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Science needs more research software engineers

nature.com

351–360 of 366 posts

Re: Science needs more research software engineers

#351
post #104
post #90

Earlier quoted context omitted.

I have never heard or read anyone, beside physicists, say codes for software code. It doesn't even make sense. Where have you seen that used?

I have never heard or read anyone, beside physicists, say codes for software code. It doesn't even make sense. Why not? "A code" is a software package which solves some kind of problem computationally. Plural, codes. I'm sure it's been in use almost as long as the programmable computers. Here's[1] a link to an article from 1968 which uses the term in the singular ("The MENE Neutron Transport Code".) [1] https://www.o…

That article appears to be written by a non-native English speaker. I don't think I've ever heard anyone refer to a software package as "a code."

Re: Science needs more research software engineers

#352

This looks great, and I would have loved to see this when I was in the lab. When the software industry says to you: "We will nearly triple your salary, you don't have to work weekends, and you also don't have to feed the mice on a Sunday night." You will 100% take this deal. I was a 10yr+ academic tool maker in biochemistry, built cutting edge microscopes, hardware, and image analysis software. My lab was successful…

Tbh the more I hear about the academia the worse it sounds.

Look I’m willing to take a massive paycut, I was starting to come around to the time cost, and hell, I’ll even work in Matlab. But:

> you don't have to work weekends, and you also don't have to feed the mice on a Sunday night

This is just wild, and if anything reminds me of low skilled near minimum wages jobs.

Re: Science needs more research software engineers

#353
post #24

I don't think scientists want research software engineers. PIs typically like to assume any and every role on a project, including software design. They don't like handing things off and letting people build modern, best practices software. You start talking about source code control, package managers, a language used in industry that they've never even heard of and don't care enough to learn about, etc., and you jus…

> They call it "codes" They/We have probably been calling it that since before you were alive. I wouldn’t be surprised if it comes from the 60s or 70s. Every group of people has their own terminology for stuff. There is no right or wrong.

Sure, there's no absolute right or wrong on terminology, but it is a sign that they're cut off from the software engineering world, which leads to a whole host of dumb practices, described elsewhere in the comments here.

As someone with a mathematics background, whenever I encounter someone in another community using mathematics (like economics or accounting or finance or whatever) using mathematical terminology that seems silly to me, it's a bad sign.

Re: Science needs more research software engineers

#354

Earlier quoted context omitted.

The next thought should be: why doesn't neo-liberal capitalism fix this problem? And: is my characterization of the problem correct? Why not start a new firm that better compensates researchers (and tool makers) for their valuable work? It seems like big tech (especially Google, and perhaps Microsoft) comes in from the commercial side and invests in R&D at reasonable rates for just this purpose! But surely if workers…

> The next thought should be: why doesn't neo-liberal capitalism fix this problem? You are the vehicle by which neo-liberal capitalism fixes the problem. By leaving academia to work for a firm directly, you are responding to a price signal sent by the industry, relaying that price signal to the academic labs. You might object, this is slower than most price signals! That's because the university environment is somewh…

> you are responding to a price signal sent by the industry, relaying that price signal to the academic labs.

Which means absolutely nothing unless a ton of other people do it as well. A handful of people here and there can be replaced.

Re: Science needs more research software engineers

#355
post #172

Earlier quoted context omitted.

seriously? in what kind of alternative reality does academia live to offer 30k?

For context, you have 7 weeks holiday, you can't get fired, your working hours are quite flexible. In France, medical expense, education is free. And outside of Paris and a few other big cities, rents are rather affordable. So all things considered, it's not a bad deal (which is why they do attract good candidates). And a typical SWE position in private sector in France would be $50-60K (of course there's variance th…

> you have 7 weeks holiday

Paid?

Re: Science needs more research software engineers

#356
post #343

Earlier quoted context omitted.

What areas of science are you interested in, and what languages/skillsets do you have? Maybe I can steer you towards some Github repos

I am interested in biology and especially neuroscience, and I have a pretty broad skill set. I have a background in graphics/GPGPU programming and enjoy building simulations.

Maybe look into Molecular dynamics?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209097/

Not an expert but this looks like the most popular repo:

https://github.com/gromacs/gromacs

Good luck!

Re: Science needs more research software engineers

#357
post #104

Earlier quoted context omitted.

I have never heard or read anyone, beside physicists, say codes for software code. It doesn't even make sense. Why not? "A code" is a software package which solves some kind of problem computationally. Plural, codes. I'm sure it's been in use almost as long as the programmable computers. Here's[1] a link to an article from 1968 which uses the term in the singular ("The MENE Neutron Transport Code".) [1] https://www.o…

That article appears to be written by a non-native English speaker. I don't think I've ever heard anyone refer to a software package as "a code."

I don't think I've ever heard anyone refer to a software package as "a code."

Then you probably haven't been around physicists, or read enough physics-related material. A non-scholarly reference which can't be easily checked online is George Dyson's "Project Orion," where Freeman Dyson (author's father) is quoted as mentioning this or that "code" as significant for the design of various Orion parts. (That should be a native enough English speaker.) The time-frame is late 1950s to early 1960s.

Re: Science needs more research software engineers

#358

Earlier quoted context omitted.

I have spoken to quite a few that made minimum wage (which is not even close to 30k).

The situation is a bit weird in The Netherlands. Some PhD students are paid employees (AiO), their gross salary is ~31000 to 40000 Euro per year (I think this is excluding vacation money, but including 13th month). Then there are PhDs that get a scholarship (bursaal), that is only around 24000-25000 gross per year. Not too long ago, there were only employee PhDs, but some universities really love the scholarship syst…

That's pretty tragic, aside from the pension - which I don't expect to receive anyway (like most everyone under 40).

Re: Science needs more research software engineers

#359

Earlier quoted context omitted.

No, if a Uni has developed some patents, and wants to 'exclusively license' them to a Pharma, that's probably a good application of that patent, they become much less worthwhile otherwise. It's a misunderstanding of the market to suggest that somehow 'the FDA will lead the trials'. This is about as likely as a manned mission to Venus, it won't happen, and it shouldn't happen for good reason (cost vastly outweighs the…

Non-exclusive licensing is the far better option. This prevents monopolization and ridiculous price increases. As far as clinical trials by exclusive license holders, those have a rather poor record of producing reliable results over the long term in many cases (Vioxx of course, there are many others). The trials should really be independently run, not controlled by the very corporations that have a vested interest i…

- 'Non-exclusive' is a non-starter for most companies, there just won't be a license.

- Some type of independent trials might be possible, but there already is a lot of oversight. That's complicated.

- 'Releasing the patents'. I'm sure everyone in the world could release all of their patents for everything, and things would be good for about 2 years, but we'd likely never see another drug produced again, ever.

Re: Science needs more research software engineers

#360
post #310

Earlier quoted context omitted.

It's very interesting that you say you find it difficult to get scientists excited about anything, because I am told pretty much the opposite. To give you the perspective, I'm a scientist and my partner is a GP. I obviously have many friends who also work in science and one thing that my partner noticed quite early after we met is that the scientist friends (and myself) would ask a lot of questions when she was talki…

In my experience, scientists do not like anything that they perceive as "soft". I like to say that the hard sciences are actually the easy ones and the soft sciences are actually the hard ones. (As it turns out, Herbert Simon also said this.) The point is that when you discuss things like design, complexity, architecture, systems thinking, etc., I've found that this does not stick, so to speak. Scientists do not see…

bmitc 1 day ago | parent | context | flag | on: Science needs more research software engineers

> In my experience, scientists do not like anything that they perceive as "soft". I like to say that the hard sciences are actually the easy ones and the soft sciences are actually the hard ones. (As it turns out, Herbert Simon also said this.) The point is that when you discuss things like design, complexity, architecture, systems thinking, etc., I've found that this does not stick, so to speak. Scientists do not see beauty in form equaling function. In my experience, scientists like learning about things they consider science-y enough for their tastes.

In my experience what you say is true for engineers (and software engineers are amongst the worse in this respect), but much less so for scientists from the hard sciences (physicists, chemists, biologists). You can also see that from many famous physicists being involved in philosophy, while many engineers consider philosophy "irrelevant talking about nothing".

> This is all painting with broad strokes, but in my experience, the most interesting intellectual conversations I've had have been with people with the least amount of degrees. I always feel when I talk to someone with a Ph.D., they're afraid to let it be known someone might know more than them and if that happens, then it's suddenly something that's not important.

Maybe we converse in very different cycles, but generally for people I know the "higher up the foodchain" the more they ask even very basic questions. In my experience you can often distinguish who is the most accomplished scientists in the room by listening who is asking the most basic questions.

All this is obviously anecdotal evidence, but is reflected also by famous accounts like e.g. Feynman's account of the challenger commission.

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