Bioinformatics

All my flash tinkering has been in VIM-- no IDE, no XML, just actionscript. It's a little tough to deal with the adobe compiler as it takes about 11 seconds to compile a large project like modestmaps on my machine. That's not good for a guess-and-check programmer. The typing does catch some errors. The worldkit project compiles instantaneously with mtasc (the predecessor to haxe )--likewise for the as2 branch of modestmaps. The flash compiler shell drops the compile time for as3 modestmaps to under 3 seconds, so I've added this to my .bash_aliases: alias fcsh="/usr/bin/rlwrap /opt/src/flex2/bin/fcsh" the rlwrap is to use readline in the flash shell--meaning I can just press up-arrow to get the previous compile command. By default, one has to paste or type the entire command again. With that, it's close to a reasonable workflow.

Living in Synteny I've been working on automating synteny mapping between any pairs of genomes. Synteny is where there's a stretch of DNA or genes in some order on chromosomeA of organismX and due to a shared evolutionary history, you can find a similar stretch of genes in order on chromosomeB of organismY. Often there are small losses and inversions, but between closely related organisms like man and mouse , there's still a lot of synteny. Plants can undergo polyploidy , following which, a species can have 2 entire copies of its genome. Over time, much of the duplicated cruft is lost, and the homologous chromosomes diverge, but if the divergence is not too great, it's still possible (actually common) to find synteny within the genome of a single organism--as well as between organisms. I've written my own algorithm to find synteny which uses python sets, and numpy array slicing to do the heavy lifting. It is quite clever [wink]. And it _almost_ works but it'...

Mash Flap I started looking into flash mapping stuff lately. For the patch I submitted to worldkit, Mikel gave me commit access! So, now the svn version of worldkit can be compiled with mtasc by typing "make". I feel unreasonably proud of that, given that much of what I did was some global search and replace stuff in VI, and then read and fixed mtasc compiler errors until they went away. It was good fun. Michal Migurski saw in that same post that I mentioned modestmaps and gave me some good ideas on getting WMS going. I just figured out how to get that working and posted a message to their overly web2.0 forums. Hopefully someone with some real actionscript skillz will clean it up. A mapping library without a good WMS interface is much less useful for most of the stuff I do. I haven't decided whether to use modestmaps or worldkit, or both. The time stuff the Mikel has done in worldkit is very cool and I haven't really looked at that yet. But I have a tim...

There's a new release of the shedskin compiler. It is able to generate fast shared libraries that can be run from CPython. It can also create binaries so I thought I'd see how it did on some code from this BMC bioinformatcs article compared to psyco and CPython. I took this iterative, brute-force ( Needleman-Wunsch ?) alignment code and modified it slightly. That's pasted here . (Notice the first line! that's how it appears in the original code). The modifications allow shedskin to infer the function and variable types. Plus, there's a couple changes I made that improve the run-time for all cases. The max() function is also in the original, but unnecessary because of python's builtin max(), however, pysco does run much faster using their hand-coded max(). For the shedskin run, I removed that extra code and used shedskin's builtin 'cause it made me feel better. The python code was run as $ time python -c "import alignment; alignment.imain()"...