AskScience, what programming language do you use?

thetripp · 11 months

Matlab.... every day. It makes dealing with (and visualizing) huge datasets so easy.

As for bioinformatics, most of the ones I know use Perl.

sitbon · 11 months

As a CS PhD student, and previous environmental science worker, I've gone through many research topics and programming languages.

I have a friend who works in the software industry and convinced me to give .NET a try, because he works with gigantic codebases that need to remain maintainable for a looong time. I gave it a go because the Mono project is so kick-ass on Linux now. I now fancy C# as the language that makes it easy to get shit done in a simple unified way. For the typical CS-working-alone research scenario, it has made my code a lot more maintainable in the long-term. For the record, I still love my smattering of Python toolkits and modules (TCP pickle protocol, anyone?).

There's this nasty habit¹ in this field where people write code, use toolkits, do all sorts of things, and then produce their pretty graphs... but nothing comes of it. Even when they share code, it becomes out of date or unmaintainable pretty quickly. There are some very notable exceptions, where the software is the center of the research- my favorite example is the ns-3 network simulator (and I'm a contributor :). A good example of something that has evolved a lot but is still not very fun to use for maintainability/Java reasons is TinyOS.

These days, I do a lot of theory and data manipulation, and still love to work with C/C++, Python, and perl, but good programming practices, along with C#, have accelerated my coding to the point where I can get shit done and move on to the real science at hand. It's good I'm finally at that point considering I've been writing code for over 15 years :)

Speaking of theory, Matlab and Mathematica are very useful tools. For those that think Matlab is good for big datasets... when you get to managing the truly big ones, PostgreSQL is the way to go. Takes a bit of effort to design the database but you will be rewarded for it. I'm actually doing that as a side business for extra cash now, and it's very profitable (and is much more impressive than the CSV files most scientists end up with).

-^1: The other nasty habit I'm dealing with now is arbitrary pseudocode used to describe algorithms. I can't contact an author about the paper he wrote 20 years ago and tell him his algorithm is either wrong (despite being the centerpiece of the paper) or that poor notation has made it impossible to implement in whatever way they intended.

So then, out the window goes my ability to compare my algorithm to theirs directly. Sometimes I blame page limits at conferences... it's easy to spot where an author decided not to explain something fully because there was still that one damn reference hanging off of the overlimit page. This practice (altogether) has been going on for 30-40 years easy.

Valeen · 11 months

I use mathematica, not a real language, but its extremely powerful and speed isn't really an issue for me. Occasionally I need to let something run over night when I am doing numerics, but that is about the extent of it. It also allows me to do all my graphic without having to export the data and mess with it in an external program like gnuplot.

oedipamatzah · 11 months

I use mostly Perl with some R thrown in for stats and graphs. The rest of my lab does most of their stuff in Python and keep trying to get me to switch to it, but I haven't gotten around to it yet.

computers_in_space · 11 months

Computational astrophysics here. Had to answer this one.

Python/Cython for manipulating and visualizing anything up to TB data.

C or Fortran for anything that needs to be fast. Maybe C++. Please note that I said Fortran (>=90) and not FORTRAN (<=77). I saw some codes still in FORTRAN66 at Princeton. Ouch.

I use a fair amount of bash, but none of it is for science. More "using a computer" type tasks. Setting up virtual environments, automating permissions, etc.

I love playing with other languages as I'm still a computer nerd at heart, but I haven't found anything else useful for getting science done.

Now for my rant:

I look down on scientists that use closed (for profit) languages. This includes commercial compilers (PGI, NAG, ifort), MATLAB (please just use Octave forchrissake), IDL, etc. You are basically making it difficult if not impossible and expensive for me to reuse your work for no good reason. The free, open source alternatives of these things are almost always faster and always more portable.

I do not understand using Perl. Anything you want to do in Perl, you can either do with a simple bash script or in a language that does not blow. Old, slow, and just plain ugly.

The one exception I make is Mathematica because nothing is as good at symbolic manipulation and sometimes you need that. It's a shame, but maybe sage/sympy will get there one day.

Oh almost forgot, using Windows for science is a joke. You can't run anything serious. Mac or linux only, no exceptions.

tl;dr: Python, C, and Fortran on Mac or linux only. Refuse to work with commercial libs like MATLAB, IDL. Laugh at Perl and Windows.

chrisamiller · 11 months

You'll likely be interested in this thread over at BioStar:

Which are the best programming languages to study for a bioinformatician?

For most of us bioinformaticians, this includes Perl, Python, R, and bash command line utilities (like sed, awk, cut, sort, etc). There are also people who code in Java, Ruby, C++, and Matlab.

So the bottom line? Whichever language lets you get the work done most easily is the right one for you. Answering this question should include a careful survey of the libraries and other code that you can pull from, as well as information on the preferences and experience of both you and your collaborators. If you're doing microarray analysis, it's hard to beat the R/bioconductor libraries, but that's absolutely the wrong language for someone wrangling most types of large sequencing data sets.

shavera · 11 months

ROOT. Almost all particle physics is done in this C++ bastardization.

electricsandstorm · 11 months

Python!

LegoForte · 11 months

I try to use Python as often as possible, but I do a lot of work in Matlab. Generally, I use Python because it's clean and consistent and beautiful, and NumPy and Matplotlib do almost everything I want. I use Matlab because it's the standard for engineering, but I always find it clunky and painful to actually program in.

A while back, I was using LabView for data acquisition and control, and then compiling that to Matlab code to hook up to an optimizer. It was a nightmare, and I ended up rewriting the entire system in Python, which made my life so much better.

blueboybob · 11 months

Used TCL as an undergrad. Now I use IDL and AWK.

Samarang · 11 months

Thanks for all the comments everyone. I knew programming languages are varied but seeing everyone putting out their preferred language is quite eye opening.

goalieca · 11 months

R and C++. I absolutely hate matlab and have started doing more and more stuff in python.

s_quark · 11 months

C++ is wonderful, although I would really like it if it would let me overload anything as an operator, overload operator precedence, treat functions like they're variables, type classes and type variables! Templates can be a pita too!

thomasballinger · 11 months

Python, then probably Matlab, c, Tcl, bash, R, perl in that order. I'm an RA at a neuroimaging lab. Learning to use basic command line tools is also not to be underestimated. If you're part of a large organization or have close colleagues, bend to convention unless you have a good reason not to. Learn competence with the language that has the library you need to start out with - we're doing Science here, not software design (unless you are).

defrost · 11 months

I play around with data in Python, Matlab, and Excel Spreadsheets (yes, seriously). I play around with concepts in Haskell and lisp.

I implement in C and often interface with Fortran, the major part of my career has been orientated towards the production of real time data acquisition / processing / interpretation instruments ( marine seismic, airborne geophysics, geomosaicing raw satellite feed, precision mapping underground chambers to monitor for wall creep, etc).

I don't so much "do science" as industrialise it.

avfc41 · 11 months

Python, mostly because ArcGIS uses it as their built-in scripting language, and they have the arcpy module. Also, everyone in my program had to learn Stata, which is what I use for statistical stuff.

a_dog_named_bob · 11 months

LabView 4 life.

2x4b · 11 months

I used C++ and Matlab for a thing a couple of years ago, now I don't do any programming (my only computer use is Mathematica/Maple for algebra checks/really hard integrals).

I know a few people who use FORTRAN, and lots of astronomy type people use IDL.

johnh2o2 · 11 months

I'm in high energy astrophysics and, in order of frequency, I use: bash scripts+awk, python, C, perl

I don't count latex but if you do, latex would be in between bash and python.

rupert1920 · 11 months

About six years ago I used FORTRAN.

Yup.

GentleStoic · 11 months

I looked into, and learnt, various options when I (re-)learn programming 2-3 years go. Now I write python code most of the time. I picked this language partly because of it has libraries that does numerical/scientific analysis (NumPy/SciPy), MVC-driven interfaces for interactive data-exploration (Enthought Traits/Chaco/Mayavi), and simple and gorgeous plotting (matplotlib). On a day-to-day basis I find that the clear syntax (e.g., compared to Java with tons of boilerplates) and relatively "un-openendedness" (unlike perl) sources of productivity. The only drawback in the years I've used it is that python can be sluggish with very large and unoptimized datasets.

I also code for fun, and python has either libraries or binding for accessing natural language analysis (NLTK), wikipedia, R, and... reddit. Some graphics program I use are also scriptable in python (e.g., nodebox), which is a bonus. For fun I'm learning Coffeescript (a dialect of Javascript), since I want to make tools that people can just run in their browsers; and coffeescript is very "python" (or ruby) like.

Technically (La)TeX is also Turing-complete, but I just use it to write manuscripts.

Sode79 · 11 months

I do almost everything in SAS

bulbousaur · 11 months

PL/I.

psygnisfive · 11 months

Haskell, Agda, Scheme for more theoretically oriented stuff (especially Agda these days). Ruby for simple scripting stuff.

cognitio · 11 months

As a physics undergrad working in a cosmology lab, I pretty much just use matlab and python. Matlab is...unfortunate, but it gets the job done when i need to whip up something quick and visual. Most of the programming in our lab is python. Most of our experiment is run by a bunch of python scripts that i really wish i understood :p

Astrokiwi · 11 months

I'm do astrophysics simulations. I use Fortran77 when I have to, upgrading it to Fortran95 when I can. I use Python for the less intense stuff, and I've started learning towards C++ because it's probably a good thing to get used to.

lumberjackninja · 11 months

Python, via SAGE; it can do pretty much anything Matlab can, but it doesn't suck. It'll also do symbolic stuff, which is pretty neat; basically, it's Matlab+Maple all rolled up into one nice package.

I also use Python for doing pre-processing of files before running them through tools I've written in other languages, by which I usually mean C. At my new job, C++ is fairly popular (it's a Microsoft shop, unfortunately), so I'm having to force myself to get over my (mostly unfounded) dislike of the language.

At the end of the day though, you use the right tool for the right job. That doesn't automatically justify the niche languages that are only used in specific scientific subfields, but at the end of the day it makes everybody's life easier if you just use C, say, for writing an operating system instead of trying to do it in FORTRAN.

devicerandom · 11 months

Python + Scipy/Numpy/Matplotlib.

At my new job, I have to use Perl, with which I have a love/hate relationship now (but I'm still learning).

I used Matlab for a while and I absolutely, totally hated it with a passion.

Wonka_Vision · 11 months

I program in MathCAD, which is not nearly as robust as Matlab.

omgdonerkebab · 11 months

Many theoretical particle physicists are using Mathematica, except for heavier computation, which requires either FORTRAN or C++. But only a relatively small number of particle theorists know a real programming language (not Mathematica)... those few who do write programs in FORTRAN or C++ that others can use without knowing the languages.

Much of particle experiment work is done in C++ now, with Python frameworks. I speak primarily of the ATLAS and CMS collaborations for the corresponding experiments at CERN, since that's where my short particle experiment experiences came from. Most of the data analysis will be in C++, while there's some overlap with theorist C++ and FORTRAN programs.

I also know some condensed matter theorists who enjoy coding in Python a lot. But the ones I know don't have that many computations to do, so they don't need something faster like FORTRAN or C++.

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