Why scientific programming does not compute • Hacker News Board

Re: Why scientific programming does not compute

#131

Post by JohnnyBrown » Thu, Jul 07, 2011, 2:31 AM UTC

ajdecon wrote: post #114

(Disclaimer: my background is in materials physics, and it may be different in other fields. But I doubt it.) Unfortunately there is very little direct incentive for research scientists to write or publish clean, readable code: - There are no direct rewards, in the tenure process or otherwise, for publishing code and having it used by other scientists. Occasionally code which is widely used will add a little to the p…

I'm working in biology now, and a good example of researchers who produce quality, documented code that other people find useful is the Knight group at UC Boulder. They write python with good docs and support, publish the algorithms they come up with in bioinformatics journals, and people cite them all the time.

Might be worth thinking about why there are incentives there and not elsewhere.

Re: Why scientific programming does not compute

#132

Post by enjalot » Thu, Jul 07, 2011, 3:05 AM UTC

eru wrote: post #88

enjalot wrote: post #24

Earlier quoted context omitted.

I'm finishing up a degree in Computational Science where we are essentially trained in computational and mathematical techniques used in the physical sciences, and all I can think about is becoming an artist. I don't think it's the science that adds value, I think it's the programming. The thing is, programming allows you to automate, simulate, measure and visualize complex processes. Science is all about complex pro…

If you are interested in programming and arts, why not have a look at computer games? (Or even modern board games, where the algorithms are run by the players themselves.)

I grew up interested in computer games, and I was lucky enough to TA a game design class at my university. I love the ability to create interactions, but my interest has recently turned to designing interactions into things that aren't normally interactive. I had a lot of fun making an interactive data visualization at a recent hackathon, and I'm hoping to do more things like that.

I personally think games and science need to get much closer together, interactive learning is so powerful, and video games can make anything fun. It's definitely something to explore, but there is still a huge divide between science and entertainment and the understanding of the people in each field.

Re: Why scientific programming does not compute

#133

Post by enjalot » Thu, Jul 07, 2011, 3:10 AM UTC

ajdecon wrote: post #114

(Disclaimer: my background is in materials physics, and it may be different in other fields. But I doubt it.) Unfortunately there is very little direct incentive for research scientists to write or publish clean, readable code: - There are no direct rewards, in the tenure process or otherwise, for publishing code and having it used by other scientists. Occasionally code which is widely used will add a little to the p…

Don't forget that a particular code might have 2 or 3 paper's worth in it, so releasing the code after 1 paper could mean getting "scooped" on another paper.

I'm left a little cynical after a Master's in computational science, and I still can't believe that open code is not part of the repeatability doctrine. I suppose my goals are not aligned with most grad students since I have no interest in an academic career (at least not after many years in industry) but I got much more satisfaction from feedback on my blog posts than publication.

Hell, each blog post is its own little publication, and it may not be peer reviewed before its published, but the amount of links to them and google searches prove that I have more than a few peers who appreciate my contributions.

Re: Why scientific programming does not compute

#134

Post by billswift » Thu, Jul 07, 2011, 3:27 AM UTC

reinhardt wrote: post #74

jzila wrote: post #33

My girlfriend is a PhD student in a pharmacology lab. I'm a software engineer working for an industry leader. Once, she and the lab tech were having issues with their analysis program for a set of data. It was producing errors randomly for certain inputs, and the data "looked wrong" when it didn't throw an error. I came with her to the lab on a Saturday and looked through the spaghetti code for about 20 minutes. Once…

Not sure how your anecdote relates to the conclusion. Forgetting, or even knowing why, to transpose a matrix is not an example of a problem that can be solved by "a basic understanding of software development". Hell, I'm sure there are many decent hackers that don't know what a matrix is, let alone spot such errors within a long sequence of computations.

I bet that they would have been more likely to have found the problem themselves had the code been cleaner and better documented.

Re: Why scientific programming does not compute

#135

Post by roadnottaken » Thu, Jul 07, 2011, 3:31 AM UTC

JohnnyBrown wrote: post #131

ajdecon wrote: post #114

(Disclaimer: my background is in materials physics, and it may be different in other fields. But I doubt it.) Unfortunately there is very little direct incentive for research scientists to write or publish clean, readable code: - There are no direct rewards, in the tenure process or otherwise, for publishing code and having it used by other scientists. Occasionally code which is widely used will add a little to the p…

I'm working in biology now, and a good example of researchers who produce quality, documented code that other people find useful is the Knight group at UC Boulder. They write python with good docs and support, publish the algorithms they come up with in bioinformatics journals, and people cite them all the time. Might be worth thinking about why there are incentives there and not elsewhere.

That is an excellent example and a good point. But, for what it's worth, the Knight lab doesn't really do any biology. Most of their biology is done by collaboration with other labs, and the people in the lab are almost entirely programmers or database people. There's nothing wrong with that, but it's more an example of programmers getting into biology than the other way around.

Re: Why scientific programming does not compute

#136

Post by salva_xf » Thu, Jul 07, 2011, 3:39 AM UTC

Could be that they are not using the correct language, If they have some domain specific language on top of common lisp for example, they will have much better code with less work, i think

Re: Why scientific programming does not compute

#137

Post by lcargill99 » Thu, Jul 07, 2011, 4:03 AM UTC

wolfgangK wrote: post #83

madaxe wrote: post #62

Earlier quoted context omitted.

Because most scientists write code in Fortran '77, which is interpreted, meaning that "code" == "program".

I would have sworn that Fortran was compiled.

It is.

Re: Why scientific programming does not compute

#138

Post by [deleted] » Thu, Jul 07, 2011, 4:39 AM UTC

gte910h wrote: post #6

I want to write a "software style guide" for journalists and their editors. Software and Code are both mass nouns in technical language. "Code" can be in programs (aka, things that run), libraries (things that other programmers can use to make programs), or in samples to show people how to do things in their programs or libraries. Some people call short programs scripts. When you feel you should pluralize "software",…

[deleted]

Re: Why scientific programming does not compute

#139

Post by ahi » Thu, Jul 07, 2011, 4:43 AM UTC

enjalot wrote: post #133

ajdecon wrote: post #114

(Disclaimer: my background is in materials physics, and it may be different in other fields. But I doubt it.) Unfortunately there is very little direct incentive for research scientists to write or publish clean, readable code: - There are no direct rewards, in the tenure process or otherwise, for publishing code and having it used by other scientists. Occasionally code which is widely used will add a little to the p…

Don't forget that a particular code might have 2 or 3 paper's worth in it, so releasing the code after 1 paper could mean getting "scooped" on another paper. I'm left a little cynical after a Master's in computational science, and I still can't believe that open code is not part of the repeatability doctrine. I suppose my goals are not aligned with most grad students since I have no interest in an academic career (at…

As far as I can tell, the two main criteria that makes a publication an academic publication:

1) Peer review is done anonymously and errors are discussed privately.

2) More people "wrote" it than read it.

Re: Why scientific programming does not compute

#140

Post by earl » Thu, Jul 07, 2011, 4:47 AM UTC

crocowhile wrote: post #63

earl wrote: post #30

Earlier quoted context omitted.

My experience is while they may be respected, they aren't paid . And I'm not a charity.

Nobody is paid for doing research. The salary of a professor is about 1/3-1/5 of what the same person may get in industry. People who do research don't do it for the money.

That's fair, but you know what those professors get? Tenure. ie not getting fired unless they're caught in bed with a live boy or a dead girl. And they typically get paid with hard money as stevenbedrick notes.