Consider working on genomics
91–100 of 299 posts
Re: Consider working on genomics
#92Where do they live? What do they do?
Like, do you need a genome interpreter? Does one exist? Are there any open source products used by the field currently? I know the names of the programs and items I'd look at to get started in AI, for example. But for genomics, it's a total mystery.
Re: Consider working on genomics
#93I think that is already accepted as good practice, and the way most people in the field work, which is part of the reason why the field is in this shoddy state right now. Because in reality, most of the time those engineers don't exist and it will never advance to the second stage, but will still be used regardless. And even if you manage to find an engineer for your team, the same problem exists in many layers down your stack.
As with most other kinds of software, the biologists should be treated as customers (or trained up to be skilled-enough engineers), as it is done in other disciplines. To create good accounting software you also wouldn't propose to have the accountant write the initial version of the software, would you?
> Many of the projects that are critical to the foundation of genomics are reaching or have eclipsed the ten-year mark. How much longer can we expect these individuals to single-handedly maintain these code bases?
What you propose sounds more like "hey, be the next idiot that commits to maintaining critical software for nothing", rather than any systemic change. The ugly secret of bioinformatics is the same one as in broader tech: Most of it runs on the backs of unpaid OSS maintainers (in this case a handful of motivated PIs that carve out some of their time for that).
If you want to have good software in the sciences, you first have to solve the OSS funding problem.
PS: the `user-select: none;` on your page is really annoying
Re: Consider working on genomics
#94Re: Consider working on genomics
#95I recently switched from software engineering on ads and web performance at a FAANG to (meta)genomics at a nonprofit startup; happy to answer questions
A. What are the broad and medium goals you work on?
B. What are your daily activities? How do they fir into (A)?
C. What does nonprofit genomics vs for profit look like from a revenue standpoint?
D. What specific technologies/stacks are you using?
E. The CRUD frontend+backend+database to serve users (and sell ads) is pretty ubiquitous in 'tech', with some branches. How does your field compare?
Re: Consider working on genomics
#9620 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…
It was my first fulltime job, and by far the most chill. People were great. The PI was laid back, the whole lab went out for beers every now and then - and not because of a mandatory startup-style 'bonding' event. We genuinely enjoyed each others company and hung out outside of work. I never had that in any other job, which were/are all commercial operations.
The vibe and the power structure felt very different. More level. There werent any purely managerial roles, everyone was doing at least a bit of 'science'. And even junior ICs like me got to coach undergrads every now and then. Most of the operational budget comes from grants, on which you have to deliver. The pay is not amazing, so most employees really are in it for the science.
Or I was still young and naive and was lucky all of the two layers of management were all nice people.
Ultimately I left, as the grant money coudnt keep up with offers I was getting.
It is still the job I am most proud of. I love talking about it, and it really sucks that even a well funded lab cant really afford market engineering rates.
Re: Consider working on genomics
#97I also experienced "software engineers" who had no idea what they were doing being given more credence because they had a PhD in some bio-related field. Oh, you got a PhD in some molecular aspect of some tiny piece of biology, and that makes you qualified to build big data systems? It did not. Apparently what that gives you is an adherence to reading decades old textbooks about database design. It was like working with a first year software engineering undergrad from twenty years ago.
To be fair, it looks like the same can be said for machine learning. Many software engineers I know are in the "machine learning space", but report that they are just operations support for data scientists, and don't actually get to learn about, let alone be involved with creating, the models they support.
If you are a software engineer, work in a software company, where engineering is the value proposition.
Re: Consider working on genomics
#98Look, I did this at multiple places for a number of years. The issue is that you often form an adversarial relationship with the scientists. They don't really want you there. They are perfectly happy just organizing everything by hand with post its and excel spreadsheets. They do not want you to mess with their flow with your software, even if it would help them to be more efficient.
Re: Consider working on genomics
#99Earlier quoted context omitted.
I have experience working in academia. I started out working for a medical school in fact, on bioinformatics. It's been a while, so I have kind of forgotten the problems, but I'll do my best. 1. Academic code. Not one institution would pass the Joel Test[1]. You pretty much covered some key points in your first paragraph, so I see not much has changed. The best predictor of how something will perform in the future is…
If you don't have a PhD, don't touch academic jobs with a 10 foot pole. They all got one, and they value the credential to a ridiculous degree. When I last worked with academia, they essentially thought of me as the same as the guy who maintains the lab equipment, not an actual collaborator on their research.
Re: Consider working on genomics
#100Several of the job boards linked don't have any job listings, most don't provide a salary range, several require advanced degrees, and none specify whether remote work is possible. If I can get a better salary and working conditions at some crappy no-name startup, why would I choose to work at an organization that respects my craft so little they haven't bothered to maintain their software for a decade?