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Consider working on genomics

claymcleod.dev

111–120 of 299 posts

Re: Consider working on genomics

#111
Hard no.

Initial code would still be developed by SME, who:

- Don't understand most programming abstractions

- Don't see the advantage of a clean codebase

- Would rather go back to their code spaghetti mess, than help figure out why some corner cases behave differently in a fresh codebase

- Would still submit changes to their code spaghetti mess and expect you to apply them to the cleaned codebase

I did what the author suggested (not in genomics, but in a different research-heavy scientific field) for a while and would not recommend it to anyone.

And that's not even taking compensation and work conditions into account.

Re: Consider working on genomics

#112
post #72

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…

>Molecular Biology of the Cell Tangential, but what are the chemistry prereqs to grasp this book?

MBC is readable by someone with an undergraduate background in science. You'd probably want basic knowledge of biology, general chemistry and organic chemistry.

It's essentially an upper-level undergraduate textbook.

Re: Consider working on genomics

#113
heh, you think scientists automatically understand computing nature?

You’ll be the janitor cleaning up their 20k LoC, one file Python with zero abstraction.

If this is already a thing at a FAANG, it will be worse at a pure science shop.

Re: Consider working on genomics

#114
Usually, scientific oriented companies or organizations have little regard for software as a domain, craft, etc. It’s just a thing that gets in the way, despite being vital. It’s almost just a utility to them rather than a differentiator and active component of the advanced work going on.

For example, the Broad Institute is super interesting, but having applied there several times, they are esoteric, to say the least, in their hiring. They pay well below market, and their process is opaque and slow and sometimes downright non-communicative. They are also not really open to remote work, so you gotta move there and commute to the heart of Cambridge. Budgets are set by folks maybe a couple years out of a PhD program, who will also make technical decisions in terms of the software design (the latter an assumption given my experience in similar places).

These organizations are also pretty traditional in their selection of stacks. Good luck trying to use a functional-first language, aside from maybe Scala (usually lots of Java stacks), and be prepared to write lots of Python, the only language that exists to many scientists. I once saw a Python signature (function name and arguments) spill over 10-20 lines, in a file over 10,000 lines long. They had given up on another software stack because “it wasn’t working for them”.

This is all painting with broad strokes, of course. But I think scientific organizations that would embrace software as a major component of their technological and scientific development would do well. There’s a lot of opportunity.

Re: Consider working on genomics

#115
post #83

The author completely neglects the downsides: - The compensation absolutely do not match the workload and education required. - The sheer number of disreputable PIs and their unrealistic goals for software. - The data is likely questionable and often underpowered. - Institutional politics. everywhere. - Marketing ("Curing Cancer"). The role is actually just juggling various bioinformatics file formats.

PIs?

Principal investigator: https://en.wikipedia.org/wiki/Principal_investigator

The person that runs a research lab, which at a university is usually a (tenured) Professor.

Re: Consider working on genomics

#116

I've worked on genomics, at the Broad. Can confirm there is a ton of toxicity. There's also a lot of smart and great people, if you can find a team specifically dedicated to software I would recommend it. Also the pay is good...for a non-profit. More broadly...shortages like this aren't because SWEs just love ad-tracking and hate health improvements. People need to be willing to pay for these services (case in point;…

Hmm as an ex-Broad employee (and now in another genomics center), what did you find really toxic about the Broad?

FWIW, I really loved Broad the people, my direct line manager and co-workers. The management was horrible and the management at DSP (not the line folks/managers) were the worst.

Re: Consider working on genomics

#117
post #83

The author completely neglects the downsides: - The compensation absolutely do not match the workload and education required. - The sheer number of disreputable PIs and their unrealistic goals for software. - The data is likely questionable and often underpowered. - Institutional politics. everywhere. - Marketing ("Curing Cancer"). The role is actually just juggling various bioinformatics file formats.

PIs?

Principal Investigators. Basically, the academics who get the grant funding and run their own research groups.

Re: Consider working on genomics

#118
Genomics was a pretty good place for software engineers that have an interest in molecular biology; however, the pay is not generally comparable with that earned in a tech industry job. Interesting (to me) is that the software engineers that I've worked with in genomics-oriented labs treat biologists and biological data as the gold standard, while the biologists in those labs are fairly reverential towards the software engineers and computational results! Of course, both are overly optimistic ... Unfortunately, the best software engineers I worked with eventually jumped to software startups or tech industry jobs.

Re: Consider working on genomics

#119
I am a career SW engineer that has worked on genomics in a startup. The field is genuinely exciting.

The endemic disease of the field is the leadership. A leadership made out of Principal Investigators forged in academia, appear simply incapable of producing any item which is not articles (or equivalents thereof).

Re: Consider working on genomics

#120
post #98

Look, I did this at multiple places for a number of years. The issue is that you often form an adversarial relationship with the scientists. They don't really want you there. They are perfectly happy just organizing everything by hand with post its and excel spreadsheets. They do not want you to mess with their flow with your software, even if it would help them to be more efficient.

Can you elaborate with some anecdotes? Why is their current workflow wrong? Why would an organization hire someone to build software if they can achieve goals with spreadsheets?

Why indeed.
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