Archive for the ‘Case studies/examples’ Category

“Should I switch to Python?”

Tuesday, November 17th, 2009

[caption id="" align="alignleft" width="140" caption="Logo owned by the Python Software Foundation"][/caption] 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 ...

Links to some great articles on programming

Monday, January 19th, 2009

[caption id="attachment_410" align="alignleft" width="300" caption="Photo by Manel"][/caption] The internet is full of smart people writing intelligently on how to write good software. Very few of these articles are from the perspective of a scientist (hence this blog!) but a lot of what they write is useful, interesting and, occasionally, entertaining. This ...

Coding case-study: (re-) writing a clustering tool

Friday, October 17th, 2008

[caption id="" align="alignleft" width="300" caption="photo by jimkster"][/caption] Over the summer, Rich has been writing a novel clustering algorithm for use with gene expression and other similar types of data.  There are some interesting facets to this (scientifically-motivated) project which illustrate some of the considerations the scientist-programmer can encounter when working on ...

Good code, bad code – an example

Friday, September 26th, 2008

[caption id="" align="alignleft" width="300" caption="Photo by jaycoxfilm"][/caption] We've written a function in pseudocode.  Twice.  Once will be using good coding practice, care and attention.  The other one won't.  Because both functions will be doing the same thing, this is a great way to see the difference that good programming practice can ...