Yee Man Chan $Id: resume.txt,v 1.1 2002/06/16 23:54:04 root Exp root $ Mobile: (408) 930-5988 E-mail: ymc@yahoo.com Homepage: http://www.welltall.com/ymc/ Location: Palo Alto, CA Work Authorization: Permanent Resident Travel: wouldn't mind Availability: 2-week notice OBJECTIVE To utilize my knowledge in Bioinformatics and Networking Software and passion in Software Development to become part of the force that makes a better world. SUMMARY An experienced UNIX/Linux software engineer specializes in various aspects of Bioinformatics as well as Network Programming. An individual that has a passion to learn new things and try new things. My experience working at a start-up equipped me with the mindset to work extra-hard as a team to beat the schedule. I feel strongly that I am up to any challenge that my next job may entail. EXPERT SKILLS C, Perl, Java, Sequence Alignment, HMM, Linkage Analysis, Gene Expression Clustering Analysis, Web Caching, Distributed Systems Design, HTTP/1.1, Binary-based/Text-based/XML-based Transaction Protocol Design, GNU development tools, Open-source software hacking, Problem Solving, Mathematics and Statistics, Encoding/Encryption Algorithms, Multilingual LANGUAGES AND SYSTEMS Computer Languages: C (7 yrs), Perl (5 yrs), Java (4 yrs), C++ (2 yrs), HTML (4 yrs), JavaScript (4 yrs), SQL (2 yrs), XML (1 yr), Visual Basic (1 yr), MIPS 2000 Assembly (1 yr), Pascal (3 yrs), BASIC (2 yrs) Bioinformatics Tools Used: BLAST, MegaBLAST, BLAT, d2_cluster, ESTScan, spidey, e-PCR, Fasta, plaid Bioinformatics API: Bioperl, NCBI Toolkit Bioinformatics Programs Hacked: Fasta, spidey Bioperl Contributions: Bio::Tools::dpAlign, Bio::Tools::HMM Protocols Known or Used: HTTP/1.1, FTP, IPv4/IPv6, TCP, SMTP, TELNET, ICPv2/ICPv3, CARP, SSH-2.0, SVODP/RTSP, DCE RPC, DCOM Encoding/Encryption Algorithms Known or Used: RSA, MD5, IDEA, Reed-Solomon Code, Base64, MPEG Demultiplexing, DES, NTLM Specific Programming Skill: CGI Programming, UNIX System/Network Programming, Pro*C, JNI C-Java/Java-C, Makefile, Java RMI, Java Swing, Java NBIO, Linux 2.2.x/2.4.x KERNEL Module Programming, Perl XS programming RDBMS: Oracle, MySQL, Postgresql UNIX System Admin Skill: DHCP, firewall, IP chains, apache, squid, Darwin Streaming Server, FTP server, webmin, crond, samba, network set-up, shell script, LVS OS: Windows NT/2000, Windows 95/98/Me, MS DOS 3.3-6.2, Windows 3.1, Red Hat Linux 6.2, Unix SunOS 5.5.1, QNX V4.23, FreeBSD 3.0-CURRENT, Digital Unix V4.0D, HP-UX 10.20, PalmOS 3.0, Netwinder Linux for ARM, Hardhat Linux 2.0 for PowerPC 405 Open-Source Software Hacked: squid-1.1, squid-2.2STABLE5, cuttlefish-1.0.4, wu-ftpd-2.6.0, netkit-ftp.0.15, ssh-2.0.13, pgp-2.6.2, pgp-6.5.1, webmin-0.79, mpgtx-1.0, squid-2.4STABLE6, samba-2.2.4, NCBI Toolkit Perl Modules submitted to CPAN (username: UMVUE): Authen::Perl::NTLM, DCE::RPC Software: MS Word, MS Excel, MS Access, MS PowerPoint, MS Visual Studio 6.0, Watcom C++, Adobe Photoshop 4.0, Adobe Illustrator 7, Changjei Input Method, Rational Rose/C++ 3.0/4.0, SAS v6.12, MATLAB 5.2, Oracle 8.0.4, AMPL, TROLL, lex & yacc, awk/gawk, vi/emacs, purify, latex, gdb/ddd, gcc/cc, gnuplot, squid-2.2STABLE5, cuttlefish-1.0.4, apache-1.3.9, Cygnus Source Navigator 4.2.2, Cygnus CodeFusion 1.0, DarwinStreamingServer-2.0.4, CVS/RCS, tcpdump API Package: Java API 1.3, Rogue Wave C++ Library 7.0, JDBC-7.0.1.2, xerces-1.2.0, cryptix Human Languages: English, Taiwannese/Hokkien, Cantonese, Mandarin, two years of college Japanese and Korean alphabets. EXPERIENCE Stanford Human Genome Center, Palo Alto, CA Software Developer Research (Aug 2002 ~ present) - Annotated chromosome 5, 16 and 19 as a member of the 10-person annotation team under the Human Genome Project - Worked with the author of spidey program to extend the program to do cross-species EST/mRNA to genome alignment - QCfed genome assemblies of stickleback and poplar tree - Performed Linkage Analysis to created Linkage Maps for stickleback markers based on the genotypes supplied. - Performed computerized sequence analysis/annotation: SNP placements, align overlapping clones, genetic markers placements, gap-filling using primer walk sequences, paired up ESTs of a cDNA - Built GO and ENSEMBL databases locally and wrote scripts to access them and analyze gene expression data we collected - Developed a reporting script to generate SNP report and also the flanking sequences for PCR purposes. Hewlett-Packard Laboratories, Palo Alto, CA Visiting Scientist (Apr 2002 ~ March 2004) - Modified squid such that it uses content digest to index web cache such that it uses a new idea to avoid duplicate data transfer. - Contributed ideas regarding the research - A paper was published at USENIX NSDI'04 as a result of the research Nokia Networks, Mountain View, CA Perl Scripting Contractor (May 2002 ~ June 2002) - Developed scripts to automate the process of converting the hardware schematics from Amber Networks to conform Nokia's standard. - Reverse-engineered the communication protocol of the hardware parts query software using tcpdump. - Wrote a perl script program to emulate the DCOM-based hardware parts query software to access the parts database in Finland. EnjoyWeb, Inc., Santa Clara, CA Member of Technical Staff (Aug 1999 - Jan 2002) - Designed a secure XML-based control protocol to ensure all information related to our content deliveries are encrypted by our proprietary RSA-based PKI architecture. - Modified FTP protocol to encrypt content with IDEA algorithm. The corresponding 128-bit key is generated randomly and exchanged via our RSA-based PKI architecture. - Developed a Java-based multi-threaded server for our control center. There are multiple components in the system. They locate each other via a central Directory Server. The most stressed units: Front-end Processing Server and Job Tracking Server are designed in such a way that multiple instances of them can be run parallelly in multiple machines to ensure scalability. - Developed a C-based multi-threaded server for our internet appliance. This software receives the download commands from the control center and then act as a client to fetch content from our Data Servers or the internet. - Modified squid to stall the flow of HTML document download in order to modify the documents. - Modified webmin such that it can act as an web interface to our internet appliance. - Managed a team of five engineers for a month - Prepared demos to secure the initial funding University of Michigan, EECS Dept, Ann Arbor, MI Undergraduate Research Assistant (Jan 1998 - Dec 1998) - Modified an open-source web cache proxy program called Squid to become a trace-driven simulator to study web traffic. - Wrote a trace-driven simulator to study our model. - Presented research progress before the research group. - Published the results of our findings. - worked in a research team of two faculties, two Ph.D. students and me University of Michigan, Engineering Research Center (ERC), Ann Arbor, MI Programmer (May 1997 - Dec 1997) - worked in a team of two Ph.D. students and 5 undergraduates - gained hands-on experience in Object-Oriented Design technique - sharpened my C++ programming skill EDUCATION University of Michigan -- Ann Arbor, Michigan Honors B.S. Mathematics & Honors B.S. Economics May 1999 (GPA 3.872) Honors Thesis: "Market-based Web Cache" SELECTED PUBLICATIONS "The DNA sequence and biology of human chromosome 19", Jane Grimwood et. al., Nature 428, 529-535 (01 April 2004) URL: http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v428/n6982/full/nature02399_fs.html Paper available at: http://www.welltall.com/ymc/academics/chr19.pdf "Design, Implementation and Evaluation of Duplicate Transfer Detection in HTTP", Jeffrey Mogul, Yee Man Chan and Terence Kelly. In Proceedings of the USENIX Symposium on Networked Systems Design and Implementation, San Francisco, CA, March 29-31, 2004 URL: http://www.usenix.org/events/nsdi04/ Paper available at: http://www.welltall.com/ymc/academics/dtd.pdf "The Case for Market-based Push Caching", Yee Man Chan, Sugih Jamin, Jonathan Womer and Jeffrey Mackie-Mason. In Proceedings of the Second International Conference on Telecommunications and Electronic Commerce, Nashville, Tennesse, October 6-8, 1999 URL: http://munin.utdallas.edu/atsma/ictec/ Paper available at: http://www.welltall.com/ymc/academics/webcache.pdf HONORS AND AWARDS Member, Phi Beta Kappa Society INTERESTS AND ACTIVITIES Senior VP of Consulting, Association of Chinese Students and Scholars at Stanford Young Phi Betes E-mail List Maintainer, Phi Beta Kappa Society Northern California Chapter REFERENCES Available Upon Request.