Perl is useful too

I subscribed the mail lists of china-pm and bio-perl-pm. Actually I didn't look into it very carefully until just now. Some guys introduce the use of perl to develop the plug-in for firefox, which shocks me a lot. Perl can be used to such a high level, but I give it up. Anyway, regret is useless. Try to grasp both Perl and Java. Be a good programmer soon.

Merry Christmas

Merry Christmas! A new year is coming. Work harder and harder!
Today I plan to finish the technical report to Keith.
Here we go.

To Be Creative

A good programmer is not always Using the codes of others, rearranging them and modifying them, but do some creative work. Create the methods and codes of their own, for others.

I want to and will be such a good programmer later.

Some interesting website

Today when I am surfing online, I found some website very interesting.
First, metabolicvisualizer, very creative website. It lets you control the contents of the involved elements, such as glucose, ATP, and so on. With your adjusting, the reactions inside the big cycle area are automatically adjusted. Very interesting.

Second, DAVID, The Database for Annotation, Visualization and Integrated Discovery. DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

A paper published in Nature Protocols describes step-by-step procedure to use DAVID:

Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. (2009) Nat. Protoc. 4:44 -57.

http://www.nature.com/nprot/journal/v4/n1/abs/nprot.2008.211.html

Note: This paper, commissioned by the Nature-branded journal -- Nature Protocols, systematically describes the rationals and procedures to use the DAVID Bioinformatics tools. By following the step-by-step procedure in the paper, readers will be able to more efficiently use DAVID bioinformatics tools for high-throughput gene functional analysis, leading to more meaningful analytic experiences and maximal satisfactory results. In this moment, subscription to Natrue web site is required to view full text. We will provide free archive-version of the paper shortly.

Using Network Alignment to serve the discovery of undealying disease

In the recent reports, the most question which was thrown to me is, what the hell of designing a network comparison algorithm can be used to? Now, Xuebing Wu et al. help me to give one answer: network alignment can be used to detect or predict the underlying disease families. (The other applications include reconstructing the phylogenetic relationships of organisms, integrating data of genome and proteome, querying the interested pathway within the known pathway databases, and so on.)

Here is the link of this paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/25/1/98?. Thank Samuel for helping download it.

The coming review and three technique report

Our annual conference would be held earlier next month, say, around Jan 5th. In addition, we will have a pre-report for the whole year work summary before that, which probably is the next Tuesday.Thus, in this week I need to start and finish a review paper,and two reports for the annual conference. One is in Chinese and the other is in English. These two coming reports are technical ones, which need a lot of data from pre-experiments. In addition to these, I also need to prepare three detailed reports for Keith for the further discussion, which are related to the three thoughts I mentioned in the last letter and also in the prepared proposal respectively.

In a word, this week I would have a heavy paper work. They would be:

1. One big review for peer review, which is on the progress of the methods network comparison applied in the phylogenetic analyses.

2. Two technical reports, one in English and another in Chinese. They are requested before the annual conference and would help me prepare the presentation.

3. Three detailed reports in line with my thoughts mentioned to Keith. In order to have a good discussion later, I need to prepare each of them as detailed as possible.

Today I would like to start with the second one, the simplest, and try to finish it.

Here we go.

What would I do today

I attend the regular biweekly report this morning.
I will try my best to write the detailed report for Keith, which will be started after a while.
For the annual conference, I need to prepare two review as requested. So I'd like to do it from now on. One is for the review on network comparison algorithm, the other is the detailed thought record on the pathway alignment and the network comparison algorithm based on the pathway alignment.

Here we go.