Why scientific programming does not compute • Hacker News Board

Re: Why scientific programming does not compute

#11

Post by pygy_ » Wed, Jul 06, 2011, 8:25 PM UTC

bh42222 wrote: post #5

As a general rule, researchers do not test or document their programs rigorously, and they rarely release their codes, making it almost impossible to reproduce and verify published results generated by scientific software, say computer scientists. Just stop doing that! Seriously, testing is not wasted effort and for any project that's large enough it's not slowing you down. For a very small and simple project testing…

You won't see any clean code written by scientists until (major) journals make it mandatory to submit code for peer review and publication.

When it happens, I hope that they'll manage to agree on a sensible license (even though I won't set my hopes too high).

Re: Why scientific programming does not compute

#12

Post by scott_s » Wed, Jul 06, 2011, 8:25 PM UTC

bh42222 wrote: post #5

As a general rule, researchers do not test or document their programs rigorously, and they rarely release their codes, making it almost impossible to reproduce and verify published results generated by scientific software, say computer scientists. Just stop doing that! Seriously, testing is not wasted effort and for any project that's large enough it's not slowing you down. For a very small and simple project testing…

The point is that since software development is not their main goal or background, their practices tend to be ad-hoc. We know the value of testing and documentation, but they do not. People don't know to stop doing something until they know it's a bad practice. And they're not going to know it's a bad practice until they discover that fact on their own (which can be a slow process) or someone teaches them (faster, but potential cultural problems).

That they should is basically a given in the article. The question is how to make it happen.

Re: Why scientific programming does not compute

#13

Post by nkassis » Wed, Jul 06, 2011, 8:26 PM UTC

sliverstorm wrote: post #3

Why not just hire comp scientists or programmers permanently? Adjust the company model, permanently segregate the work?

I'm lucky to be in a lab with enough funding for this. This is rarely the case. In medical science it's easy to get large grants and pay programmers in something like biology the programmer is usually that guy that learned perl since he's already getting paid to do science.

Grad students probably wrote the majority of the tools used in my lab and it shows because when they leave the knowledge of the different issues and bugs in the software that they had goes with them. Years later they resurface and no one has any idea of the thought process of the original author.

It's quite annoying. We have such a project right now that is a basic piece of software we use for all our research. There is no current funding for someone to sit there and clean up the code. Most funding agencies want new work not maintenance work to be done with their money. There just isn't any incentives anywhere for this.

Someone will just reinvent the wheel probably.

Re: Why scientific programming does not compute

#14

Post by neutronicus » Wed, Jul 06, 2011, 8:26 PM UTC

bh42222 wrote: post #5

As a general rule, researchers do not test or document their programs rigorously, and they rarely release their codes, making it almost impossible to reproduce and verify published results generated by scientific software, say computer scientists. Just stop doing that! Seriously, testing is not wasted effort and for any project that's large enough it's not slowing you down. For a very small and simple project testing…

The thing about scientific code is that it's often a potential dead end. The maintenance phase of the software life cycle is not as assured as it is in industry.

Writing good engineering software is not the scientist's goal so much as demonstrating that someone else with a greater tolerance for tedium (also someone better-paid) could write good engineering software.

Re: Why scientific programming does not compute

#15

Post by MasterScrat » Wed, Jul 06, 2011, 8:27 PM UTC

saulrh wrote: post #2

Something I heard from one of my professors once: "A programmer alone has a good chance of getting a good job. A scientist alone has a good chance of getting a good job. A scientist that can program, or a programmer that can do science, is the most valuable person in the building."

Similarly, from Zed Shaw (http://learnpythonthehardway.org/book/advice.html) :

"People who can code in the world of technology companies are a dime a dozen and get no respect. People who can code in biology, medicine, government, sociology, physics, history, and mathematics are respected and can do amazing things to advance those disciplines."

Re: Why scientific programming does not compute

#16

Post by archgoon » Wed, Jul 06, 2011, 8:30 PM UTC

MasterScrat wrote: post #15

saulrh wrote: post #2

Something I heard from one of my professors once: "A programmer alone has a good chance of getting a good job. A scientist alone has a good chance of getting a good job. A scientist that can program, or a programmer that can do science, is the most valuable person in the building."

Similarly, from Zed Shaw ( http://learnpythonthehardway.org/book/advice.html ) : "People who can code in the world of technology companies are a dime a dozen and get no respect. People who can code in biology, medicine, government, sociology, physics, history, and mathematics are respected and can do amazing things to advance those disciplines."

This seems at odds with the statement from the article

"There needs to be a real shift in mindset away from worrying about how to get published in Nature and towards thinking about how to reward work that will be useful to the wider community."

EDIT: What the heck is wrong with this? We have two opinions on the perceived value of programmers in scientific enterprises, one from someone who works in the field (David Gavaghan) and another from Zed Shaw. I'm highlighting that Zed's perception is not universally agreed upon.

Re: Why scientific programming does not compute

#17

Post by gte910h » Wed, Jul 06, 2011, 8:30 PM UTC

szany wrote: post #7

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",…

Actually it's a science thing. In a scientific context "code" is understood to mean "program". For example: http://scholar.google.com/scholar?q=%22population+synthesis+... I'm not sure why this is though.

What an excellent idea: Generate new jargon that's incompatible with the jargon used from the field you suck at.

Perhaps concerned scientists and editors should reject the bifurcation here and take on the lingo of the field that creates the tool they have to use and need to learn better as a first step in learning to program in a more responsible manner?

Re: Why scientific programming does not compute

#18

Post by prospero » Wed, Jul 06, 2011, 8:30 PM UTC

sliverstorm wrote: post #3

Why not just hire comp scientists or programmers permanently? Adjust the company model, permanently segregate the work?

I did some work on data visualization for the astrophysics department when I was in college. I started to work with the simulation code, but found that the math was sprinkled everywhere, which made it really difficult for me to make structural changes without risking the integrity of the program.

One of the most elusive skills for self-taught programmers is how to structure code properly. A good architecture would allow domain experts and non-expert programmers to coexist, but that would require throwing away a lot of existing spaghetti code written by domain experts, which is not going to be a popular decision.

Re: Why scientific programming does not compute

#19

Post by scott_s » Wed, Jul 06, 2011, 8:30 PM UTC

One of the main sources in the article is a study from the 2009 Workshop on Software Engineering for Computational Science and Engineering. One of the workshop's organizer's has a report of the overall conference which is interesting: http://cs.ua.edu/~carver/Papers/Journal/2009/2009_CiSE.pdf

Re: Why scientific programming does not compute

#20

Post by pvarangot » Wed, Jul 06, 2011, 8:31 PM UTC

sliverstorm wrote: post #3

Why not just hire comp scientists or programmers permanently? Adjust the company model, permanently segregate the work?

It's usually outside of the scope of what you can pay for using a grant, and grants are currently the "standard" way to fund science. In this particular case also the permanently part won't get along with with grants being given for specific goals and also for fixed periods of time.