Open2Dprot Subprojects Module List and Contributed Related Projects

Open2Dprot Subprojects Module List
and Contributed Related Projects

These tables summarizes open source subprojects for the Open2Dprot pipeline modules and other associated projects. The latter may use similar data or provide other types of related analyses. Modules that are not currently released are grayed out in the table. Pre-alpha status indicates that the data structures, menus, and XML schema will undergo change and the program is not ready for release. Beta status indicates that the data structures, menus, and XML schema may undergo changes as it is being validated after the program is released. Design prototype status indicates that a user interface GUI has been constructed with some supporting structures. Source code for all modules is available on the Files mirror and CVS browser. Additional support files (sample data, public .jar libraries, etc) are available when you use the download the files.

1. Open2Dprot pipeline subprojects

Open2Dprot consists of a series of coordinated Open2Dprot pipeline processing modules. Raw proteomics expression data in the form of 2D gel images, 2D LC-MS peak datasets, preprocessed protein array expression data, etc. is input to the pipeline as is information about the experiment (MIAPE type information) is accessioned into the database. The pipeline does a sequential data reduction using various alternate pipeline processing steps to do this data reduction. Finally, the data mining can proceed using the Composite Samples Database (CSD) that was constructed.

The Pipeline Control Program, also called Open2Dprot, schedules and runs the modules in the pipeline after doing a data-dependency analysis on what data exists and what data needs to be created by running parts of the pipeline to proceed to the next stage in the pipeline. It then runs the pipeline to eventually construct the CSD.

1.1 Modules available for Open2Dprot pipeline - subprojects

Open2Dprot consists of a series of coordinated Open2Dprot pipeline processing modules. The pipeline control program scheduler, also called Open2Dprot, schedules and runs the modules in the pipeline after doing a data-dependency analysis. By using standard XML as the "glue" between modules, it should be possible to substitute alternate modules at the various pipeline steps. As pipeline modules and alternate modules become available, they are added to this table. [There are several alternate processing modules that are possible candidates.] We encourage the donation of alternate pipeline processing modules which will be added to this table. Modules can reside at open2dprot.sourceforge.net or at alternate contributors' Web sites.

We use a common O2Plib library in the Open2Dprot pipeline modules. This helps ensure that they use the same conventions, data structures and XML data interchange schema formats.

Subproject Home Download Documentation Overview (PDF) PDF documents Version Revision history Status Pipeline step

Open2Dprot (see below) Open2Dprot Open2Dprot Open2Dprot Open2Dprot Open2Dprot Open2Dprot
overall design [Overall design]

Open2Dprot scheduler program Open2Dprot Open2Dprot Open2Dprot Open2Dprot Open2Dprot Open2Dprot Open2Dprot Open2Dprot
pre-alpha
program [scheduler]

Accession module Accession Accession Accession Accession Accession Accession Accession Accession
Beta [1]

Seg2Dgel module Seg2Dgel Seg2Dgel Seg2Dgel Seg2Dgel Seg2Dgel Seg2Dgel Seg2Dgel Seg2Dgel
Beta [2]

Landmark module Landmark Landmark Landmark Landmark Landmark Landmark Landmark Landmark
Beta [3]

AutoLandmark module AutoLandmark AutoLandmark AutoLandmark AutoLandmark AutoLandmark AutoLandmark AutoLandmark AutoLandmark
pre-alpha [3]

CmpSpots module CmpSpots CmpSpots CmpSpots CmpSpots CmpSpots CmpSpots CmpSpots CmpSpots
Beta [4]

BuildCSD module BuildCSD BuildCSD BuildCSD BuildCSD BuildCSD BuildCSD BuildCSD BuildCSD
pre-alpha [5]

CSDminer CSDminer CSDminer CSDminer CSDminer CSDminer CSDminer CSDminer
design prototype [6]

O2Plib O2Plib.jar O2Plib O2Plib O2Plib O2Plib O2Plib O2Plib
Beta --common--

Subproject Home	Download	Documentation	Overview (PDF)	PDF documents	Version	Revision history	Status	Pipeline step
Open2Dprot	(see below)	Open2Dprot	Open2Dprot	Open2Dprot	Open2Dprot	Open2Dprot	Open2Dprot overall design	[Overall design]
Open2Dprot	Open2Dprot	Open2Dprot	Open2Dprot	Open2Dprot	Open2Dprot	Open2Dprot	Open2Dprot pre-alpha program	[scheduler]
Accession	Accession	Accession	Accession	Accession	Accession	Accession	Accession Beta	[1]
Seg2Dgel	Seg2Dgel	Seg2Dgel	Seg2Dgel	Seg2Dgel	Seg2Dgel	Seg2Dgel	Seg2Dgel Beta	[2]
Landmark	Landmark	Landmark	Landmark	Landmark	Landmark	Landmark	Landmark Beta	[3]
AutoLandmark	AutoLandmark	AutoLandmark	AutoLandmark	AutoLandmark	AutoLandmark	AutoLandmark	AutoLandmark pre-alpha	[3]
CmpSpots	CmpSpots	CmpSpots	CmpSpots	CmpSpots	CmpSpots	CmpSpots	CmpSpots Beta	[4]
BuildCSD	BuildCSD	BuildCSD	BuildCSD	BuildCSD	BuildCSD	BuildCSD	BuildCSD pre-alpha	[5]
CSDminer	CSDminer	CSDminer	CSDminer	CSDminer	CSDminer	CSDminer	CSDminer design prototype	[6]
O2Plib	O2Plib.jar	O2Plib	O2Plib	O2Plib	O2Plib	O2Plib	O2Plib Beta	--common--

2. Contributed Associated or Related Projects

We had added some additional non-pipeline open source projects that may use similar data or common software modules. They may be useful for performing other types of analysis on data used by Open2Dprot provide other types of analyses.

Contributed
Project Home Download Documentation Overview (PDF) PDF documents Version Revision history Status

Flicker program Flicker Flicker Flicker Flicker Flicker Flicker Flicker Flicker

MAExplorer program MAExplorer MAExplorer MAExplorer MAExplorer MAExplorer MAExplorer MAExplorer MAExplorer

TMAP/ProtPlot project ProtPlot Protplot TMAP (ProtPlot) ProtPlot ProtPlot ProtPlot ProtPlot ---

Contributed Project Home	Download	Documentation	Overview (PDF)	PDF documents	Version	Revision history	Status
Flicker	Flicker	Flicker	Flicker	Flicker	Flicker	Flicker	Flicker
MAExplorer	MAExplorer	MAExplorer	MAExplorer	MAExplorer	MAExplorer	MAExplorer	MAExplorer
ProtPlot	Protplot	TMAP (ProtPlot)	ProtPlot	ProtPlot	ProtPlot	ProtPlot	---

03/20/2006