zen talk

The second day of metabolic modelling work introduced me to more installation stuff required to complete the platform set-up. This all started when I was going through the vignette of the R package sybil and trying to run the example analysis shown in the vignette. I tried to run the flux balance analysis example and it said that I needed glpkAPI. It turns out that I have to first install GNU GLPK. The glpk that was available on ubuntu repository didn't work. So, I installed glpk as follows wget http://ftp.gnu.org/gnu/glpk/glpk-4.48.tar.gz wget http://ftp.gnu.org/gnu/glpk/glpk-4.48.tar.gz.sig sudo gpg --keyserver keys.gnupg.net --recv-keys 5981E818 sudo gpg --keyserver keys.gnupg.net --recv-keys 5981E818 ./configure make make install After this, I tried installing glpkAPI using install.packages , but it didn't work (even with --configure-args specified correctly). Downloading the package to the local drive and installing it from the command console worked. Here is the...

I wanted to start analysing genome-scale metabolic models. I am interested in metabolic modelling to study human diseases. At least as of now, my idea is to use R for the analysis. This post describes all the technical set-up that I am doing on my ubuntu 10.04 LTS machine in order to eventually start working with these models. As I am interested in human metabolic network, my model of interest is the reconstructed human metabolic model, recon 2. I googled to see where I can download it from. It has a web site http://humanmetabolism.org/. But the model is available for download from the supplementary material of this paper . There was a zip file that contained many files which I interpret as the generic human model and cell specific models for a variety of cell types. I first wanted to see the contents of these files with my eyes. I know that I could open these files with any text editor, but I also knew that there is something called SBML editor which is specifically designed fo...