PeptideAtlas software
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Current revision Tfarrah (Talk | contribs) |
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| + | This is an evolving document about the PeptideAtlas code base, begun by Terry Farrah in June 2009. | ||
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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/[devXX/]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== | + | * $PIPELINE refers to /net/db/projects/PeptideAtlas/pipeline. |
| - | 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. | + | ==Before a PeptideAtlas build== |
| + | In /regis/sbeams/bin is mostly stuff useful before building PeptideAtlas -- converting file formats and searching -- but some of it is useful during the build process: | ||
| + | Mayu (used during step07 of build pipeline), calctppstat.pl (summary of TPP results on a single experiment), updateAllPaths.pl (used when moving pepXML and protXML files to new directories), showProteins.pl (summary of proteins in pepXML). | ||
| + | |||
| + | Mayu is the only one of the above called explicitly during the build process. Perhaps it should thus be stored in $SBEAMS or $PIPELINE, or at least linked there. | ||
| + | |||
| + | ==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 | ||
| - | I am not sure why there are two locations. | + | Some of the software needed for the analysis step is in $SBEAMS/lib/scripts/PeptideAtlas: PAidentlist2mayu.pl, update_proteotypic_scores.pl, update_search_batch_statistics.pl. |
| ==Loading a PeptideAtlas build== | ==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 also outlined in [[Building Peptide Atlas]]. |
| These are all in $SBEAMS: | These are all in $SBEAMS: | ||
Current revision
This is an evolving document about the PeptideAtlas code base, begun by Terry Farrah in 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).
- $PIPELINE refers to /net/db/projects/PeptideAtlas/pipeline.
Contents |
Before a PeptideAtlas build
In /regis/sbeams/bin is mostly stuff useful before building PeptideAtlas -- converting file formats and searching -- but some of it is useful during the build process: Mayu (used during step07 of build pipeline), calctppstat.pl (summary of TPP results on a single experiment), updateAllPaths.pl (used when moving pepXML and protXML files to new directories), showProteins.pl (summary of proteins in pepXML).
Mayu is the only one of the above called explicitly during the build process. Perhaps it should thus be stored in $SBEAMS or $PIPELINE, or at least linked there.
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 of the software needed for the analysis step is in $SBEAMS/lib/scripts/PeptideAtlas: PAidentlist2mayu.pl, update_proteotypic_scores.pl, update_search_batch_statistics.pl.
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.
