Learn about the Browser

This list is sorted by increasing technical complexity: the first steps require only a webbrowser, the last ones a Linux webserver.

Use the browser website

• Video tutorials and slides by Openhelix
• Basic materials written by the gurus: The User's guide and the FAQs.
• A similar page to this one "Learning about the browser"
• Type in (manually) a couple of custom tracks in different formats
• Subscribe to the mailing list or search through it. Most everyday questions have already been asked by someone else so searching gives you an answer usually faster than asking on the mailing list.

Download the data of the genome browser (sequences and annotations)

• Be aware that internal coordinates (not website) are 0-based!
• Unlike Gbrowse and Ensembl, UCSC is storing the data partially in SQL (coordiantes, outline of x-y-plots) and partially in flat text files (sequences, alignments, details of x-y-plots)
• Table Browser: The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles):
  • Table Browser, Example session
• SQL-stored data (FAQ):
  • Public mysql access
  • The all.joiner file, describes relations between all database tables
  • For all genes-related tables, there is a graphical map (sub-optimal layout :-)
• Flat-file data: Download from the ftp server (stored in /gbdb on browser servers)
  • Text file formats

Install a copy of the browser on your own machine (Unix or Mac)

• The old documentation website with developer documentation
• See also the next section about source tree installation, as the source tree toolset includes all CGI scripts for the UCSC browser installation (but you don't need to compile it, binaries for mirrors are provided at http://genome.ucsc.edu/admin/mirror.html#step6)
• Create a mirror of the UCSC site:
  • FAQ: mirror a complete browser
  • Almost the same document, but on the wiki, some more info
  • Mirror only selected genomes
  • Adapt your cgi-bin/Hg.conf file for your mirror
  • Be prepared that you'll need to create at least and also download parts of the hg18. At least mouse genomes still depend on it.
  • Updating the data automatically from UCSC
  • Pro and cons of storing custom tracks in MySQL or as flat files
  • How are cookies handled by the browser?
  • Do not try to change the default locations /gbdb, it's not difficult to move into something else than /var/wwww
  • Local_tracks_at_mirror_sites

Compile the UCSC source tree and analyze genomes yourself

• • What is the the source tree ?
  • What is available in the Kent source utilities ?
  • Some important tools are already compiled (even for windows!) from here
  • Compile all tools (includes the browser webserver) yourself
  • You need to set some environment variables before you start the compilation
  • Walkthroughs for...
    • MacOS X users
    • Debian and Ubuntu
    • CentOS Notes
    • Windows: see [1] but your mileage may vary to get everything to compile.

• • The most common problem on the mailing list are harmless warnings that trigger errors. To ignore these, which is usually safe, remove the -Wall option from the makefile
  • See also the textfile README.building.source README.building.source
  • searching through the archives or the Technical-FAQ-Category of the wiki when you have problems

Modify your own copy of the browser

• Add tracks to your own mirror:
  • Charles Sugnet's presentation about TrackDB
  • How_to_add_a_track_to_a_mirror
  • color codes
  • The structure of the trackDB
  • The trackDB statements
  • When you run into problems, search through the mailing list when you have problems and read the documentation in the directory kent/src/product
  • a similar place with hgSearchSpec docs and statistics (the system to search for ids) can be found completely off-track
• Create a browser for a completely new genome

Making Of: How the UCSC genome annotations are created

• How the UCSC folks created their tracks:
  • The UCSC's makeDb-files are a log of all commands that are necessary to re-create all annotations for a particular genome.
  • Some explanations how to read the makeDb files: bashVsCsh
  • Notes on the history of the internal tools: Autosql. Blastz. Chains and nets
• Whole-genome multiple alignments (Chains_Nets)
  • Mm9_multiple_alignment
  • Whole-genome alignment pipeline: Angies mental model and Max's howto
• How to create a browser for a new genome from scratch
• Genbank Updates

Statistics, overviews

• Gene_Set_Summary_Statistics
• Web hit statistics of the UCSC browser