I started working at a genomics company about a couple of years ago and my experience is very different from the post. Although there might be a handful of bioinformatics tools that are quite old, the ones at the heart of of operations are worked on by teams and reasonably maintained, and although I agree with the headline that there's a lot of work to be done in the area - my perspective is a little different. Although this doesn't apply to all genomics companies, I'm at a company that has a lab, and the software we write makes the lab about 8x more efficient and the next generation of sequencing technology will bring sequencing costs down by about 5x. Meanwhile the science and literature keep pushing further and newer generations of physicians are putting a stronger emphasis on genomic counseling. Thanks in part to the power of viral sequencing data the government is starting to trust laboratories that bring valuable and actionable insights. I think all of those combined with the fact that CRISPR technologies are getting further along puts genomics in a unique position. TLDR; yes genomics is exciting and on the brink of something big, but no it's not a dumpster fire that needs saving. Oh and as a bonus - I get to work with really smart scientists and they are very friendly :)
Consider working on genomics
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Re: Consider working on genomics
#16220 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 got me extremely excited about genetics and bioinformatics, highly, highly recommend this book to any software person I meet who is interested in biology. As to the work environment, it seems to be extremely varied depending on the lab and team your on. I came from a number of years doing web development in marketing and finance before joining an R1 university research lab, and in many w…
Any particular edition of Molecular Biology of the Cell you’d recommend? I just looked up the 7th edition on Amazon (seems like the latest) and it’s $300 USD. Oof.
Re: Consider working on genomics
#163I recently switched from software engineering on ads and web performance at a FAANG to (meta)genomics at a nonprofit startup; happy to answer questions
F. The parent article mentions solutions are often custom made by one person. Can problems in the field be reduced such that extensible open-source frameworks could be applied? The way we have frameworks for webdev?
I'm very new to this area, and am really not the right person to ask, but I'll try my best ;)
In general you have frameworks when lots of people are trying to solve a large number of problems that look similar at the start and then will diverge. That's pretty web specific. I think instead in bio you mostly get (and will keep getting) modular tools and pipeline standardization.
Re: Consider working on genomics
#164Usually, 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…
> Good luck trying to use a functional-first language, aside from maybe Scala
While they've moved away from it in the last few years, the Broad Institute had a huge investment in Scala. It's been in use there since at least 2010 and I believe longer. The primary software department was almost entirely Scala based for several years. That same department had pockets of Clojure as well.
Re: Consider working on genomics
#165What 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…
> But is there still algorithmic low hanging fruit?
I would say no unless looking at the frontiers of what is done in the wet lab which might require new analytical tools. But this stuff is probably much easier for and much better aligned with someone doing CS in academia.
My impression that there is quite some space for ML-based approaches including DL. But even there I would not call it low-hanging.
Re: Consider working on genomics
#166Earlier 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)
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
I worked with Bob some ~20 years ago at Berkeley. he showed up one day to check out the seminars and see if he could "help out" after having sold his database company to Intel. he said he'd been trained as a physics guy in the 80s but there were no real jobs so he started a software company instead. He joined my advisor's group (it helped a lot, because at the time most journals wouldn't publish a paper submitted from a home address).
He proceeded to completely understand hidden markov models and protein sequence alignment and was immediately hacking improvements to HMMER. However, Sean Eddy couldn't understand his optimizations (Sean has to know how HMMER works at all times) and so Bob went off and made his own tools like MUSCLE.
One of the reasons he can do this is, well, he's a programmer/math genius, and the other reason is that HMMs and protein alignments are a fairly well understood and programmable thing these days.
Still blows me away we train up all these people to be scientists when there are no jobs for them in that role.
Re: Consider working on genomics
#167I'm most definitely not an expert in this area, but I have recently taken interest in learning about "succinct data structures", which from what I understand have their place in bioinformatics.
It's been a challenging topic to learn about, because most of the information comes from Computer Science papers and articles where the information is presented in a very formal, mathematical way, which I am just not used to.
Normally when thinking about data structures and algorithms, we're mostly concerned with optimizing for speed. Space complexity is not usually as big of a consideration. Succinct data structures are all about creating ways to achieve good runtime performance while representing the data in a "compressed" format. I think this comes in handy when doing things like DNA sequencing since data sets are so large.
I'm excited to check out some of links in the post, and in case any one else is interested in learning more about succinct data structures, here's a few resources I'd recommend:
Prof. Ben Langmead's YouTube channel: https://www.youtube.com/user/BenLangmead/featured
Alex Bowe's blog has some good content: https://www.alexbowe.com/articles/
Prof. Erik Demaine's "succinct" lectures from his adv. data structures course at MIT on YouTube: https://www.youtube.com/watch?v=3Y2weLDiUWw
Edward Kmett's Haskell live coding session going into some details about succinct: https://www.youtube.com/watch?v=9MKEmNNJgFc
There's also a lot of research papers, which you should be able to find by searching for "succinct data structures" (Jacobson, Munro, Brodnik, Raman, Rao, Navaro, Sadakane just to name a few). I at least have a basic CS undergraduate degree, but many of these papers are over my head, but I have still been able to slowly understand more and more. Some I had to purchase.
Re: Consider working on genomics
#168I work in genomics, this is very true. I know of some modernization efforts, ie by companies working with new file formats, like GenomSys [0] with mpeg-genomics [1].
It feels like it’s going very slowly though. The field just really depends on their Unix philosophy tools, there is a lot of gzipped text files that are piped through bash scripts and tool like awk and grep. It works, mostly, but there is a lot of weirdness.
Re: Consider working on genomics
#16920 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…
Having worked (as a consultant/contractor) for a few businesses in the field, I can say that my experience was closer to "grateful for your help" than to "an overpaid lab assistant". I even recall once, in a meeting, being referred to (by a senior staff scientist with a Ph.D.) as "the technical guy", causing me to wonder at how someone who does gene sequencing thinks of programming as being more technical. But, YMMV.
> causing me to wonder at how someone who does gene sequencing thinks of programming as being more technical
Everything you don't understand looks complicated from the outside.
Re: Consider working on genomics
#170I recently switched from software engineering on ads and web performance at a FAANG to (meta)genomics at a nonprofit startup; happy to answer questions
Are there any open source tools/projects worth contributing to that don't need specialized infrastructure, proprietary data, or a PhD in the field to understand?