Why scientific programming does not compute • Hacker News Board

Re: Why scientific programming does not compute

#81

Post by jzila » Wed, Jul 06, 2011, 10:26 PM 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 suppose the tie-in is simply that we hackers think differently from scientists. It's much easier for us to visualize a complex tree of logic than for people who are not accustomed to it. The second purpose of the anecdote was to illustrate that there is a complete lack of software testing knowledge within the scientific community, or even the recognition of the need for it. All of the "testing" they do is on production data. There is no unit testing anywhere.

Re: Why scientific programming does not compute

#82

Post by madaxe » Wed, Jul 06, 2011, 10:31 PM UTC

reinhardt wrote: post #75

xxd wrote: post #73

Earlier quoted context omitted.

This wouldn't be a healthcare startup in SF, would it?

I shudder to think that such a "company" could be developing health-related software.

You should see the shit they design pharmaceuticals with.

Re: Why scientific programming does not compute

#83

Post by wolfgangK » Wed, Jul 06, 2011, 10:33 PM UTC

madaxe wrote: post #62

szany wrote: post #7

Earlier quoted context omitted.

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.

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

I would have sworn that Fortran was compiled.

Re: Why scientific programming does not compute

#84

Post by eru » Wed, Jul 06, 2011, 10:38 PM UTC

john_b wrote: post #72

gallamine wrote: post #44

I'm a PhD student in Electrical Engineering. I'm currently working on a Monte Carlo-type simulation for looking at the underwater light field for underwater optical communication (no sharks!). I'm doing the development in MATLAB and I recently put all my code up on Github ( https://github.com/gallamine/Photonator ) to help avoid some of these problems (lack of transparency). Even if nobody ever looks/uses the code, I…

I'm a M.S. student in mechanical engineering facing a similar situation, except I haven't put any code on Github (my advisor wants to keep it proprietary, but I probably would not bother putting it up even if he were ok with it). I've written around 15000 lines of MATLAB for my research and only a handful of people will ever need to see it. Some is well-structured and nicely commented, but other parts are incomprehen…

I wonder whether our priorities for research are misguided. Isn't research about extending the knowledge of humanity? Writing and passing on readable code would probably advance us further in total, than everyone starting basically from scratch.

(I'm not faulting you, you just react to the incentives.)

Re: Why scientific programming does not compute

#85

Post by eru » Wed, Jul 06, 2011, 10:41 PM UTC

pwang wrote: post #66

szany wrote: post #7

Earlier quoted context omitted.

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.

Yes, I hear this all the time. I know that the fancy course 6 kids here on HN would poo-poo it, but it's a very common usage in scientific computing. I can imagine the origins and can hypothesize about why it persists (the festering petri dishes of programming culture that is "grad school"), but don't have a definitive answer. John Tukey is widely credited with coining the term "software" in print in 1958, but I'll w…

And even `programming' has lots of uses. Like in linear or dynamic programming. Or even in strength training.

Re: Why scientific programming does not compute

#86

Post by _delirium » Wed, Jul 06, 2011, 10:41 PM UTC

gte910h wrote: post #17

szany wrote: post #7

Earlier quoted context omitted.

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?

I think you have the chronology backwards. The use of "code" as a mass noun dates to the 1960s at the earliest (actually, I can't find a good example before the 1970s in brief searching), while the use of "code" as a singular noun to mean "implemented algorithm", and "codes" as the plural, dates back at least to the 1950s.

As one of many examples, here's a 1955 survey article compiling a list of "available digital computer codes for nuclear reactor problems": http://www.osti.gov/energycitations/product.biblio.jsp?osti_...

Re: Why scientific programming does not compute

#87

Post by rflrob » Wed, Jul 06, 2011, 10:42 PM UTC

Where do most programmers get this exposure to best practices like version control, unit testing, etc? I took a few early-mid level CS classes, and there was a relatively cursory emphasis on readable code, there was barely any on any of the sorts of things that lead to well-maintained projects. If these are the sorts of things that one learns at your first internship, then it's no wonder that academics in other disciplines don't have any exposure to it.

Re: Why scientific programming does not compute

#88

Post by eru » Wed, Jul 06, 2011, 10:44 PM UTC

enjalot wrote: post #24

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."

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.)

Re: Why scientific programming does not compute

#89

Post by bendmorris » Wed, Jul 06, 2011, 10:45 PM UTC

rflrob wrote: post #87

Where do most programmers get this exposure to best practices like version control, unit testing, etc? I took a few early-mid level CS classes, and there was a relatively cursory emphasis on readable code, there was barely any on any of the sorts of things that lead to well-maintained projects. If these are the sorts of things that one learns at your first internship, then it's no wonder that academics in other disci…

The vast majority of students are never exposed to these concepts and those who are usually teach themselves. We've been teaching a class called "programming for biologists" that teaches practical skills that are needed in scientific computing - simple database use, version control, etc. - and we've seen huge demand from students and faculty members in many departments.

Re: Why scientific programming does not compute

#90

Post by orborde » Wed, Jul 06, 2011, 10:45 PM UTC

ahi wrote: post #9

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",…

"he attempted to correct a code analysing weather-station data from Mexico." This annoys me, and it is everywhere. It indicates the writer has no idea what they're writing about and presumes that it's not a process but a matter of getting the right answer. "Hold on a sec, let me get out my Little Orphan Annie's Secret Decoder Ring." (sibling deleted and moved here)

The biggest howler I saw was "The SSI unites trained software developers with scientists to help them add new lines to existing codes, allowing them to tackle extra tasks without the programs turning into monsters."