zen talk

"Theory that would not die: how Bayes' rule cracked the Enigma code, hunted down Russian submarines, and emerged triumphant from two centuries of controversy" by Sharon Bertsch McGrayne. Just came across it, and it appears to be a very promising read. The very first page mentions some practical problems that Bayes' rule helped solve in its early days: - To demonstrate the innocence of Captain Alfred Dreyfus, a French artillery officer - To set rates for insurance premiums - To decode German Enigma cipher thereby arguably saving the Allies from losing the WWII - To locate a missing hydrogen bomb and to locate Soviet submarines - To assess the likelihood of a nuclear accident - To verify the authorship of the Federalist Papers. Each of these applications is worth a look :-)

Is it possible to prevent cancer by making life style changes? This question just crossed my mind and I immediatedly Googled. The answer was a very clear yes. That is, it is possible to decrease the risk of cancer in people who are at high risk for cancer. It is also possible to reduce the complications and prolong life after cancer treatment. Best of all, many of the required life style changes are simple and doable. At a quick glance, these are most noted life style changes: - Healthy diet: at least five portions of fruits and vegetables per day (one portion = 80 grams). High fiber.  Whole grains. Less red meat. Less saturated fats. Less salt and sugar. Less processed food. - Active life style. Exercise. - Keep good weight. Obesity is a risk factor. - Avoid smoking. Avoid tobacco. - Be mindful of your alcohol intake i.e. keep it low or avoid. - Take special measures to reduce exposure to UV radiation. - Reduce exposure to pesticides and environmental pollutants. F...

I bought 10Mbps ADSL network connection from Saunalahti . It works all perfect except for this little glitch I had with it: from my Linux Mint Debian Edition (LMDE) or Ubuntu machine, I could not get the wireless network. While a windows machine and two android phones can access the wifi signals from the modem, the Linux machines can't even see the SSID of my network. In the beginning when I had just setup the modem I could access the wireless network from my LMDE machine. I started noticing the problem with the network, when I turned off my ADSL modem one day and in the evening turned it on. While all other machines got the connection as soon as the modem was up, my Linux machine could not detect the signal. After a little bit of messing around, I concluded that, for Linux to receive the wireless signal without a problem and to get the connection after the modem restarts, I need to follow the following protocol. I need to turn the wifi off on the modem by pressing a blue butto...

Google turns up many posts explaining how to install the ATI catalyst proprietary drivers on LMDE. Take this post as just an additional information. In my case, the installation did not work until I accidentally installed another package, x11-xserver-utils.  Thus, in my case, the installation of the drivers was as follows: sudo apt-get install x11-xserver-utils sudo apt-get remove --purge fglrx* sudo apt-get update && sudo apt-get install fglrx-driver fglrx-control sudo /usr/bin/aticonfig --initial sudo reboot I think the reason it worked this way was because computer couldn't recognize the correct graphic device version before the installation of x11-xserver-utils.

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...

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...