Getting Started on the UCSC Genome Browser Project Team

Software Engineering Technical Information

kent/src. The source tree for the Genome Browser, BLAT, related libraries, etc. Check out your own copy using git.
kent/src/README. This text file in the source tree describes coding conventions, make instructions, and the major library modules in the code.
See how well you do on Galt's Git quiz.
Genome Browser wiki. Lots of user-level and technical information about the Genome Browser, source code, mirrors, handy scripts, etc.
How to enable search using hgFindSpec, written by Angie Hinrichs.
The Parasol Parallel Batch System. Documentation on the batch processing system used on the cluster, written by Jim Kent.
autoSQL and autoXml: Code generators from the genome Project. Jim's initial paper on these tools (Linux Journal, 2002).
XML, SQL, and C. Jim's paper about tools for mapping between C and XML data structures, etc. using autoXml, autoDtd, sqlToXml and xmlToSql (Dr. Dobb's, 2006).
Hiram's Wiggle Presentation. Talk given 11/18/04.
Vim Tricks. Tricks for setting up vim to edit R code and to switch between .c files and their corresponding .h files, written by Krish Roskin.

New & Improved Sermon on Software Engineering. Jim's presentation about software engineering on the Genome Browser project (Genecats meeting 28 Oct 02).
CGI Build Process
A Tutorial on NFS v.s. Native I/O: how to find the best place to do something faster. A mini-tutorial from Paul on when and why you should use native I/O instead of network I/O.
Jim Kent's Web Programming Mini Tutorial. Short tutorial on setting up a home page and a CGI-bin directory on a CSE computer at UCSC. Links to information on HTML and CGI scripting.

Evolution and the Santa Cruz Browser. Jim's presentation on chaining and netting at CSHL 2003.
Chain format. Information on chain format.
Net format. Information on net format.
Evolution in Action. Jim's presentation at the Genecats meeting on 1 Feb 2002.
Improving Gene Prediction using Pseudogenes. Robert's presentation at the Genecats meeting on 21 Oct 02 2002.
Information on axt format. See also Human-Mouse Alignments with BLASTZ in Genome Res 13:103-107.
Evaluating Local Structure Alphabets for Protein Structure Prediction. Rachel Karchin's dissertation.