Programming for Scientists

How to…optimise Matlab

image from wikipedia

Matlab is a language that’s used a lot in science and for good reason.  It’s quick to code in, plus there are loads of built-in functions and packages available for many of the tasks that Programmer-Scientists might find themselves involved in.  The main issue that a language like Matlab faces is that it’s slower than languages like C++ and FORTRAN, which can be inconvenient when dealing with resource-intensive tasks like data analysis, statistical modelling or numerical simulation.  But fear not!  We proudly present our guide to how to optimise your Matlab code.

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Posted in Optimisation | 2 Comments »

Scripting for science papers

image by marco annunziata

Scientist-Programmers write a lot of scripts.  It’s part-and-parcel of “trying stuff out”, it’s a quick way to get some number crunching done on those data, and it’s very useful for generating the figures and tables that you need for that paper you’re writing.  In this article, I give a quick once-over of some of the things I’ve learned over the years about using scripts as a scientific tool.

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Posted in Craft of coding, The Scientist-Programmer, The basics of... | 1 Comment »

“Should I switch to Python?”

Logo owned by the Python Software Foundation

Rich has recently been considering switching to the Python programming language.  Currently, Matlab is the language of choice in his department for rapid development and prototyping of code.  It’s very good at this, but Mathworks (the company who produces Matlab) have been tinkering with the licencing terms, leading to hassles where none should exist.  This is very frustrating and leads to the thought that it might be nice to use a free language where this will no longer be an issue.

But of course things are not quite that straightforward.  Matlab is used for good reason – it’s very good at what it does.  So is it worth the effort to stop using Matlab and instead learn to use Python?  In this article we discuss some of the things that’ll need to be considered. Read the rest of this entry »

Posted in Case studies/examples, Choosing a programming language | 15 Comments »

Writing code for a big scientific collaboration

Photo by ralphbijker

One of the striking thing about scientific software is the range of different contexts in which it’s needed.  Scientists need quick-and-dirty scripts to process their data and plot their results; they need prototypes so that they can experiment with new statistical techniques; and they sometimes need to build new software tools that they’ll use again and again in their research.  While a lot of this will be for their own personal research, sometimes the Scientist-Programmer finds themselves developing software as part of a large scientific collaboration.  This has some particular requirements. Read the rest of this entry »

Posted in The Scientist-Programmer | No Comments »

The ‘programming for scientists’ link montage

Continuing our theme of gathering together useful stuff for the scientists-programmer we present a list of interesting, useful, informative and possibly fun links. Enjoy!

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Posted in Uncategorized | 1 Comment »