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Consider working on genomics

claymcleod.dev

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Re: Consider working on genomics

#291

Post by pengwing »

jinto36 wrote: post #198
pengwing wrote: post #26

Can you provide a list of the top problems in that space? Much rather try to understand them deeply myself and build a company solving them than just getting a job.

Protein structure prediction was a huge deal, which is why AlphaFold received so much fanfare. It is actually pretty good. The next step is to predict where multi-protein complexes would interact- which is not just as simple as predicting the structure of two proteins independently and then trying to fit them together like a puzzle, because the the interactions can also change the structure. While it's not as hard as…

So if I understood you correctly then further lowering the cost of experimentally determining protein targets could be a viable way forward that is completely orthogonal to computational methods?

Re: Consider working on genomics

#292

Post by x0x0 »

otoburb wrote: post #274
lebovic wrote: post #175

I'm a software engineer who works on genomics. I see a lot of negativity in this thread, which mirrors my experience: in most places, you'll be paid like a researcher with the respect of a lab assistant – unless you have a PhD and a postdoc. That said, it's possible find work that's respected and pays well. Most of that kind of work is happening in the context of startups or freelancing. My favorite example of this i…

>> I see a lot of negativity in this thread, which mirrors my experience: in most places, you'll be paid like a researcher with the respect of a lab assistant – unless you have a PhD and a postdoc. As an outside observer to this area, something doesn't add up. It sounds like software tooling is desperately needed to advance the entire field across the board, yet it seems that few startups or founders are attempting t…

> As an outside observer to this area, something doesn't add up. It sounds like software tooling is desperately needed to advance the entire field across the board

This is hardly the only place in society where X is desperately needed, but people don't want to pay for it, and continue to suffer through the underprovision of X.

Here, software engineering is simply not viewed as prestigious or important, or often, even as valuable. The science is viewed as valuable. A lack of bugs or rigorous software engineering practices... nobody cares.

Some of it is a phd is a prestige competition, and dirty engineers being comped on par with people who spent (cough wasted cough) a decade or more of their life in college/post-docs just won't do.

And a piece of it is the scale of the investment needed. Imagine a couple million LOCs with only manual testing. Your two weeks of writing tests is a tiny drop in the bucket. Retrofitting reasonable software dev standards on these projects is enormously expensive.

Finally, there's an inescapable volume issue. Suppose I build a hot new confocal microscope and I sell 300 of them for low hundreds of thousands each. I have 2 teams of devs ($2M/year/team) for 2 years on analysis code, for a $8m investment. That's $27k/machine. That's real tough math to make work. Whereas Google pays gmail engineers really well, in part because they spread those costs over a billion users.

Re: Consider working on genomics

#293

Post by aaauaucuggaa »

heuermh wrote: post #288
aaauaucuggaa wrote: post #158

I will add Mammoth Biosciences to the list. We are looking for Software Engineers, Data Engineers, Data Scientists and more. https://mammoth.bio/careers/

Had a glance at the team page on the Mammoth website, curious to learn more about how the various roles fit together. Mind sharing a way to get in touch?

Sure, feel free to drop me am email at kylem at mammothbiosci.com

Re: Consider working on genomics

#294

Post by ethbr0 »

x0x0 wrote: post #292
otoburb wrote: post #274

Earlier quoted context omitted.

>> I see a lot of negativity in this thread, which mirrors my experience: in most places, you'll be paid like a researcher with the respect of a lab assistant – unless you have a PhD and a postdoc. As an outside observer to this area, something doesn't add up. It sounds like software tooling is desperately needed to advance the entire field across the board, yet it seems that few startups or founders are attempting t…

> As an outside observer to this area, something doesn't add up. It sounds like software tooling is desperately needed to advance the entire field across the board This is hardly the only place in society where X is desperately needed, but people don't want to pay for it, and continue to suffer through the underprovision of X. Here, software engineering is simply not viewed as prestigious or important, or often, even…

> Here, software engineering is simply not viewed as prestigious or important, or often, even as valuable. The science is viewed as valuable.

Specifically, publishing is viewed as valuable. And publishing is a frozen-in-time snapshot.

Ergo, all the things that drive quality software elsewhere (SRE, maintainability, interpretability) simply don't exist as incentives.

> [Low product sales count is] real tough math to make work. Whereas Google pays gmail engineers really well, in part because they spread those costs over a billion users.

Also a great observation. Most cutting edge is, by definition, mostly custom. It's really hard to amortize even incredibly valuable things over tiny population counts and still pay market software engineering wages.

Re: Consider working on genomics

#295

Post by aednichols »

maxFlow wrote: post #269
aednichols wrote: post #235

Earlier quoted context omitted.

Current Broad SWE with 5 years’ tenure. Feel free to ask any questions. I’m in the “bunch of software people together” department so it’s not as insular or PI driven as working in a lab. I still mostly like the role but it has become more generic over the years as the department acquiesced to the working ways & programming languages of outside private funders.

1. Could you share a bit about your stack? I'd be specially interested about the data engineering side of things if possible. 2. As a SWE, how deep into biology/genetics concepts have you had to go during your tenure?

1. I'm on the product engineering side rather than data, but from what I know, Scala is still heavily entrenched. New projects are all in Java; other languages are effectively disallowed.

2. I learned a fair amount in the 2017-2019 time frame but with the pandemic and increased specialization my pace has decreased. Lunchtime talks are just not as fun to attend on Zoom. Another possible explanation is that my curiosity has been satisfied, and someone with more curiosity could get more out of it.

Re: Consider working on genomics

#296

Post by aednichols »

noname123 wrote: post #284
geoffjentry wrote: post #244

Earlier quoted context omitted.

A really hard aspect to this is that there's a massive impedance mismatch between the research & production side of things. Working in the research side is pretty straightforward - although software development practices are going to be a lot looser & faster. Working in a production environment is straightforward, it's like any other software job. But - working at the confluence of those two states is incredibly diff…

Fwiw I acknowledged the good people directly from the Cromwell team on a presentation recently due to the incredible support/help somebody & their team provided my team. The WDL/Cromwell community has grown and I've heard people mention it everywhere now (far away from the Broad) and it's in no small part due to that team and its former leadership.

Hey, that's my project! (And geoffjentry is my former boss.)

Nice to hear the praise, thank you. The project has changed a lot over time and inevitably left some disappointed people filing Github issues (CWL, non-cloud backends, etc).

It's really unique and enjoyable working on OSS that has a strong community, it is the highlight of my career.

Re: Consider working on genomics

#297

Post by aednichols »

isoprophlex wrote: post #67
mdlm wrote: post #22

Those who are interested in the Broad Institute can reach out directly to me at mdelamaz@broadinstitute.org

Do you do fully remote positions, from non-US timezones (eg. Western Europe)?

[Also at Broad] Must be a US resident except for exceptional cases (e.g. world-renowned scientist).

Re: Consider working on genomics

#298

Post by sargstuff »

whatever1 wrote: post #267
sargstuff wrote: post #255

Earlier quoted context omitted.

Umm..... software weather modeling systems map equations that may change daily completely due to modeling / assumptions change.

Funny you mention weather because I have worked in the field. We had to make a change in the discretization scheme, and pretty much all of the assumptions of the super optimized parallelized production version had to be thrown away, to the point that we had to abandon it completely. Software engineering needs well defined boundaries to design between them and test edge cases. When we are doing fundamental research we…

> "Funny you mention weather because I have worked in the field. We had to make a change in the discretization scheme, and pretty much all of the assumptions of the super optimized parallelized production version had to be thrown away, to the point that we had to abandon it completely."...

Ah, so initial pixilation for front fonts weren't unicode compatible? :-)

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