Archive for August, 2008

Count time in c/c++

Sunday, August 31st, 2008

It is not that difficult to count time in C++ between two designed points. Here is how I did it.

#include < ctime >

time_t tstart, tend;

tstart = time(0);
//your scripts
tend = time(0);
cout << “It took ” << difftime(tend, tstart) << ” second(s).” << endl;

It worked fine for me.

Well, if you want to be as precise as possible, then use the following C code, which is at microsecond resolution:

#include <time.h>

double tstart, tstop, ttime;

tstart = (double)clock()/CLOCKS_PER_SEC;


tstop = (double)clock()/CLOCKS_PER_SEC;

ttime= tstop-tstart; /*ttime is how long your code run */

Book on protein denaturation

Friday, August 29th, 2008

I accidentally found there is an impressive book on protein denaturation, its title is Physicochemical Aspects of Protein Denaturation. The author is Savo Lapanje, he seems a very good writer based on my first impression of the book. I’d like to read and also recommend the book.

PLoS on facebook and video on nucleosome occupancy patterns

Tuesday, August 26th, 2008

It is good to know that PLoS Computational Biology is on Facebook. I immediately became a fan of it on facebook. Exploring the PLoS CB facebook, I found that there is a video on nucleosome occupancy patterns which is very interesting. Also, “surprisingly” the speakers/authors are all from UT Austin! Nice to know.

Here is the link to the video.

SciVee: make your research known

Also, the scivee website seems a very good platform for communicating scientific results and opinions. People actually post their own video of their own research on scivee. This is cool. You actually expand your audience without being restricted to any conference, symposium, workshop… I’m definitely going to watch some of them anytime.

ISMB 2008 summarize

Wednesday, August 6th, 2008

ISMB 2008 fever is not over yet. For example. There is a very interesting blog on ISMB 2008. It is actually quite useful.

One thing came out strong for me after the conference is that it is very inspiring/productive to talk to collages about your research. You would be amazed by the feedback you get, I know I am. Also, I talked to several people about their research and learned a great deal out of the conversation. Just to list a few.

Ramiro Barrantes is doing co-evolution of amino acids based on both sequence and structure.

Thomas Abeel use DNA denaturation energy as profiles to predict core promoter.

Hagit Shatkay carefully parsed the literature in protein subcellular localization so that she could come out with a better localization predictor (than TargetP, MultiLoc, PLOC).

David Jaffe presented his lots of work on several types of array analysis. My impression is that he has a variety of accesses to enormous data resource. Some of his results are biologically intuitive. For example, two types of histone methylation, H3K4 and H3K27 function in reverse way of DNA methylation. H3K4 methylation turn on transcription initiation while H3K27 turns it off.

Peter Karp developed a program that infers transporter function. He parsed the literature of tranporters annotation and then create modules to record their chemical reaction.

Ludovica Montanucci presented her work on using SVM to classify thermostability gain/loss of sequence mutation. She collected all genes/proteins of a thermophilic and mesophilic genomes and made pair of similar proteins so that one protein of a pair is from thermophilic and the other one of the same pair is from the mesophilic. Then she used SVM to learn and the n predict thermostability changes(gain/loss) of sequence mutation. Yana Bromberg made a good comment that she ought to try her method on ProTherm, a database for experimental determined melting temperatures of mutants. I’m glad that I had a chance talking to Yana more in the lunch break.