I started at UCSF on Nov. 9, 1998. Most of the materials I work other than those for the SACS training seminars are either for a secure web server or for UCSF grant projects and therefore impossible to show to the general public.

I will post completed projects on this page in various areas what are open to the public and give descriptions of materials that are firewalled.

UCSF grant projects:

PMT grant - provide bioinformatics expertise to identify exons for the studied genes, responsible for prototyping the PMT result web pages and organizing the data received from the campus Genomic Core facility for further analysis
PGA grant - provide instructional expertise, develop materials for and conduct workshops (workshops given several times a year)

I am involved in developing software for local SACS use as well as for special projects on campus.

Software development:

plain - display program for showing SNPs on non-transmembrane proteins (5' UTR and 3' UTR regions also shown)
TOPO2 - totally rewritten TOPO program now in python and its web site
color-pb - a tool to colorize GCG's prettybox postscript output file
exon finding tool - a python program to search NCBI databases for exons starting with an accession number for a mRNA sequence
topo - enhancements to the TOPO program for visualization of transmembrane proteins started at WSU, software has been ported and partial transmembrane segment display added

SACS has its own interface to a number of GCG programs as well as other commonly used sequence analysis programs. My contribution to this effort includes.

GCG interfaces:

Stringsearch, peptidesort, coilscan, hthscan, translate, fitconsensus, testcode, stemloop, bestfit, gap, compare, distances, plotsimilarity, pretty, prettybox, and prime
Other interfaces:

Memstat (transmembrane prediction), MultAlin (multiple alignment), selected Phylip programs (phylogenetics) and AutoBlast (a means of doing automatic BLAST searches at NCBI on a periodic basis).

SACS offers a seminar training series to help UCSF users become more familiar with using its resources. This series has evolved over the course of time, with the earliest ones being less polished than the later ones.

Training seminars I have given.

Spring 2003
4/02/03 - UNIX: - PDF	5/07/03 - BLAST: - PDF
4/09/03 - WEB: - PDF	5/07/03 - Multiple alignments: - PDF
4/16/03 - GCG: - PDF	5/21/03 - Characterization [Protein]: - PDF
4/23/03 - EMBOSS: - PDF
Winter 2003
No seminars due to the move
Fall 2002
9/25/02 - UNIX: - PDF	10/30/02 - Binary Alignments: - PDF
10/02/02 - GCG: - PDF	11/06/02 - BLAST: - PDF
10/09/02 - EMBOSS: - PDF	11/13/02 - Multiple Alignment: - PDF
10/16/02 - WEB: - PDF	11/20/02 - RasMol (by request): - PDF
10/23/02 - Characterization [Protein]: - PDF
Summer 2002
7/24/02 - UNIX: - PDF	8/07/02 - Multiple Alignments: - PDF
7/31/02 - GCG: - PDF	8/14/02 - Alignment Visualization: - PDF
Spring 2002
4/03/02 - UNIX: - PDF	5/08/02 - BLAST: - PDF
4/10/02 - GCG: - PDF	5/15/02 - Multiple Alignment: - PDF
4/17/02 - EMBOSS: - PDF	5/22/02 - RNA Folding: - PDF
5/01/02 - WEB: - PDF
Winter 2002
1/16/02 - UNIX: - PDF	2/13/02 - EMBOSS: - PDF
1/23/02 - WEB: - PDF	2/20/02 - BLAST: - PDF
1/30/02 - Locating Data: - PDF	2/27/02 - Characterization [Protein]: - PDF
2/06/02 - GCG: - PDF	3/06/02 - Multiple Alignments: - PDF
Fall 2001
9/26/01 - UNIX: - PDF	10/31/01 - BLAST: - PDF
10/03/01 - GCG: - PDF	11/07/01 - Multiple Alignment: - PDF
10/10/01 - WEB: - PDF	11/14/01 - Characterization [Protein]: - PDF
10/17/01 - Locating Data: - PDF	11/28/01 - EMBOSS: - PDF
10/24/01 - Binary Alignments: - PDF	12/05/01 - RasMol(by request): - PDF
Summer 2001
7/11/01 - WEB - PDF	7/25/01 - RasMol (by request) - PDF
7/18/01 - BLAST - PDF
Spring 2001
3/28/01 - UNIX: - PDF	5/02/01 - BLAST: - PDF
4/04/01 - GCG: - PDF	5/09/03 - Multiple Alignment: - PDF
4/11/01 - WEB: - PDF	5/16/01 - Characterization [Protein]: - PDF
4/18/01 - Locating Data: - PDF	5/23/01 - Characterization [DNA]: - PDF
4/25/01 - Binary Alignments: - PDF	5/30/01 - Alignment Visualization: - PDF
Winter 2001
1/24/01 - UNIX: - PDF	2/21/01 - Binary Alignment: - PDF
1/31/01 - GCG: - PDF	3/01/03 - BLAST: - PDF
2/07/01 - WEB: - PDF	3/07/01 - Multiple Alignment: - PDF
2/14/01 - Locating Data: - PDF	3/14/01 - Characterization [Protein]: - PDF
Fall 2000
9/20/00 - UNIX: - PDF	10/25/00 - BLAST: - PDF
9/27/00 - GCG: - PDF	11/01/00 - Multiple Alignments: - PDF
10/04/00 - Locating Data: - PDF	11/08/00 - Characterization [DNA]: - PDF
10/11/00 - Simple Database Searching: - PDF	11/15/00 - Characterization [Protein]: - PDF
10/18/00 - Binary Alignment: - PDF	11/29/00 - Phylogenetics: - PDF
Summer 2000
7/12/00 - UNIX and Your SACS Account - PDF	7/19/00 - GCG - PDF
Spring 2000
3/29/00 - Bioinformatics Introduction: - PDF	5/03/00 - Alignment Visualization - PDF
4/05/00 - Database Searching: - PDF	5/10/00 - WWW Analysis: - PDF
4/12/00 - Using Blast: - PDF	5/17/00 - Protein Analysis: - PDF
4/19/00 - Binary Sequence Alignment: - PDF	5/24/00 - Transmembrane Proteins: - PDF
4/26/00 - Multiple Sequence Alignment: - PDF	5/31/00 - Phylogenetics: - PDF
Winter 2000
2/02/00 - Bioinformatics Introduction:	2/23/00 - Database Searching:
2/09/00 - Protein Analysis:	3/01/00 - Multiple Sequence Alignment:
2/16/00 - Binary Sequence Alignment:	3/08/00 - Phylogenetics:
Fall 1999
9/29/99 - Bioinformatics Introduction:	11/11/99 - Internet and WWW Analysis:
10/13/84 - Binary Sequence Alignment:	12/01/99 - Primer Selection:
10/27/99 - Protein Analysis:
Summer 1999
7/29/99 - Alignment Visualization:	8/18/99 - Transmembrane Proteins:
Spring 1999
4/21/99 - Bioinformatics Introduction:	6/09/99 - Internet and WWW Analysis:
5/05/99 - BinarySequence Alignment:	6/23/99 - Primer Selection:
5/19/99 - Protein Analysis:
Winter 1999
1/20/99 - Bioinformatics Introduction	3/03/99 - Internet andWWW Analysis:
2/03/99 - BinarySequence Alignment:	3/24/99 - Primer Selection:
2/17/99 - Protein Analysis:

under construction