from Hacker News

Introduction to Genomics for Engineers

by froggychairs on 11/24/22, 6:44 PM with 81 comments

• by glofish on 11/25/22, 12:08 AM

  Those looking for a proper and comprehensive introduction into genomics from a programmer's perspective should try the Biostar Handbook:

  https://www.biostarhandbook.com/

  I have learned so much from it.

  It is an introduction into what is like to do genomics in a scientific environment. The content at the link the OP posted appears to be an oversimplified, high level and naive overview

• by dddiaz1 on 11/24/22, 10:09 PM

  I have absolutely loved working in genomics. I am a huge believer that genomics will be a huge part of healthcare in the future, and i have two examples to motivate that point that I think may be interesting to the reader.

  1) The Moderna vaccine was made with the help of illumina genome sequencing. They were able to sequence the virus and send that sequence of nucleotides over to moderna for them to develop the vaccine - turning a classically biology problem, into a software problem, reducing the need for them to bring the virus in house.

  2) Illumina has a cancer screening test called Galleri, that can identify a bunch of cancers from a blood test. It identifies mutated dna released by cancer cells. This is huge, if we can identify cancer before someone even starts to show symptoms, the chances of having a useful treatment dramatically go up.

  Disclaimer: I work for illumina, views my own.

  I wrote some more about why genomics is cool from a technical point of view here (truly big data, hardware accelerated bioinformatics) : https://dddiaz.com/post/genomics-is-cool/

• by civilized on 11/24/22, 8:26 PM

  Really glad to see this, but it reminds me of the earlier HN post that said engineers don't go into genomics because it doesn't pay and requires a lot of investment in learning biology.

• by faizshah on 11/25/22, 1:59 AM

  One of my favorite books in this space is “BioInformatics Data Skills.” It’s just nice concise coverage of a lot of basic tech skills like git, bash, tmux etc. and then coverage of basic bioinformatics skills.

  For me coming from a SWE background the computational skills are very easy to pick up especially if you work with bioinformaticians you can ask questions. It’s the genomics knowledge that is very difficult for an engineer to acquire.

• by ramraj07 on 11/25/22, 12:09 AM

  Starts with “ This Guide is written specifically by and for computer scientists and engineers”

  And yeah it shows - contrived example after another, and honestly not a great description of anything.

  If you want to truly understand genomics you have to understand how biology works. And honestly it’s great info for anyone even if you’re not getting into genomics or whatever.. why would you not want a working model of how life is put together? In that case I’d just recommend dusting off a biochem or cell bio text book and reading just the first 5-8 chapters. Typically they lay it out very simply from basic principles and the authors have far more experience and understanding and writing help than this weird tutorial course thing.

• by ALittleLight on 11/24/22, 10:24 PM

  I didn't get this from skimming the first page - but what will this let me do? If I take this course will I be able to mess with a cell or will I just learn some stuff about biology.

  I saw a recent Lex Friedman podcast where the guest talks about "bioelectric patterns" and somehow getting a worm to grow a second head by messing with those patterns. I would absolutely start on this course now if it was a realistic pathway to doing something like that.

• by guy4242 on 11/26/22, 12:29 AM

  It's difficult to get into this field if you don't have a graduate degree. I was a double major, Computer Science and Biochemistry, with a minor in Biotechnology. I sent my resume to many biotech and pharma companies, but could not even get an interview. A lot of the jobs said you need 0 years experience if you have a PhD, but 10 years experience if you have a Bachelors. Now that I have 10 years experience as a developer, I've forgotten almost everything I learned in my science education, and I've lost interest.

• by gravelc on 11/25/22, 1:23 AM

  Don't want to be too disparaging, but this to me doesn't seem to be an 'Introduction to Genomics', but more an introduction to read mapping and variant detection in human (or more broadly diploid) genomes.

  Genomics stretches vastly beyond this - assembly and annotation to start with.

  I'd argue the most interesting problem space for software engineers is outside of what is covered in the document.

• by rainmaker124 on 11/25/22, 3:00 PM

  CS person with biology PhD here. The mix of biology and computation is huge, and with the right skill set, interdisciplinary unicorns make tons of money. If you want to see how computation and biology mix, first dive into a standard university Intro Biology course, and then with that foundation, look into computational biology & bioinformatics (they're distinct). You'll find that genomics is only one piece of a much bigger and absolutely fascinating story.

  To get that basic biology foundation, another post mentioned an EdX Intro Biology course, that would be a terrific start, or just get a recent university-level intro biology textbook. It's not terribly difficult material and you'll be in far better shape than reading a biology-for-laypersons pamphlet.

• by yuppiepuppie on 11/24/22, 9:54 PM

  Genomics is where I started learning how to program. Having worked as bench scientist in a genetics lab I understood nothing about my lab mates research when they were showing me python scripts of their analysis. Which initially got me curious. Now having been in the in the industry developing apis for large companies for the past 8 years, I’d be keen to get back into it. Any ideas where to start or find jobs in the space? I would love to go back into the space.

• by lordofgibbons on 11/25/22, 3:01 AM

  I find the field extremely interesting, but I wish the pay in genomics was better. Compared to fang/unicorn type companies, their pay is way below market and it's really hard to justify the massive pay cut.

• by qualudeheart on 11/25/22, 5:02 AM

  Does this touch on recent developments in information biology?

• by penciltwirler on 11/24/22, 9:03 PM

  Nicee, but I feel like really the only thing you need to know as an eng is DNA -> RNA -> Protein. Sometimes RNA -> DNA via reverse transcriptase. Everything else is just normal Python scripting.

• by Exendroinient00 on 11/25/22, 5:03 PM

  Surely sellouts working on ads won't interject the comment section.