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- Software:Prequips (1386 bytes)
3: ...p://prequips.sourceforge.net '''Prequips'''] is a software environment for integration, visualization and an...
5: '''Integration''': The software is capable of integrating mass spectrometry data ... - Software:Prequips:Inclusion List Builder (3897 bytes)
22: === Software ===
25: * '''NEW''' [http://www.prequips.org/download/software/prequips_0.97_win32.zip Prequips 0.97 + Inclusion...
26: * '''NEW''' [http://www.prequips.org/download/software/prequips_0.97_macosx.zip Prequips 0.97 + Inclusio... - Software:Overview (3074 bytes)
1: ...cs tools, many of which are integrated into the [[Software:TPP|TPP]] project.
5: '''Please see the [[Software:TPP|TPP page]] for descriptions of the pipeline a...
7: The TPP software distribution integrates the following programs:
9: ...mary]], [[Software:MzXML2Search|MzXML2Search]], [[Software:MsXML2Other|MsXML2Other]],
10: [[Software:readmzXML|readmzXML]], [[Software:mzStar|mzStar]] - Software:msBID (1414 bytes)
4: ==Getting the software==
5: ...ftware for LINUX [http://tools.proteomecenter.org/software/msBID_linux.tar.gz here]
6: ...ware for Windows [http://tools.proteomecenter.org/software/msBID_windows.tar.gz here]
16: ==Environment to run the software== - Software:SBEAMS (2104 bytes)
13: ==Getting the software==
17: * [http://tools.proteomecenter.org/software/sbeams.installnotes sbeams.installnotes] - Instal...
19: * [http://tools.proteomecenter.org/software/sbeams-0.22.1.tar.gz sbeams-0.22.1.tar.gz] - SBEA...
21: * [http://tools.proteomecenter.org/software/GDGraph-1.35a.tar.gz GDGraph-1.35a.tar.gz] - Cust...
23: ...e] ''Note: You might find a newer version of this software by following this link.'' - Software:PeptideProphet (1728 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
5: ...s now a core part of the Trans-Proteomic Pipeline software distrubtion. - Software:ProteinProphet (6941 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
5: ... an integral part of the Trans-Proteomic Pipeline software distribution.
40: '''IPROPHET:''' iProphet, or InterProphet, is software under development that further processes PeptideP... - Software:XPRESS (1756 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
8: .... For those SEQUEST users interested in using the software, ThermoFinnigan has an implementation of XPRESS i... - Software:ASAPRatio (1791 bytes)
2: ==Getting the software==
3: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
9: ... consuming and tedious before. A byproduct of the software is to identify outlier peptides which may be misi... - Software:Libra (1189 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.''' - Software:Pep3D (1087 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.''' - Software:TPP (8915 bytes)
8: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio]]
9: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:XPRESS]]
10: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:Libra]]
11: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:SBEAMS]]
14: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:ProteinProphet]] - Software:Petunia (464 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] Windows/Cygwin distribution, or directl... - Software:SpecArray (1001 bytes)
2: ==Getting the software==
3: Please download this software from the [http://sourceforge.net/project/showfile...
6: ...les under identical LC-MS settings. The SpecArray software suite include several closely integrated programs...
8: ...data (''Note: Pep3D is also integrated into the [[Software:TPP|TPP]]'') - Software:ReAdW (1604 bytes)
6: ...the Xcalibur software suite; you must obtain this software from ThermoFinnigan.
14: ...ll only work under Windows with Thermo's XCalibur software installed.
16: ==Getting the software==
18: ...s software is no longer included in the current [[Software:TPP|TPP]] distribution.'''
22: Additional methods for obtaining the software are: - Software:mzStar (1909 bytes)
5: ...s many bugs and improves speed. Please see the [[Software:mzWiff|mzWiff]] page for more information.
9: ...t download the appropriate converter for your own software.)
18: library provided by the Analyst software, which is therefore required to be present on the...
21: ...-only and requires an installation of the Analyst software on the same computer. The version of mzStar must...
23: ==Getting the software== - Software:Cytoscape (722 bytes)
3: Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction ne...
6: ...Schwikowski B, and Ideker T. (2003) "Cytoscape: A software environment for integrated models of biomolecular...
8: ==Getting the software== - Software:XLink (3210 bytes)
8: The software used for automated analysis contains three progra...
28: ==Getting the software==
30: ...org/software/xlink/XLINK_Software_Tools.zip XLINK_Software_Tools.zip]
32: ...ools/XLINK_Software_Manual_0.93.html Version 0.93 Software Manual]
35: ...e/xlink/deprecated/XLINK_Software_Tools.zip XLINK_Software_Tools.zip] - Software:PeptideSieve (6357 bytes)
8: ...entification scoring functions of database search software, providing a panel of reagents for protein quanti...
10: The software consists of a single C++ program. The input is e...
18: ===Getting the software===
22: A [http://tools.proteomecenter.org/software/PeptideSieve/PeptideSieve_v0.51.static.with.GUI.s...
24: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:PeptideSieve:Build here]. - Software:SPE (46 bytes)
Page text matches
- Main Page (6445 bytes)
1: ...)''' is committed to providing free, open-source, software projects in support of cutting-edge proteomics re...
12: ...up] for important notifications of updates to our software.
17: ==The [[Software:TPP|Trans-Proteomic Pipeline (TPP)]]: MS2 proteom...
18: ...ans-Proteomic Pipeline (TPP) is a completely free software
23: ...ch engines, including the bundled X!Tandem search software (from The GPM) and [http://comet-ms.sourceforge.n... - Prequips:Eclipse Setup (5641 bytes)
16: ...ed to have administrator privileges to set up the software.
20: ...to add the other features. Simply go to '''Help > Software Updates > Find and Install ...'''. Select '''Sear... - Software:Prequips (1386 bytes)
3: ...p://prequips.sourceforge.net '''Prequips'''] is a software environment for integration, visualization and an...
5: '''Integration''': The software is capable of integrating mass spectrometry data ... - Windows Installation Guide (4572 bytes)
9: * '''Make sure that you have rights to install software on your computer''' (i.e. Admin privileges)
25: ...010 SP1 (x86), and the .NET Framework 3.5/4.0 SP1 software packages Microsoft ''which may already be install... - TPP:Supported Search Engines (1578 bytes)
18: [http://proteomics.ucsd.edu/software-tools/ms-gf/ MSGF+]
21: [http://proteomics.ucsd.edu/software-tools/inspectms-alignment/ Inspect]
30: [[Software:ProbID|ProbID]]is an open-source, freely-availabl... - Software:Prequips:Inclusion List Builder (3897 bytes)
22: === Software ===
25: * '''NEW''' [http://www.prequips.org/download/software/prequips_0.97_win32.zip Prequips 0.97 + Inclusion...
26: * '''NEW''' [http://www.prequips.org/download/software/prequips_0.97_macosx.zip Prequips 0.97 + Inclusio... - Software:Overview (3074 bytes)
1: ...cs tools, many of which are integrated into the [[Software:TPP|TPP]] project.
5: '''Please see the [[Software:TPP|TPP page]] for descriptions of the pipeline a...
7: The TPP software distribution integrates the following programs:
9: ...mary]], [[Software:MzXML2Search|MzXML2Search]], [[Software:MsXML2Other|MsXML2Other]],
10: [[Software:readmzXML|readmzXML]], [[Software:mzStar|mzStar]] - TPP:Windows Cygwin Installation (7499 bytes)
9: ...r to installing the SPC software. By default the software installs and uses the Apache2 webserver. The Apac...
14: # Download the [http://tools.proteomecenter.org/software/TPP_Cygwin_Setup.exe TPP_Cygwin_Setup.exe install...
22: ...C:, you must CHANGE the path to c:\cygwin, or the software WILL NOT work!<br/>Keep the other options set to ...
64: === Reininstalling the TPP Software ===
75: ...ccasionally it will be necessary to uninstall the software, for example, in the case of an incomplete or bro... - Software:msBID (1414 bytes)
4: ==Getting the software==
5: ...ftware for LINUX [http://tools.proteomecenter.org/software/msBID_linux.tar.gz here]
6: ...ware for Windows [http://tools.proteomecenter.org/software/msBID_windows.tar.gz here]
16: ==Environment to run the software== - Software:SBEAMS (2104 bytes)
13: ==Getting the software==
17: * [http://tools.proteomecenter.org/software/sbeams.installnotes sbeams.installnotes] - Instal...
19: * [http://tools.proteomecenter.org/software/sbeams-0.22.1.tar.gz sbeams-0.22.1.tar.gz] - SBEA...
21: * [http://tools.proteomecenter.org/software/GDGraph-1.35a.tar.gz GDGraph-1.35a.tar.gz] - Cust...
23: ...e] ''Note: You might find a newer version of this software by following this link.'' - TPP:Documentation (46 bytes)
1: Please see the main [[Software:TPP|TPP]] page. - TPP:Frequently Asked Questions (5647 bytes)
9: ...evel of computer expertise is required to use the software?===
10: ...nd greatly reduces the complexity of of using the software.
12: ...=Do I need to run the TPP GUI in order to use the software?===
31: ...401, which is not used by any typically installed software. TPP-related webpages will be accessed by http:/...
57: ...nce from the TPP users community and / or the SPC software developers. - TPP:7.0.0 Release Notes (6884 bytes)
27: ...rters. This is potentially inefficient for legacy software that calls readHeader() and readPeaks() independe... - TPP:Installing on Mac OSX (12870 bytes)
13: ...nix shell commands and installing and configuring software. - Software:PeptideProphet (1728 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
5: ...s now a core part of the Trans-Proteomic Pipeline software distrubtion. - Software:ProteinProphet (6941 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
5: ... an integral part of the Trans-Proteomic Pipeline software distribution.
40: '''IPROPHET:''' iProphet, or InterProphet, is software under development that further processes PeptideP... - Software:XPRESS (1756 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
8: .... For those SEQUEST users interested in using the software, ThermoFinnigan has an implementation of XPRESS i... - Software:ASAPRatio (1791 bytes)
2: ==Getting the software==
3: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
9: ... consuming and tedious before. A byproduct of the software is to identify outlier peptides which may be misi... - Software:Libra (1189 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.''' - Software:Pep3D (1087 bytes)
1: ==Getting the software==
2: '''This software is included in the current [[Software:TPP|TPP]] distribution.'''
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