Today in my theatre!

Today I watched two movies. The first one was '12 Angry Men' - a brilliant classic, and the second one is Over the hedge, a cool and funny cartoon movie! I enjoyed watching both! After that, I went out to the gym to disprove that I am a couch-potato :P. I was in gym after a long time (especially, going there alone with my self motivation is something that doesn't happen!), and spent there more than 90 minutes of an industrious exercise :O.

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Setting up R packages for CBM of genome-scale metabolic models on Ubuntu 13.10

Long ago, I posted here the steps involved in setting up R packages for performing constraint based modelling (CBM) of genome scale metabolic models. It was Ubuntu 10.04 LTS back then. Now, I am trying to reproduce the same set-up on Ubuntu 13.10. As a quick summary, we need the following R packages: "sybil", "sybilSBML", and "glpkAPI". The "sybilSBML" R package requires the Bioconductor package "rsbml" which requires "libsbml" library, which in turn depends on "swig". The "glpkAPI" is an R wrapper for glpk library which is the optimization engine. I have been able to install all these packages by executing the following steps. 1. Install swig from ubuntu repositories. sudo apt-get install swig 2. Install python-dev from ubuntu repositories. sudo apt-get install python-dev 3. Install openjdk from ubuntu repositories. sudo apt-get install openjdk-7-jdk 4. Install libxml2 and libxml2-d...

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Set up for analysing genome-scale metabolic models on ubuntu

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...

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