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Seattle Proteome Center Software Tools Wiki
Welcome to the Seattle Proteome Center (SPC) software tools wiki. This wiki is primarily intended as means of sharing user documentation for the SPC tools. We encourage outside contribution, but please make your edits responsibly.
- To edit or create pages, log in before you start editing pages. Thanks!
- The tools change rapidly, so make a note of what version you are using if you edit information.
Latest TPP version: 3.2.1 (June 20, 2007)
News:
- New wiki accounts are temporarily disabled. Due to high levels of spam we've temporarily halted creation of new accounts. We will open the wiki again when we have stronger anti-spam measures in place. In the meanwhile, anyone who wants an account can contact Josh (you should be able to find email contact through the spctools-discuss newsgroup website, see below.)
- For developers: The Sashimi project has migrated to Subversion (SVN) from CVS. Please see the spctools-discuss newsgroup for more info.
- The Windows/Cygwin TPP distribution now includes X!Tandem with the K-Score plugin! While the PeptideProphet model is still undergo refinement, this brings us closer to offering a completely open-source, free proteomics solution!
SPC Software
The SPC is committed to providing open-source, free software to support proteomics research. The SPC Software Overview page lists (almost) all of the open-source software projects produced at the SPC. Major projects:
- TPP: our proteomics pipeline software is described on the Trans-Proteomic Pipeline (TPP) Overview page.
- Open Data Formats: You can learn more about the SPC-developed open-formats on the Formats page.
- SBEAMS Project: SPC's high-powered LIMS database system.
- Prequips project: initial work on an MS data integration and visualization system.
Links
SPC Links
- newsgroups: subscriptions highly recommended for SPC Tools users
- spctools-discuss discussion group: very active, daily discussions ranging from installation to data processing. All users, new and experienced, encouraged to participate.
- spctools-announce discussion group: infrequent, important notifications of updates to our software
- Sashimi Project Page on SourceForge: Of interest to developers-- our code repository and software distribution site.
- SPC Proteomics Course: Next course is November 5-9, 2007
- Seattle Proteome Center (SPC) general website: about our organization.
- Sashimi Website: an older documentation site, mainly containing useful information about the mzXML format.
Non-SPC, related links
- The Gaggle project: The ISB's data interaction, visualization, and exploration system, increasingly integrated with the TPP
- Cytoscape Project: Network visualization tool, integrated with the Gaggle.
- PeptideAtlas: The world's largest public repository of MS/MS spectra, developed and hosted at the ISB.
- Intro to Systems Biology course offered at the ISB
Wiki Guidlines
- These tools change rapidly. Please include the version when describing anything.
- These pages should not be used to report bugs. Please use the appropriate support avenues
Refer to MediaWiki user's guide for an introduction to formatting and editing pages.
