Some interesting books!

Among many other hundreds of books which I should be reading, this essential biochemistry seems to be one! Credit goes to Jukka Nurminen, our cross-business area collaborator for introducing the book. Though shalt be read, Mr. Biochemistry! The second book that Jukka introduced was Bioinformatics: sequence and genome analysis. Well, I was familiar with this book earlier; so this was a reminder for the relevance of this book to me, now more than ever!

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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...

Chetta idea - 1

Alternative title: proposal for a health care project. Diseases such as hypertension (high blood pressure), diabetes, obesity are becoming so common nowadays. It is hard to find people with no diseases. The lifestyle is certainly to be blamed. But what is the use if we just shut our mouth after finding the right thing to blame? Or how would I be different if I leave it there. So, here is a proposal for an automatic health-care system. Well, I know there maybe some treatments, but the idea here is to prevent the diseases. But, prevention really demands prediction of the disease occurrance much before the disease symptoms show off. But, since I am not a palmist or an astrologist, my proposal is to develop a method to stop the disease as soon as its onset or the symptoms appear. OK... it will become more clear as I go with the concrete examples. I would like to concentrate on hypertension and diabetes, because they appear to be the most common diseases. As most of you know, the best cure...

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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