PeptideAtlas software

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The core data in PeptideAtlas is a large set of peptides organized into individual builds according to organism and sample type (for example, Yeast, Human Plasma, or Human Glycocapture). A peptide may belong to multiple builds.

$SBEAMS below refers to /net/dblocal/www/html/[devXX/]sbeams (as of June 16, 2009). $PIPELINE refers to /net/db/projects/PeptideAtlas/pipeline.

Creating ("building") a PeptideAtlas build

A collection of csh, bash, and perl scripts, plus various text, XML, and csv files, all outlined in Building Peptide Atlas.

Many of these are in $PIPELINE:

  • $PIPELINE/recipes -- notes on how to create and load a build; not executable
  • $PIPELINE/run_scripts -- shell scripts for running the build pipeline
  • $PIPELINE/bin -- mostly perl scripts, called directly or indirectly from the scripts in $PIPELINE/run_scripts

Some are in $SBEAMS.

I am not sure why there are two locations.

Loading a PeptideAtlas build

A collection of perl scripts, all or most of which execute SQL queries on the SBEAMS database. These are also outlined in Building Peptide Atlas.

These are all in $SBEAMS:

  • $SBEAMS/lib/scripts/PeptideAtlas
  • $SBEAMS/lib/perl/SBEAMS/ -- general SBEAMS perl modules
  • $SBEAMS/lib/perl/SBEAMS/PeptideAtlas -- perl modules for PeptideAtlas

Displaying PeptideAtlas via web interface

Perl scripts, mostly in $SBEAMS/cgi/PeptideAtlas.

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=PeptideAtlas_software"
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