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. | 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/sbeams (as of June 16, 2009). | + | $SBEAMS below refers to /net/dblocal/www/html/[devXX/]sbeams (as of June 16, 2009). |
| ==Creating a PeptideAtlas build== | ==Creating a PeptideAtlas build== | ||
| A collection of csh, bash, and perl scripts, plus various text, XML, and csv files, all outlined in [[Building Peptide Atlas]]. | A collection of csh, bash, and perl scripts, plus various text, XML, and csv files, all outlined in [[Building Peptide Atlas]]. | ||
| - | ==Loading PeptideAtlas== | + | |
| + | Many of these are in /net/db/projects/PeptideAtlas/pipeline/bin. | ||
| + | |||
| + | 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 [http://db.systemsbiology.net SBEAMS] database. | A collection of perl scripts, all or most of which execute SQL queries on the [http://db.systemsbiology.net SBEAMS] database. | ||
| + | |||
| + | 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== | ==Displaying PeptideAtlas via web interface== | ||
| Perl scripts, mostly in $SBEAMS/cgi/PeptideAtlas. | Perl scripts, mostly in $SBEAMS/cgi/PeptideAtlas. | ||
Revision as of 21:33, 18 June 2009
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).
Creating 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 /net/db/projects/PeptideAtlas/pipeline/bin.
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 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.
