[HN Gopher] Introduction to Genomics for Engineers
___________________________________________________________________
Introduction to Genomics for Engineers
Author : froggychairs
Score : 99 points
Date : 2022-11-24 18:44 UTC (4 hours ago)
(HTM) web link (learngenomics.dev)
(TXT) w3m dump (learngenomics.dev)
| penciltwirler wrote:
| 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.
| epgui wrote:
| I'm a biochemist + software engineer, and while I understand
| where you're coming from, IMO that's a very harmful/self-
| sabotaging attitude.
|
| As soon as you start touching science, _everything_ is
| important.
| greazy wrote:
| ...no. There is more to genomics than python scripting. This is
| widely incorrect assumption.
|
| A new generation of bioinformaticians and computational
| biologists are using rust, go, and the web to create, share and
| deliver.
|
| Checkout nextclade.org
| aquafox wrote:
| You do know that there are things like epigenetics, DNA repair
| (using specialized proteins), RNAi, post-translational
| modifications, metabolites (just to name a few)?
| otherme123 wrote:
| Sooner or later you'll have to learn all the other stuff in the
| linked page: file formats used only in genomics, structural
| variants, NGS, evolution, regulation, polygenics, etc.
| dddiaz1 wrote:
| 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/
| agumonkey wrote:
| what kind of math/cs/algorithmic skills do you think one should
| work on to get a job in this kind of company ?
| pinkwinds wrote:
| Purposefully blocked for certain countries?
|
| "The Amazon CloudFront distribution is configured to block
| access from your country."
| civilized wrote:
| 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.
| firstplacelast wrote:
| https://news.ycombinator.com/item?id=33671264
|
| ^Most recent discussion I've seen.
|
| I worked in genomics, left this year because you're underpaid
| and often disregarded "IT-help" that assists wildly over-
| educated and underpaid people driving the actual research in
| 95% of cases.
| tetris11 wrote:
| Thats why you stay though, the people are interesting and the
| work is meaningful and you directly see the fruits of your
| labors whilst contributing to a codebase that is by default
| open source.
| [deleted]
| fncivivue7 wrote:
| firstplacelast wrote:
| People aren't anymore interesting than anywhere else.
|
| Work is no more meaningful than anywhere else. It's a big
| "selling point" for the industry, but it's just a way to
| get people to get paid less (yay you're making the world
| better than all those garbage people serving coffee or
| healing sick people or keeping your lights on or optimizing
| the routes of the goods you have delivered). If you want
| sustainable systems, trying to be a martyr and work for
| less only screws this up long term.
|
| Code-base is not open-source. It's biotech R&D, there is
| zero culture of sharing outside your organization within
| industry. You can present high-level things at conferences
| and such, but you'll have to rip the raw data out of their
| dead hands...not happening.
|
| I've been in too many conversations about building software
| to serve larger groups in this industry. It can happen, but
| it can't currently and nobody wants it. Confident someone
| will find a solution, but everyone wants their own home-
| grown solutions in their own walled-gardens that no one has
| access to.
|
| Data and the things it can/can't tell you are held tightly
| in these companies. I was at a pharma a couple years ago
| where researchers were explicitly told they COULD NOT test
| certain compounds in a certain way because they did not
| want a trace of this data to exist while they were trying
| to push compounds through the FDA.
| bsder wrote:
| The reason why San Diego has such a craft brew scene is that it
| has a lot of underpaid microbiologists.
| zosima wrote:
| Working with genomics technology is too far away from the money
| to become rich from. There are too many middlemen in-between
| technology and application.
|
| But it's a fun subject, and as the technology develops, middle
| layers will disappear and then the money from expertise will
| become better.
|
| The number of people that are both capable software developers
| and has a good understanding of cellular biology are quite few
| and will probably remain so for the foreseeable future.
| jltsiren wrote:
| I don't think middlemen are the issue.
|
| In biotech, the end goal is a physical product or a service
| performed by a doctor or another highly paid professional.
| Those don't scale as well as software. The ratio of users to
| developers is also low. You are likely developing software
| for many niche tasks, which does not scale either.
|
| And if you are considering roles in the academia, your
| productivity is not going to be high enough to justify a
| competitive salary. Productivity, in monetary terms, is
| defined by the amount of money you can bring in. Either
| directly on indirectly. In the academia, that usually means
| grants. You may be able to argue successfully to a funding
| agency that one software engineer is worth two postdocs, but
| not four.
| yuppiepuppie wrote:
| 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.
| chairhairair wrote:
| I have a similar story with chemistry. I'd also like to get
| back into the sciences, but I'm not sure how relevant
| programmers are.
| ALittleLight wrote:
| 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.
___________________________________________________________________
(page generated 2022-11-24 23:00 UTC)