Pythooooon

I’ve written previously about the Daaaaave algorithm for using ‘omics data to predict fluxes through a metabolic network. We originally implemented the algorithm in MatLab, and released the code as supplementary material to the paper [1]. But the journal (BMC Systems Biology) messed up: changing the file names, and breaking the code.

We’ve tried to get them to fix this. Unsuccessfully.

So instead, I’ve put the code on sourceforge github [2]. And since MatLab sits uncomfortably with my cardigan-wearing, open source approach to science, I’ve reimplemented the algorithm in python there, too.

References

1. Lee D, Smallbone K, Dunn WB, Murabito E, Winder CL, Kell DB, Mendes P, Swainston N (2012) “Improving metabolic flux predictions using absolute gene expression data” BMC Systems Biology 6:73.
   doi:10.1186/1752-0509-6-73
2. http://github.com/u003f/daaaaave

A python