Brian Chan

I was hired as an undergrad programmer in my sophomore year since April 2001. My main job title is to write standalone and web interface to process and visualize bioinformatics data. I have learned and become proficient in designing and developing software. I also acquired some amount of bioinformatics knowledge to facilitate the background coding of each of my program. Under the supervision of Alex Kozik, I managed to complete and achieve the following:

DiagHunter and GenoPix2D publication

I played a small part in this project by writing code for the GenoPix2D visualization plot. This paper was published on Genome Biology on Sept 19th, 2003.
http://genomebiology.com/2003/4/10/R68/

Contig Viewer

This graphical viewer displays contig assembly and other related info. There are many options implemented to customize the output image and text for the researchers. Two versions have been developed with very similar background coding but different usages. One is an online PHP version, the other one is a standalone Python version.
http://cgpdb.ucdavis.edu/database/chromat_viewer/CV_main.php (php version)
http://www.atgc.org/Py_ContigViewer/ (python version)

Python BLAST info viewer

It is designed to view results of BLASTX search of the set of ESTs (or contigs) against Arabidopsis predicted proteins. The viewer displays graphical alignments for the first three best hits (if found) from BLAST report as well as intron-exon positions for Arabidopsis protein sequence.
http://cgpdb.ucdavis.edu/SNP_Discovery/BlastViewer/

xgeolocate - IP locator

It looks for the respective geographical location(s) from the netgeo server, then it plots the result on a world map. After plotting, the result can be saved into a data output file. Next time the user can directly plot the locations on the world map with that data file as an input file.
ttp://www.atgc.org/geolocate_1_2/

Graph9

This Graph9 program does clustering based on adjacency matrix. An adjacency matrix representation of a graph is a V-by-V array of Boolean values, with the entry in row v and column w defined to be 1 if there is an edge connecting vertex v and vertex w in the graph, and to be 0 otherwise.
http://www.atgc.org/BlastParser/Graph9_Program.html

BLAST parser

Almost any bioinformatician wrote at least once in his/her lifetime a BLAST parser for some particular needs. Major advantages of our parser are automatic generation of the "Matrix file" suitable for protein/sequence clustering analysis, and generation of the "Two Hits File" which helps to distinguish orthologs from paralogs in the case of BLAST search of one genome against another, for example: Lettuce/Sunflower COS candidates (Conserved Orthologs Set) web page.
http://cgpdb.ucdavis.edu/BlastParser/Blast_Parser.html

Sequence Retrieval by Keywords

Blast Search Parser matches a given a keyword with the words in BLAST hit description line. If the description line contains a searchable word, a cutoff value is compared. Blast Search Parser will extract the contig with the largest expectation value above the cut off value.
http://cgpdb.ucdavis.edu/database/sms/blast_search_DB_parser.php

Though these programs are free to use, they are written under thoughtful planning and careful coding. I hope you find them useful for your professional and maybe even personal use. If you are looking for a programmer to help you develop some useful software, please do not hesitate to contact me by email (birdchan@ucdavis.edu).

I am looking forward to furthering my education in the field of Computer Science. My academic goal is to obtain a PhD in Computer Science.