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Consider working on genomics

claymcleod.dev

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Re: Consider working on genomics

#251

Post by boldlybold »

quest88 wrote: post #147
boldlybold wrote: post #141

Earlier quoted context omitted.

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.

I contribute to Nextflow core (https://nf-co.re/) It's more of a collection of pipelines than traditional software, but there are users all around the world and a good community.

Most of the packages on bioconda (https://bioconda.github.io/) are open source. But you probably want to find a sub-field that interests you most before finding a project.

In grad school, we also had an ex-google software engineer volunteer with us one day a week. It was very impactful for many members of the lab to learn good engineering practices, and it wasn't at all like the sentiment others in this thread are expressing where engineers were "janitors".

Re: Consider working on genomics

#252

Post by sseagull »

aWidebrant wrote: post #134

"From my experience, what works incredibly well is a partnership between biologists and software engineers: the biologists first come up with the first concept of the tool, which is purely focused on ensuring good results. After this first iteration is completed, engineers then come in and rewrite the tool using modern engineering practices with things like speed and reliability in mind." Like others have pointed out…

I’m more familiar with chemistry, but a lot of times the scientist is the one who needs to make the first iteration to prove their idea. It’s often the case you really don’t understand the problem until you actually program/run the idea in at least a quick and dirty way.

But the role of the software engineer after that is invaluable in making that idea accessible and reproducible.

Re: Consider working on genomics

#253

Post by sargstuff »

CoastalCoder wrote: post #31
pestatije wrote: post #15

Earlier quoted context omitted.

> This state of affairs makes it difficult for anyone other than the original author to contribute to these code bases, further cementing the one-maintainer policy. Who wants to fix other peoples code mess? This is a no-no if you want to promote a job opening.

I've seen this also in several software systems that started life in a CS grad department. (Not all the same university.) The original authors' quirks get enshrined in the code base, and its neigh impossible to fix until they leave the company that commercialized it.

sorta like the original calculus thesis.

Re: Consider working on genomics

#254

Post by [deleted] »

clmcleod wrote: post #197
aWidebrant wrote: post #134

"From my experience, what works incredibly well is a partnership between biologists and software engineers: the biologists first come up with the first concept of the tool, which is purely focused on ensuring good results. After this first iteration is completed, engineers then come in and rewrite the tool using modern engineering practices with things like speed and reliability in mind." Like others have pointed out…

Yeah I think this is fair enough after reading it back. However, that was not exactly my intention here, and I think this is a case of me needing to be more careful in my wording. When I said that software engineers add in the speed and reliability, I didn't mean they _only_ add in the speed and reliability: just that these two tenants of good software engineering where accounted for in this "correct" way of doing th…

[deleted]

Re: Consider working on genomics

#255

Post by sargstuff »

whatever1 wrote: post #152

These should be separate in academia. SWEs cannot write code that maps equations that may change daily completely due to modeling / assumptions change. Too much focus on modularizing, premature optimization, useless unit testing etc. Who cares about all these if the underlying model is wrong? If things are stable enough to go into production then the code should leave academia and be re-written properly by SWEs, not…

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

Re: Consider working on genomics

#256

Post by iainctduncan »

I worked for a while at a consultancy supporting genomics through LIMS (lab info management software) customization, so not really genomics, but in the genomics biz (big genomics companies were our clients). For me, it was the least interesting software work I have done in my 20 year coding career. On the other hand, for people who just wanted a steady pay cheque and to go home at 5pm, it was a good gig. But man, software that moves samples and test tubes and their data around, it could be cars in a parking lot for all that the science makes it interesting.

We had bad attrition to both more interesting and higher paying work. (I left for both after a year at the consultancy)

Re: Consider working on genomics

#257

Post by sargstuff »

_Wintermute wrote: post #172
didip wrote: post #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.

You'll be lucky if it's python, most likely thousands of lines of R by someone who doesn't know how to write a function or declare dependencies.

Ummm... messy python/R sounds lot better than messy numerical analysis in fortran with NO programming standards because has been used/modified for over 50+ years.

Mainly because can find / write software to analyze & reorganize modern structured languages such as python & R into something recongnized in programming field as appropriate approach/structure.

Re: Consider working on genomics

#258

Post by sargstuff »

robertlagrant wrote: post #144

> 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 th…

> "Yes I can add methylation analysis in three weeks,"

virtual or reprogram the robotic arm?

Re: Consider working on genomics

#259

Post by _dain_ »

neilv wrote: post #155

When considering software roles in science organizations, forget assumptions you might make about a typical tech job, joining a bunch of other software and hardware people -- or you'll risk accidentally ending up on the other side of a distorted status system (not the side that normally pampers techbros). You need to feel out the particular person you'll be reporting to on how well they personally respect and underst…

your parenthetical paragraphs are bigger than your paragraph paragraphs

Re: Consider working on genomics

#260

Post by tejtm »

jdeaton wrote: post #200
tdullien wrote: post #91

So if one was financially independent and wished to write something open-source in that field, where would the highest impact be?

Invent a new file format (or a few) for storing genomics data. They're all the rage in the bioinformatics field. Make sure not to document its semantics so that its implementation is the only spec.

Ahh a "reference implementation" connoisseur
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