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| Revision as of 21:38, 29 June 2007 Jtasman (Talk | contribs) (adding x!tandem link to new section) ← Previous diff |
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| ==Links== | ==Links== | ||
| - | *[http://www.proteomecenter.org Seattle Proteome Center (SPC) general website]: about our organization. | + | ===SPC Links=== |
| - | *[http://www.proteomecenter.org/course.php SPC Proteomics Course]: Next course is '''November 5-9, 2007''' | + | |
| *newsgroups: '''subscriptions highly recommended for SPC Tools users''' | *newsgroups: '''subscriptions highly recommended for SPC Tools users''' | ||
| **[http://groups.google.com/group/spctools-discuss spctools-discuss discussion group]: very active, daily discussions ranging from installation to data processing. All users, new and experienced, encouraged to participate. | **[http://groups.google.com/group/spctools-discuss spctools-discuss discussion group]: very active, daily discussions ranging from installation to data processing. All users, new and experienced, encouraged to participate. | ||
| **[http://groups.google.com/group/spctools-announce spctools-announce discussion group]: infrequent, important notifications of updates to our software | **[http://groups.google.com/group/spctools-announce spctools-announce discussion group]: infrequent, important notifications of updates to our software | ||
| *[http://www.sourceforge.net/projects/sashimi Sashimi Project Page on SourceForge]: Of interest to developers-- our code repository and software distribution site. | *[http://www.sourceforge.net/projects/sashimi Sashimi Project Page on SourceForge]: Of interest to developers-- our code repository and software distribution site. | ||
| + | *[http://www.proteomecenter.org/course.php SPC Proteomics Course]: Next course is '''November 5-9, 2007''' | ||
| + | *[http://www.proteomecenter.org Seattle Proteome Center (SPC) general website]: about our organization. | ||
| *[http://sashimi.sourceforge.net Sashimi Website]: an older documentation site, mainly containing useful information about the [[Formats:mzXML|mzXML]] format. | *[http://sashimi.sourceforge.net Sashimi Website]: an older documentation site, mainly containing useful information about the [[Formats:mzXML|mzXML]] format. | ||
| *[http://www.sbeams.org SBEAMS Project]: SPC's high-powered LIMS database system. | *[http://www.sbeams.org SBEAMS Project]: SPC's high-powered LIMS database system. | ||
| + | ===Non-SPC, related links=== | ||
| *[http://gaggle.systemsbiology.org The Gaggle project]: The ISB's data interaction, visualization, and exploration system, increasingly integrated with the [[Software:TPP|TPP]] | *[http://gaggle.systemsbiology.org The Gaggle project]: The ISB's data interaction, visualization, and exploration system, increasingly integrated with the [[Software:TPP|TPP]] | ||
| *[http://www.cytoscape.org Cytoscape Project]: Network visualization tool, integrated with the Gaggle. | *[http://www.cytoscape.org Cytoscape Project]: Network visualization tool, integrated with the Gaggle. | ||
Revision as of 23:30, 11 July 2007
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, simply create an account (link on the top right of the page) 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: 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.
- Prequips project documentation.
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.
- SBEAMS Project: SPC's high-powered LIMS database system.
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.
