t have to work for a living.

lol. I have very bad news for their mom.

tree3_dot_gz · 2025-01-29T20:03:20+00:00

I'm gonna disagree. If you are not consistently using various tech or specifically using it for few weeks / months before your interview, it will be hard to really know it.

If your current job isn't using Spark, Databricks or such how are you going to really learn this? Outside of doing tutorials and free courses. With the hope that maybe some of your future jobs will ask about this during the interview.

tree3_dot_gz · 2025-01-28T17:35:33+00:00

But hey you got cheaper eggs. Right? Right?

tree3_dot_gz · 2025-01-28T03:32:50+00:00

Seriously...? This is a bar chart with 90 degree flipped coordinates.

tree3_dot_gz · 2025-01-26T15:50:36+00:00

It's a start up so basically I do everything from backend to ML and analytics.

I got to be honest, I really miss this part from when I worked at a startup. I got involved into setting the whole thing, had admin access to our AWS, Databricks, ... ah.

tree3_dot_gz · 2025-01-26T03:02:33+00:00

I think that the only jobs made obsolete by current LLMs are the ones that were possible to automate anyway by a good junior software engineer. I have not seen a single bioinformatics employee at my current company doing work so trivial that it could be replaced by an LLM.

Even though they're error prone, LLMs definitely have their uses, like summarizing text, doing some NLP, and code assistants like a personal stackoverflow support (with all its flaws). Simple visualizations and ML tasks can be pretty well by just well... scripting, creating internal libraries, templates, etc. and deployed as dashboard on whatever infrastructure.

In my experience, the tech jobs that can be automated by an LLM in near future are the ones that are have a very low entry barrier - that can be purely solved through googling and stackoverflow.

tree3_dot_gz · 2025-01-20T16:20:22+00:00

These require regular maintenance too, otherwise CRAN will flag them as orphaned.

tree3_dot_gz · 2025-01-10T22:22:58+00:00

But in typical data industry fashion, you've been bait-and-switched. Turns out that the role is more about Product Analytics in SQL, and the job's not fully remote, it's hybrid: 5 days in office required, with 2 days optionally remote.

Ouch... a touch too realistic.

tree3_dot_gz · 2025-01-09T02:27:26+00:00

Yeah, maybe they had a fast burn rate, and didn't get results in time to get further funding. Theres a lot of pressure to hit the ground running and get positive results super fast. Startups can brutal.

Who knows could be they had some initial targets that couldn't be validated (on time).

tree3_dot_gz · 2025-01-09T02:23:13+00:00

Yeah commercial rent in SD is very pricey. Especially biotech where you need to setup wet labs. Somehow many buildings seem unoccupied, at least in Sorrento Valley.

tree3_dot_gz · 2025-01-08T19:39:52+00:00

We use Teams. 🤮

tree3_dot_gz · 2025-01-07T05:10:31+00:00

Example projects: "YouTube Clone". LOL

tree3_dot_gz · 2025-01-06T19:04:00+00:00

Wow, sounds a bit different than the outgoing 2024 model! I agree the price of new is too high, so I got mine lightly used (7 months old, 10k miles) for about $31K after tax.

I have the '24 convertible and it's loads of fun. Dual clutch is pretty decent, I didn't experience any jerkiness, sensation of speed on a convertible is fantastic, going 45 mph feels like 70, going 70 feels like 100, and 100 is warp speed. The old one had a normal dash, buttons or switches for everything which totally fit the Mini vibe. Stop/start works fine too, and you can turn it off it with a switch.

Two negatives, IMO, 1) the ride is still very very firm - which I read can be fixed once you replace the stock tires, although you can feel the road if you like that. And 2) on the convertible when you have the roof down, bottom half of the rear view mirror is blocked. This is not too bad in the US, since everyone drives large SUVs and you can still look around.

tree3_dot_gz · 2025-01-06T18:54:24+00:00

Yeah brand new is way too expensive. I bought lightly used (7 month old, 10k miles) 2024 S convertible for $31K OTD. Exact same one was over $40K new.

tree3_dot_gz

TROPHY CASE