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Consider working on genomics

claymcleod.dev

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Re: Consider working on genomics

#81

Post by cratermoon »

anonymous_bio wrote: post #36

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 is a nightmare. Going from one to another is an exercise in the philosophies of ontologies.

Re: Consider working on genomics

#82

Post by cratermoon »

the_only_law wrote: post #78
anonymous_bio wrote: post #36

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.

> The role is actually just juggling various bioinformatics file formats. I need an advanced degree for that?

You do in academia. Otherwise you might as well be washing dirty labware for all the respect you get.

Re: Consider working on genomics

#83

Post by boppo1 »

anonymous_bio wrote: post #36

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.

PIs?

Re: Consider working on genomics

#84

Post by pclmulqdq »

cratermoon wrote: post #58
clmcleod wrote: post #12

Earlier quoted context omitted.

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…

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

#85

Post by foobiekr »

My first job offer out of college for compsci was for a genomics research company that desperately needed software engineers. At the time they were storing sequences as ATGC strings in an oracle database using perl scripts. It was really below even undergraduate-level basic stuff.

The offer was $38k a year. About two days later, I got my second offer, $50k from a game company, and then a real offer, $60k, which I took. This was in the late 1990s.

That was 20+ years ago, of course, but I sort of wonder if things have changed. I frankly think a lot of SWE work for fundamentally evil, socially destructive companies, and I honestly don't think you have to to earn a good living, but you also don't have to work for companies that deliriously underpay you.

Re: Consider working on genomics

#86

Post by fnbr »

cjbgkagh wrote: post #40
clmcleod wrote: post #12

Earlier quoted context omitted.

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…

I charge a high rate not because I need the money but because I need to stop people from wasting my time. I’ve worked at these places before where they exploit your altruism and dedication to craft to extract more work out of you for less. Concretely one of the places refused to hire a frontend dev to help so I got stuck wasting time churning frontends. Charging more encourages them not to do that.

Yeah. It’s one thing if the only way the job is worse is in pay, it my experience has been that if the pay is significantly worse, the job is worse off in every way.

Re: Consider working on genomics

#87

Post by uvesten »

Anecdata, but I did a master’s in bioinformatics a few years ago, and as part of that I spent about a year in a human genomics lab.

I fully agree that the software used is really bad in general, but what is worse is the level of IT literacy among the PhD’s and post-docs from the biology side. (Also statistics, I guess a lot of p-hacking is the result of authors simply being clueless…)

After finishing my thesis, I was offered to stay and work at the lab. After thinking about it, and accepting, I was told that funding wasn’t secured yet, but that it should come ”any day now”…

Thanks, but no thanks.

Anyway, I fully see the need for professional software engineers in this field, but job security and even job availability (aside from the low salaries) in academia is abysmal, so I don’t think the current situation will change any time soon.

Re: Consider working on genomics

#89

Post by rossdavidh »

AlbertCory wrote: post #27

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…

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.

Re: Consider working on genomics

#90

Post by cycomanic »

cratermoon wrote: post #63
jwilber wrote: post #32

Earlier quoted context omitted.

Or, and hear me out here for a second, people go where they’re most valued. Why would someone volunteer to go work somewhere where they’ll get less money, have less flexibility, be treated as second-class employees, have less work perks, etc. when so many alternatives exist? Doubly so in this economy. Maybe genetic companies should catch up in workplace etiquette instead of recommending that SWE’s lower their expecta…

> be treated as second-class employees The pay isn't all that important to me, as long as I can live on it, but this. It was so obvious when I was working in academia that because I wasn't myself an academic that I was just lab help, no better than the person who washes the test tubes and beakers.

I don't quite understand this post. In my experience lab technicians in academia are highly valued (however I mostly have experience with clean room staff), however they are support for the researchers, who drive the research agenda (well actually it's the funding primarily). What exactly do you expect to not be what you call "a second class citizen"?
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