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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!
Recent posts

SolydXK linux laptop overheating

For the last couple of days, my home computer with SolydXK was overheating. The situation was so bad that, by the time I can gain control of the machine, it gets so overheated that it shuts down automatically as the critical temperatures have reached. I initially suspected acpi_call (just a hunch, because I have set up the OS on this machine quite recently and haven't tweaked the system much yet, except turning off the discrete graphics card using acpi_call ). But removing the corresponding kernel module didn't do the trick. I booted into recovery mode, edited the /etc/rc.local to prevent loading the acpi_call kernel module and turning off the discrete graphics card. Although this sounds counter intuitive, because usually turning on the discrete graphics card causes the overheating, I saw some errors related to acpi_call during boot time too, which is why I targeted that first. But a reboot after exiting the recovery mode, now without acpi_call loaded, didn't prevent th

Early applications of Bayes' rule?

"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 :-)

Prevention of cancer. Is it possible?

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. Fact: 40%

ZyXEL VMG3326 D20A ADSL modem Linux wireless network problem

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

Installation of ATI catalyst propreitary driver on LMDE (Linux Mint Debian Edition)

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.

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