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Consider working on genomics

claymcleod.dev

101–110 of 299 posts

Re: Consider working on genomics

#101
Yes, Genomics may be important, but are there really that many jobs for software developers? (same could be said for many other important fields - I recently saw an article about how software engineers should move to green energy - but who is going to pay them?)

Re: Consider working on genomics

#103

20 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…

Is it feasible to do any meaningful work in this field without joining a team? (e.g. as a solo hobbyist/entrepreneur)

Re: Consider working on genomics

#104
post #73

I 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?

Re: Consider working on genomics

#105
In addition to genomics, the other area that could greatly benefit from professional SWE experience is imaging. Many of the most effective techniques today combine microscopic images with genomics- for example variable transcriptomics approaches. Imaging is a more natural fit for people who like to work with dense, visualizable matrices, although genomics data is now trending more towards matrices (all genes x some observable metric).

Re: Consider working on genomics

#106

Several 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?

I think your phrase here sums up how many people feel: > 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 This is changing in my experience, albeit slowly. And really, this is what I'm calling on us, as a community, to do better on. The reason you _would_ work at these organizations is because (1) the subject-matter is really…

How are we "as a community" going to be able to improve this?

It's ultimately down to the cultural norms of the field, as well as the realities of academic funding.

I was a research software engineer (RSE) for the best part of a decade. The best thing that happened to me was being made redundant when my funding ran out, and being forced to work in industry. What a difference (and wholly for the better).

The reasons you give are all nice positives, but they all ultimately are very emotionally manipulative. You're asking people to act against their own self-interest. But this isn't really for the benefit of humanity. It's for the benefit of the PIs who run the research groups, and keeping their little empires running. But the cost to the individual is great. You're sacrificing salary, a career track, advancing your own skills to the full, and in many cases the opportunity to have a life: being able to afford a home and support a family.

In retrospect I, and many others like me, do feel that we were taken advantage of to some degree.

I spent several years on a massive grant, then several years on lots of small short-term grants (12 months, 6 months, 3 months). You can't risk getting a mortgage when you have no guaranteed employment. And it's also very stressful not knowing if you'll be employed in three months time every three months. And unlike in a company, RSEs don't really have a proper career track. There's no real progression. You're a hired help.

RSEs are not treated equally with academics. Let's be really honest about that. We're not. I even had a PhD in the subject area and you're still beneath all of the "real" academics. We're not "partners" in their work. We're the dogsbody's.

If these people want software developers with real chops to work in the field then they need to pay a competitive salary, have a proper career track, and really fix the job stability. And they also need to properly respect the expertise RSEs bring. Unless all of those are fixed, a career in industry will continue to be the only rational choice.

This won't happen though. Tenured academics refuse to consider paying the going rate because that would mean the "hired help" would be earning considerably more than they do. I had already topped out the salary band when I left, and I was earning more than most of the junior-mid-career academics. They are, of course, on fairly poor salaries. They too would earn vastly more in industry, but are mostly unwilling to consider that option as a rule. Their loss. If they truly respected the value they were getting, then they would pay for it. It will not happen though. Most of academia is about climbing the greasy pole and not about advancing the state of the art; there's just no way they'll permit others to sit higher on the salary pyramid than they do.

At least in industry skill and competence and the ability to deliver are highly-valued, and companies will gladly pay for people who are proven to deliver. In practice the work I do in industry (biomedical) has far more positive impact upon the world than anything I did in the academic niche I used to occupy, and is also vastly more enjoyable, with a lot more responsibility and technical depth.

Are you personally planning to stick it out for the whole of your career? Because if I could give you the advice I would have liked to have given myself, it's that you should properly think about where you want your career to go in the medium to long term, and decide when (not if, but when) you will exit to move to industry. Use it as an opportunity to gain some useful skills, and move on to where your skills will be properly valued.

Re: Consider working on genomics

#107
post #47
post #41

> Google Genomics. Careers link. > Microsoft Genomics. Careers link. Google and Microsoft probably know how to make software? Side note: why does this page have user-select: none on body? It's annoying; what does it accomplish?

Google Genomics is now aka Google Cloud Life Sciences. There's also their sister company Verily that operates in this space.

There is also a research group: https://health.google/health-research/genomics/

Re: Consider working on genomics

#108

The author completely neglects the downsides: - The compensation absolutely do not match the workload and education required. - The sheer number of disreputable PIs and their unrealistic goals for software. - The data is likely questionable and often underpowered. - Institutional politics. everywhere. - Marketing ("Curing Cancer"). The role is actually just juggling various bioinformatics file formats.

> just juggling various bioinformatics file formats Your other points are spot on. This one I want to address specifically. The file formats. Academics love their incredibly over-engineered file formats. MARC. SGML. DICOM. HL7. RDF. Those are just the ones I know. Universally, they try to cover every corner case that anyone could ever imagine. Academics absolutely love their ontologies. Just implementing one of them…

HL7 is't technically an academic file format, it's an industry standard interchange format for health data.

DICOM is for radiology.

RDF and SGML, well, they're from the same era as XML, so yeah.

Re: Consider working on genomics

#109
post #72

20 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 Tangential, but what are the chemistry prereqs to grasp this book?

Fwiw, I studied humanities, do a lot of pop science reading in my spare time, and I'm able to appreciate it. There are more detailed and technical sections I skim or skip, but the overviews are fantastic. Incredible description of, for example, the sheer wonder we should all experience at the fact that all life starts as a single cell.

Re: Consider working on genomics

#110
Call me when non-tech fields learn to treat engineers as equal partners rather than disposable labor.

Academia? Yeah they're going to be one of the last to realize, PIs don't want to cede any power in their little fiefdom. Very familiar with the dynamics there.

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