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Advice to a young computational biologist

Fri, 2007-03-16 13:45 — Greg

Just when I though Bosco was posting too much poetry, he comes out with this truly excellent post on advice for young computational biologists. Bosco has managed to distill his 10 years of experience into eleven succinct points that are relevant to not only those just starting out in computational biology, but experienced hackers as well. This post is a must read, I highly recommend his advice in point four on using configuration files. It is a simple way of adding value to scripts, by extracting out the parameters into a config file and then writing another script to iterate over different values. Python has a default module for this, with many other third party options. And of course point eight, using command line plotting software, my current favorite is Ploticus.


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Sun, 2007-03-18 09:20 — mako

interact with your data

Thanks for the link Greg. Better than reading PhD comics all day (http://www.phdcomics.com/comics.php). As a fan of Xlisp-stat, I've long been looking for some interactive plotting software. My gift today is a nice toy which is almost solves what I was (almost) drove to write myself out of frustration. The problem: interacting with your visual data (plots). The new toy which makes data exploration fun again (I tend to use R) : iplots (http://www.rosuda.org/iplots/), a java graphing R package that allows "callbacks" to R data structures. Very cool, seamless install. It's not perfect, as all calls seem to have to orignate from R; the use of >iset.selected() in R calls the data points highlighted in the graph. But there are some right-click graph transformation features scattered here and there; I assume that the iplots project will continue to evolve.

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Fri, 2007-03-16 18:53 — michael

Config files

Configuration files are particularly useful in compiled languages such as java and C.
The runtime behavior can be changed without needing recompilation.
I don't know about C, but Java has the Properties class for parsing config files.