Having spent a frustrating hour or so trying to update a mac application bundle I thought I’d share a couple of things which caused no end of confusion and aren’t what you’d expect and are therefore likely to catch out those working with application bundles for the first time. Basically I was finding that although…
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Dynamically setting the java heap size at runtime
One of the oddities about java programs is that they require you to set a maximum heap size when you start the program. What this means in effect is that you need to be able to predict the memory usage of your program before it starts, and whatever heap size you set needs to be…
Adding custom chromosome name mappings into SeqMonk
When loading data into SeqMonk the program has to try to connect the chromosome names used in your data file with those which are present in the genome one which your project is based. In many cases there won’t be an exact match between the two – many mapping programs report file names in their…
How good is ‘good enough’ for research software
There are two linked problems which seem to face me with every piece of software I write for research use: When is the software complete enough to write a paper on it How to manage the versions and project description I think that although similar questions arise within software written for general use, their answers…
Scientific Instrument Software
As a bioinformatician I find myself spending too much of my time working around poor software supplied with scientific instruments. I’m continually amazed that hardware which can cost hundreds of thousands of pounds is very often let down by the control and analysis software supplied with it. I suspect that the fault for this lies…