Getting Started on the UCSC Genome Browser Project Team

Setup

• Get an SOE computer account application from katye@soe.ucsc.edu in the CBSE office. On the application, be sure to request that you be added to the protein UNIX group (it should be your default). For information on accessing your SOE email account, read this.
• Get accounts on the development machines and the cluster from one of our systems administrators: cluster-admin@cse.ucsc.edu
• Add compbio specific information to your .cshrc, .profile, etc. and create a hg.conf file. See the sample .cshrc and hg.conf files in the Other Technical Links section below.
• Add yourself to the genecats mailing list. Caveats for subscribing: do NOT use your regular login password as your mailing list password. Be sure to provide the email address that you plan to use for posting messages to the mailing list - posting from any another address will be unsuccessful.
• Get an account on the RT bugtracking system from ann@soe.ucsc.edu
• If you're interested in hearing comments, questions, and problems from our external users, subscribe to our mailing lists: genome, genome-mirror, and genome-announce.
• If you have problems with SOE software, hardware, or accounts, send email to the systems administrators or talk to Jorge, Erich, Chester, or Victoria.

Learning about the Genome Browser

• UCSC Human Genome website. Familiarize yourself with the Genome Browser, Table Browser, Gene Sorter, and BLAT.
• Genome Browser User's Guide. User documentation for the Genome Browser, Table Browser, Gene Sorter, and BLAT. Also contains information on creating a custom annotation track, and descriptions of the standard tracks displayed in the Genome Browser.
• Table Browser User's Guide. User documentation for the Table Browser, including several examples of advanced queries.
• Gene Sorter User's Guide. User documentation for the Gene Sorter.
• Proteome Browser User's Guide. User documentation for the Proteome Browser.
• Genome Graphs User's Guide. User documentation for Genome Graphs.
• Session Management User's Guide. User documentation for Genome Browser sessions.
• OpenHelix Training Materials. Online help and training materials on the UCSC Genome Browser.
• The Human Genome Browser at UCSC. Jim Kent's initial paper on the Genome Browser (Genome Research, 2002).
• The UCSC Genome Browser Database. Paper on the browser database (Nucleic Acids Research, 2003). Also refer to Jim's internal paper on the browser database, The Genome Browser Database.
• BLAT - The BLAST-Like Alignment Tool. Jim's initial paper on BLAT (Genome Research, 2002).
• The UCSC Table Browser data retrieval tool. Initial paper on the Table Browser (Nucleic Acids Research, 2004).
• The UCSC Proteome Browser. Initial paper on the Proteome Browser (Nucleic Acids Research, 2005).
• The UCSC Genome Browser Database: update 2006. Browser updates during 2005 (Nucleic Acids Research, 2006).
• The UCSC Genome Browser Database: update 2007. Browser updates during 2006 (Nucleic Acids Research, 2007).
• The UCSC Genome Browser Database: 2008 update. Browser updates during 2007 (Nucleic Acids Research, 2008).
• The UCSC Genome Browser Database: update 2009. Browser updates during 2008 (Nucleic Acids Research, 2009).
• The ENCODE Project at UC Santa Cruz. Description of UCSC Genome Browser resources for the preliminary phases of the ENCODE project (Nucleic Acids Research, 2007).
• The UCSC Known Genes. Initial implementation of the Known Genes annotation (now replaced by the updated UCSC Genes annotation on recent human and mouse assemblies) (Bioinformatics, 2006).
• Genome Browser Publications link. Selected publications by the UCSC Genome Bioinformatics group and collaborators.
• The Sordid Details of the Genome Browser at UCSC. Jim's presentation about the technical workings of the Genome Browser (Genecats meeting 18 Jan 02).
• The Human Genome User's Guide. On-line tutorial in Nature Genetics for using web browsers as tools to browse and analyze genomic data. The publication features the UCSC Genome Browser along with NCBI's Map View and the Ensembl Genome Browser.
• Displaying Your Own Annotations in the Genome Browser. Learn how to create a custom annotation track for the browser.
• Planning Next Five Years. Highlights from the 2007-2012 NHGRI Grant.

Software Engineering Technical Information

• kent/src. The source tree for the Genome Browser, BLAT, related libraries, etc. Check out your own copy using CVS.
• kent/src/README. This text file in the source tree describes coding conventions, make instructions, and the major library modules in the code.
• CVS Tutorial. Info and tutorial on using the UCSC Comp Bio CVS source respository. Also refer to the CVS--Concurrent Versions System information manual. For more information on CVS branching, see the Branching and Merging chapter.
• See how well you do on Mark's CVS quiz.
• Genome Browser wiki. Lots of user-level and technical information about the Genome Browser, source code, mirrors, handy scripts, etc.
• How to Add a Track to the Genome Browser. Chuck's presentation on the steps involved in adding an annotation track (Genecats meeting on 25 Jan 2002). See also the file "addTrack.txt" in /kent/src/hg/doc.
• How to enable search using hgFindSpec, written by Angie Hinrichs.
• The KiloKluster: Where is Everything?. Information about the kilokluster, /scratch, /scratch/i, written by Hiram Clawson.
• Setting up ssh. Information on setting up ssh-agent in a Gnome session, 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).
• Genome Browser Engineering Do's and Don't's. A list of some important things to keep in mind (and to keep your coworkers happy) when processing data, using the cluster, and making tracks.
• 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.

Software Engineering Process

• New & Improved Sermon on Software Engineering. Jim's presentation about software engineering on the Genome Browser project (Genecats meeting 28 Oct 02).
• The Browser Software Development Cycle.
• The Genome Browser CGI Build Process. Procedure used to build, test, and release a new set of Genome Browser binaries, written by Ann Zweig.
• Genome Browser Project QA links. Link to QA home page.
• The RT Bugtracking System. Donna's presentation on RT and how to use it to enter and track bugs.

Other Technical Links

• Computer Resources at CBSE. Jorge's presentation on CBSE computing resources at the Genecats meeting on 21 Feb. 2002 (Old, but not untrue).
• Using the KiloKluster. Patrick's presentation on the kiloKluster at the Genecats meeting on 21 Feb. 2002 (Old, but not untrue).
• Human Genome Browser Mirroring (Or, The Wild Side of Bulk Data Trasfer). Paul's presentation on mirroring the Genome Browser at the Genecats meeting on 21 Feb. 2002 (Old, but not untrue).
• 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.
• School of Engineering (SOE) Technical FAQ. Technical topics (including some generic ones) of interest to SOE users.
• Poster HOWTO. Kate's writeup of how to make a poster for CSHL.

Molecular Biology and Bioinformatics Links

• 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.

Travel

• Travel information. Reimbursement policies, etc., from Katy Elliott.

Historical

• The /gbdb fileserver. Information on the /gbdb fileserver and how it affects development work on the Genome Browser, written by Angie Hinrichs.

• Last updated (partially): 6 March 2008.