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...

I ordered this a-link pad 10 on 16.5 (from: (http://www.a-link.com/fi/PAD10/product.php) . It is a totally whimsical decision because there are no reviews about it in the internet. I picked up my tablet from a-link "store" in Tuomarila on 18.5. After I picked up, I went to VTT and charged it there while I was working. After that I got it home and have been testing. Test results (cons) in no specific order: 1. As of now, the touch doesn't work. Luckily I enabled under developer settings an option to show the visual feedback on touch. Because of that I know the reason why the tablet doesn't respond to touch. Apparently, there is a huge error the tablet makes as to where I touch. So, when I want to touch an OK button which is in the middle of the screen and put I finger right on the button, the tablet interprets my finger to be somewhere on the bottom left corner! For this reason, I am not able to use the tablet for the last 30 minutes. Since I am able to se...

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.

Recently battery life on my laptop (acer aspire 3820TG) has reduced quite heavily. I could not pin point any specific reason, but I thought that it has decreased significantly after I had brought ubuntu one into use. Without spending too much time on why the battery life reduced, I started googling tips for saving battery life on ubuntu. The following post gave very relevant tips, with very detailed explanation. http://ubuntuforums.org/showthread.php?t=1157408 So, I decided to activate the laptop-mode. In fact, doing so has apparently been even more easy than what was described in the above ubuntu forums post. All I had to do was to install laptop-mode-tools. sudo apt-get install laptop-mode-tools In fact, the laptop-mode-tools actually came out of box with quite sensible settings pre-configured, so I didn't have to do any extra work to get the laptop-mode working! The only thing I did was to install powertop and check that powertop had no more suggestions when I was running on b...

Mahatma Gandhi said, "you be the change you want to see in the world". Because virtues are universal, you might have heard the same words, possibly said in different ways, from different people. I wouldn't like to preach anyone, but several situations in the recent past compelled me to write this text now. However, I am not preaching anything. I am just trying to contemplate on Gandhiji's valuable words... for the benefit of myself and also for others. I however think that many many of these "others" will benefit from mulling over these words. However, when I say contemplate, I also mean putting action into it. By putting action to substantiate the contemplation, we all will primarily benefit ourselves because we will enjoy the resulting improved quality of life. And we will benefit our friends and families by putting less "expectation" or "load". Change is always "uncomfortable". It doesn't come for free! The primary step i...

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...