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Consider working on genomics

claymcleod.dev

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Re: Consider working on genomics

#141

Post by boldlybold »

olalonde wrote: post #103
AlbertCory wrote: post #27

20 years ago I got interested in "bioinformatics." I loved learning something about molecular biology, after all those years of hearing about DNA and not understanding it. And "Molecular Biology of the Cell" is, hands down, the greatest textbook ever written. That said: a lot of the comments are spot on. You're working in a field where the hard scientists and business people rule and you're a helper. Maybe they're gr…

Is it feasible to do any meaningful work in this field without joining a team? (e.g. as a solo hobbyist/entrepreneur)

If you have a software background and can get some basic domain knowledge, there's lots of open source projects that could use your contribution.

Doing fundamental reseach is a taller order. But lots of software, tools, pipelines etc need maintainers, optimizations...

Re: Consider working on genomics

#142

Post by boldlybold »

mherdeg wrote: post #136

What is the opportunity here -- writing new algorithms, implementing them accurately, optimizing them for special execution architectures, or just building more usable tools? I remember Manolis Kellis sprinkled some pretty interesting genomic questions into his Algorithm class's problem sets. There were a number of cool problems about optimally aligning strings, searching within text, etc. This was like 15 years ago…

We're only starting to see the age of genomics accelerated by GPUs. I think it's still early if you have the technical background.

Re: Consider working on genomics

#143

Post by pclmulqdq »

clmcleod wrote: post #46
AlbertCory wrote: post #27

20 years ago I got interested in "bioinformatics." I loved learning something about molecular biology, after all those years of hearing about DNA and not understanding it. And "Molecular Biology of the Cell" is, hands down, the greatest textbook ever written. That said: a lot of the comments are spot on. You're working in a field where the hard scientists and business people rule and you're a helper. Maybe they're gr…

> That said: a lot of the comments are spot on. You're working in a field where the hard scientists and business people rule and you're a helper This definitely was the culture when I started working in the field 6 years ago. However, the culture has shifted (at least where I work) to where biologists and engineers are equal partners that work together on solving these problems. For those organizations that are not t…

That may be the case for engineers with PhDs and scientific credentials, but I'm not so sure that is true of normal developers who did not play the academic game. I'm not going to take a job based on the eventuality of a culture shift, and I don't think you should either.

This isn't just genomics, by the way. Scientific computing folks are very similar.

Re: Consider working on genomics

#144

Post by robertlagrant »

> Of course, this would not be the fault of the individuals who maintain the software, who are often brilliant: it's just simply not fair to expect individuals to ensure this consistency using their own, ad-hoc processses

I think this is a little generous. Engineers of all stripes should take responsibility for their work. If they say, "Yes I can add methylation analysis in three weeks," then they should make sure that means it's made well, with tests and all. I've definitely encountered people who don't communicate the scale of the task, and for most of them it's because they don't do software engineering; they do informatics scripting.

Re: Consider working on genomics

#145

Post by noname123 »

I just want to add my $0.02 to respond to the low pay and low respect as a Software Developer/Engineer in the genomics. This is 100% true and also not true [bear with me]... you get it back in the back end.

First the comp, most people think about the income they get as in levels.fyi TC. IMHO, The no. 1 value add is working for an academic center is the freedom in both time and spirit you get in pursuing your interest and the side ventures & hustles which eventually compounds. The hours are very reasonable in academia and in most places, you can take classes internally on campus or get reimbursed for it and get supportive managers who let you take time off from work to study. Or just great WLB to pursue something you really enjoy. And this compounds both spiritually and financially.

Just a data point of one, I took an online data science degree whilst working like 15hrs/week and 25hrs on classes. From the classes, I got the bug to apply data science I learned on my degree and on the genomics analysis job to apply to the financial markets/automated trading. Now over the past 4 years, I've achieved CAGR of 35%, and sharpe of 2.5 where my options trading portfolio capital gains outsizes consistently my W-2 pay and keep me par on L5 of FAANG engineer. To give you an idea, my other co-workers have gone into side-hustles real estate (not sure about now) or running day-care to great success. Yes because you have that much free time.

Now autonomy/academic stimulation, I would not give it up for the world even if I was doing it for free. Previously I was working for a "hot tech" company where I was bored out of my minds cranking CRUD widgets and re-learning JS frameworks every year and attending BS lunch n' learn work sessions of new crappy libraries with hipster names. In genomics, you get to apply traditional stat techniques (bioconductor), deep learning techniques (tensorflow, AlphaFold, GANs) and learn latest sequencing protocols (scRNASeq, ChIPSeq, CRISPR screenings) and learn the biology domain too (immunology, viral responses, cell regulatory networks, synthetic biology. It's like being on the front-seat to a movie cinema or basketball court where the scientific evolution is happening. You're learning something new everyday and you are at the center of it all as PIs, wet lab bench scientists all depend on you to perform the analysis and build the pipelines... and 8 years in, and I'm still excited with the only disappointment that I will never learn it all.

Obv. a subjective data point of one, but I just want to add my data point just in case somebody out there on the fence. Yes sometimes you can truly have it all.

Re: Consider working on genomics

#146

Post by jesse__ »

Shameless self-promotion incoming.

I'm interested in contributing to this field. I have significant experience in 3D graphics, game engines, compilers and language runtimes. I'm a competent low-level engineer.

There's a lot of red-flags in this thread about adverse working conditions, but I'm running under the assumption there are a handful of companies out there that work with a software-minded approach.. ie. respect SWEs for who they are and what they do. If you represent one such company, and are looking for engineers who have a keen eye for performance and architecture, I'd love to hear from you.

jesse@scallywag.software

https://scallywag.software/resume.html

EDIT: Largely interested in remote roles, but could relocate for the right offer.

Re: Consider working on genomics

#147

Post by quest88 »

boldlybold wrote: post #141
olalonde wrote: post #103

Earlier quoted context omitted.

Is it feasible to do any meaningful work in this field without joining a team? (e.g. as a solo hobbyist/entrepreneur)

If you have a software background and can get some basic domain knowledge, there's lots of open source projects that could use your contribution. Doing fundamental reseach is a taller order. But lots of software, tools, pipelines etc need maintainers, optimizations...

Which projects? That seems like a good place to start.

Re: Consider working on genomics

#149

Post by rleigh »

cycomanic wrote: post #90
cratermoon wrote: post #63

Earlier quoted context omitted.

> be treated as second-class employees The pay isn't all that important to me, as long as I can live on it, but this. It was so obvious when I was working in academia that because I wasn't myself an academic that I was just lab help, no better than the person who washes the test tubes and beakers.

I don't quite understand this post. In my experience lab technicians in academia are highly valued (however I mostly have experience with clean room staff), however they are support for the researchers, who drive the research agenda (well actually it's the funding primarily). What exactly do you expect to not be what you call "a second class citizen"?

Are you really, really serious?

Academia is a hugely elitist pyramid with well-demarcated layers, and the lab technicians are at the very lowest level of the pecking order, down with the cleaning staff.

They might be "needed", but by and large are they really "well respected" or "valued"? Not really, sad to say.

Re: Consider working on genomics

#150

Post by attractivechaos »

olalonde wrote: post #103
AlbertCory wrote: post #27

20 years ago I got interested in "bioinformatics." I loved learning something about molecular biology, after all those years of hearing about DNA and not understanding it. And "Molecular Biology of the Cell" is, hands down, the greatest textbook ever written. That said: a lot of the comments are spot on. You're working in a field where the hard scientists and business people rule and you're a helper. Maybe they're gr…

Is it feasible to do any meaningful work in this field without joining a team? (e.g. as a solo hobbyist/entrepreneur)

Difficult but possible. For example, Robert Edgar [1] works alone and is one of the most productive developers in this field.

[1] http://drive5.com

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