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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.
Latest TPP version: 4.1.1, November 14, 2008. download latest TPP software directly; read the TPP documentation
News:
The TPP release system moved from cygwin to a true native Windows installation with the 4.0.0 release. We thank Insilicos for their continued major contributions to the project. The 4.0.0 release also brings full support for the new mzML 1.0 standard, a joint effort of the HUPO PSI, SPC, vendors, and others.
- The next SPC Tools Course will be held April 27 through May 1, 2009, at the ISB in Seattle. Space is limited so sign up soon!
- Note: 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 Natalie (you should be able to find email contact through the spctools-discuss newsgroup website, see below.)
Please see the TPP Recent Updates page for more news items.
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 include:
- TPP: our proteomics pipeline software is described on the Trans-Proteomic Pipeline (TPP) page.
- For information about the (sometimes confusing!) relationship between the many software projects that integrate with the TPP, either as compatible search engines, or as projects that repackage and redistribute the TPP itself, please see the TPP:Related Tools page.
- Open Data Formats: You can learn more about the SPC-developed open-formats, which include mzXML, pepXML, and protXML, on the Formats page.
- SBEAMS Project: SPC's high-powered LIMS database 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: The next course is scheduled for May 12-16, 2008
- 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.
