5 ms·

honest question: what if your science isn't maths/physics/data? I'm a chemist and from what i can see there's @#$@# all out there in FOSS land.

by jgamman 11y ago

TheLogothete 11y ago
Use R! https://cran.r-project.org/web/views/ChemPhys.html https://cran.r-project.org/web/views/ChemPhys.html https://cran.r-project.org/web/views/Pharmacokinetics.html https://cran.r-project.org/web/views/Pharmacokinetics.html
- jhbadger 11y ago
  I doubt anyone doing data analysis is unfamiliar with R, as it is the current standard. The push to use Python, or Julia, or a version of Lisp (hey, we had that in the 1990s -- us olds remember xlispstat) for data analysis is coming from the people who find R to be a rather unpleasant language. Which is a subjective opinion, obviously, but not an uncommon one.
  - baldfat 11y ago
    Learning Functional Programming (I learned Racket) makes R great since it really is a functional language.
- deleted 11y ago
  [deleted]
analog31 11y ago
Excellent question. Here's my chemistry cred: I'm married to a chemist, related to a couple more, and have worked in an area related to analytical chemistry, though I got my degree in physics, 2+ decades ago. So here are some generalizations. While in school, I noticed that the physics students were far more interested than the chemistry students, in math and computer stuff. Maybe we were computer science wannabees, or maybe we guessed (correctly in my case) that proficiency with computers would make us more employable. This was true in both undergrad and grad school. And there's a long tradition of physicists stealing ideas from math and computation for solving physics problems. When I was in school, computation was considered to be a specialized branch of chemistry, but was at the forefront of physics. Another difference is that the physics students were generally more interested in making our own tools. The current "maker" and "hacker" trends are old hat for small-lab experimental physicists. Chemistry has always been a bigger field than physics, which I suspect has attracted more interest in making commercial equipment and software. I've noticed in an industrial setting, that managers are often looking for closed solutions that can't be modified by the user, either for regulatory reasons or adversarial labor-management attitudes. The industry wants your boss to think that letting you make your own tools is either dangerous, or a waste of your time. In contrast, even in industry, physicists still have to make our own tools. And management already knows that we're freaks. ;-) So the absence of FOSS tools for chemistry doesn't shock me.
- isolate 11y ago
  > I've noticed in an industrial setting, that managers are often looking for closed solutions that can't be modified by the user, either for regulatory reasons or adversarial labor-management attitudes. The industry wants your boss to think that letting you make your own tools is either dangerous, or a waste of your time. It's interesting to consider in this context that workers owning the means of production is what links the GPL with Marxism.
  - analog31 11y ago
    It took me way too many years to discover FOSS, but after getting hooked on it, I find that I'm actually more motivated and creative when I'm using tools that nobody owns.
entee 11y ago
There are some tools out there, for example Open Babel: http://openbabel.org/wiki/Main_Page http://openbabel.org/wiki/Main_Page which has some python bindings built in. I set some of this up for myself during my PhD but it was occasionally kind of a pain sometimes to get it to work. Also at the time I was a bit of a noob so there's that :). It has some nice features for handling chemical structures, I used it mostly for translating one format into another and computing fingerprints, but I think more can be done. In general I'd agree with @analog31, biology has some good OSS tools, physics has some good OSS tools, but you get to the bridging discipline of chemistry and you find very few. My theory re. organic chemistry and biochemistry applications: it's way more profitable to be closed source. In contrast to the other two fields (gross generalization I know, but somewhat true) there's a very large market for commercial software in Pharma. If someone is willing to pay top dollar, especially an industry that is paranoid about IP and therefore tends to (rightly or wrongly) prefer closed, proprietary solutions, then that's where software will end up.

honest question: what if your science isn't maths/physics/data? I'm a chemist and from what i can see there's @#$@# all out there in FOSS land.

by jgamman 11y ago

honest question: what if your science isn't maths/physics/data? I'm a chemist and from what i can see there's @#$@# all out there in FOSS land.

TheLogothete 11y ago

Use R! https://cran.r-project.org/web/views/ChemPhys.html https://cran.r-project.org/web/views/ChemPhys.html https://cran.r-project.org/web/views/Pharmacokinetics.html https://cran.r-project.org/web/views/Pharmacokinetics.html

jhbadger 11y ago
I doubt anyone doing data analysis is unfamiliar with R, as it is the current standard. The push to use Python, or Julia, or a version of Lisp (hey, we had that in the 1990s -- us olds remember xlispstat) for data analysis is coming from the people who find R to be a rather unpleasant language. Which is a subjective opinion, obviously, but not an uncommon one.
- baldfat 11y ago
  Learning Functional Programming (I learned Racket) makes R great since it really is a functional language.
deleted 11y ago
[deleted]

analog31 11y ago

Excellent question. Here's my chemistry cred: I'm married to a chemist, related to a couple more, and have worked in an area related to analytical chemistry, though I got my degree in physics, 2+ decades ago. So here are some generalizations. While in school, I noticed that the physics students were far more interested than the chemistry students, in math and computer stuff. Maybe we were computer science wannabees, or maybe we guessed (correctly in my case) that proficiency with computers would make us more employable. This was true in both undergrad and grad school. And there's a long tradition of physicists stealing ideas from math and computation for solving physics problems. When I was in school, computation was considered to be a specialized branch of chemistry, but was at the forefront of physics. Another difference is that the physics students were generally more interested in making our own tools. The current "maker" and "hacker" trends are old hat for small-lab experimental physicists. Chemistry has always been a bigger field than physics, which I suspect has attracted more interest in making commercial equipment and software. I've noticed in an industrial setting, that managers are often looking for closed solutions that can't be modified by the user, either for regulatory reasons or adversarial labor-management attitudes. The industry wants your boss to think that letting you make your own tools is either dangerous, or a waste of your time. In contrast, even in industry, physicists still have to make our own tools. And management already knows that we're freaks. ;-) So the absence of FOSS tools for chemistry doesn't shock me.

isolate 11y ago
> I've noticed in an industrial setting, that managers are often looking for closed solutions that can't be modified by the user, either for regulatory reasons or adversarial labor-management attitudes. The industry wants your boss to think that letting you make your own tools is either dangerous, or a waste of your time. It's interesting to consider in this context that workers owning the means of production is what links the GPL with Marxism.
- analog31 11y ago
  It took me way too many years to discover FOSS, but after getting hooked on it, I find that I'm actually more motivated and creative when I'm using tools that nobody owns.

entee 11y ago

There are some tools out there, for example Open Babel: http://openbabel.org/wiki/Main_Page http://openbabel.org/wiki/Main_Page which has some python bindings built in. I set some of this up for myself during my PhD but it was occasionally kind of a pain sometimes to get it to work. Also at the time I was a bit of a noob so there's that :). It has some nice features for handling chemical structures, I used it mostly for translating one format into another and computing fingerprints, but I think more can be done. In general I'd agree with @analog31, biology has some good OSS tools, physics has some good OSS tools, but you get to the bridging discipline of chemistry and you find very few. My theory re. organic chemistry and biochemistry applications: it's way more profitable to be closed source. In contrast to the other two fields (gross generalization I know, but somewhat true) there's a very large market for commercial software in Pharma. If someone is willing to pay top dollar, especially an industry that is paranoid about IP and therefore tends to (rightly or wrongly) prefer closed, proprietary solutions, then that's where software will end up.