Narges Habibi's Blog

2011 in review

nhabibi — Sun, 01 Jan 2012 02:09:39 +0000

The WordPress.com stats helper monkeys prepared a 2011 annual report for this blog.

Here’s an excerpt:

A San Francisco cable car holds 60 people. This blog was viewed about 1,700 times in 2011. If it were a cable car, it would take about 28 trips to carry that many people.

Click here to see the complete report.

Academia.edu

nhabibi — Thu, 10 Mar 2011 02:08:54 +0000

It is a web site to follow others’ academic works. Try it!

PS: This is mine. Look at the followers!

Starting Again!

nhabibi — Mon, 28 Feb 2011 12:38:04 +0000

After a long time, about 1.5 year, I returned to my blog. The motivation is starting the PhD in Jan. 2011 in UTM (University Technology Malaysia). I am by research and I am thinking of Bioinformatics again. Living and studying here for me has some advantages and disadvantages, but in average it is OK.

I hope to write here more regularly.

My M.Sc. Thesis

nhabibi — Wed, 29 Apr 2009 12:20:19 +0000

Finally I defended my master thesis on 29 April 2009 successfully. The viva session was great and the referees appreciated the amount of time and effort spending on the thesis. The title is “Contact Map Prediction Using Committee Machine Approach”, with score “19.75″

The moments after defense are great and unbelievable. I can’t describe the feel of freedom now! I want to rest forever!

Thanks to God, my family, my friends and my professors. Thanks

How Web 2 Are You?

nhabibi — Tue, 13 Jan 2009 08:07:31 +0000

Take this quiz, interesting. My score was awful!

Social Web Usage Ladder

nhabibi — Thu, 06 Nov 2008 10:19:29 +0000

web usage ladder

(source)

PS: Well, I’m almost on the top step!

Flower Web 2.0

nhabibi — Sat, 18 Oct 2008 07:46:55 +0000

(source)

Conference Alert

nhabibi — Thu, 09 Oct 2008 08:48:11 +0000

This is a good way to be informed about incoming conferences. Just subscribe and determine the filed/fields.
I don’t know how much complete it is, but is good enough.

PS: care about the ending “s” in the URL!!!

Pdb-L Mailing List

nhabibi — Thu, 14 Aug 2008 14:29:28 +0000

I don’t have so much experiment with mailing lists, but this one is great! A number of knowledgeable and helpful people in the field, around the world.

Special thanks to Dr. Kevin Karplus, professor of Bioinformatics at University of California, Santa Cruz, for his useful and detailed responses.

Protein Contact Map Prediction

nhabibi — Wed, 28 Nov 2007 12:20:15 +0000

Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.

(Source: Wikipedia)

As the definition indicates, bioinformatics is an interdisciplinary field, hard but interesting.

The studies in bioinformatics are categorized in three groups: Genomics, Proteomics and Transcriptoemics. (Now we have some biology, You would like it! Skip, if your not interested. )

Genomics is the study of an organism’s entire genome. the genome of an organism is its whole hereditary information and is encoded in the DNA. This includes both the genes and the non-coding sequences of the DNA. More precisely, the genome of an organism is a complete DNA sequence of one set of chromosomes.

Proteomics is the large-scale study of proteins, particularly their structures and functions. The proteome of an organism is the set of proteins produced by it during its life, and its genome is its set of genes.

The transcriptome is the set of all messenger RNA (mRNA) molecules, or “transcripts”, produced in one or a population of cells. Unlike the genome, which is roughly fixed for a given cell line (excluding mutations), the transcriptome can vary with external environmental conditions. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being actively expressed at any given time. The study of transcriptomics examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA microarray technology.

Proteins are large organic compounds made of amino acids arranged in a linear chain. Proteins are essential parts of organisms and participate in every process within cells.

A protein contact map represents the distance between every two amino acids of a three-dimensional protein structure in a two-dimensional matrix. It can be used to describe the similarity between protein structures and prediction of tertiary structure. These maps are either predicted from protein sequence or calculated from a given structure.

Contact map prediction is a problem in bionformatics. Several approaches have been proposed, each one with a degree of success. We are working now on the subject. You can take a look at my seminar report and presentation, both in Persian.

More information:
- Computational Methods for Protein Structure Prediction and Modeling: Volume 1: Basic Characterization – Chapter 8

PS: Can you guess Why my “Blogroll” is empty?