Forrest Sheng Bao's Cyberhome

by Forrest Sheng Bao http://fsbao.net

I have lotta Python programs for bioinformatics research. I wanted to put them onto the web. I only developed Web apps in PHP before. And it seemed to be a big pain for porting a Python program to the web. But, I figured out in 5 minutes.

First, you need an Apache server on your Linux/Mac OS/Windows box. If you are gonna use data base, you need a database server. There are tons of blogs addressing these issues. So I won't be gossipy here. Suppose everything we mention below happens on your server-even web browsing.

by Forrest Sheng Bao http://fsbao.net

If you are looking for a program to do genome localization of small sequences, such as small RNAs, you can use our program as described in this paper: Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis. PLoS ONE 4(3): e4971. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004971 Please cite our paper if you use our program in your papers. Here is a short How-to.

My program is written in Python. So you have to install a Python interpreter first. On most Linux distributions, Python is already installed. On Mac and Windows, please go to http://www.python.org/download/ to download the installation program. Python 2.x is recommended coz I didn't test on Python 3.0.

by Forrest Sheng Bao http://fsbao.net

Since 2008, I have been helping Dr. Xie, Dept. of Biological Sciences, Texas Tech University on bioinformatics computing. I worked happy with his Post-Doctoral researcher Dr. Qi, who is now with Indiana University. I plan to write down some instructions so that new PhD students can work happy with me as Dr. Qi did.

Workstation software configurations:

by Forrest Sheng Bao http://fsbao.net

MySQL official documentation provides two ways to backup. One is mysqldump. Another is mysqlhotcopy. But I don't like mysqlhotcopy since I don't like seeing so many table files. So I like mysqldump, giving me just one sql file.

mysqldump --user=root -p drupal > newdrupal-20080614.sql