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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: ...y of which are integrated into the [[Software:TPP|TPP]] project.
3: ==The Trans-Proteomic Pipeline (TPP) Project==
5: '''Please see the [[Software:TPP|TPP page]] for descriptions of the pipeline and these...
7: The TPP software distribution integrates the following programs:
9: ...mary]], [[Software:MzXML2Search|MzXML2Search]], [[Software:MsXML2Other|MsXML2Other]], - 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23: ...e] ''Note: You might find a newer version of this software by following this link.''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: ...oftware 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: ...oftware 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...
46: ...developer Henry Lam had to say in May 2008 on the TPP developers' forum: - Software:XPRESS (1756 bytes)
1: ==Getting the software==
2: ...oftware 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: ...oftware 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: ...oftware is included in the current [[Software:TPP|TPP]] distribution.'''
17: ...dition file using the built-in utility within the TPP web UI (Petunia), or by using a text editor. - Software:Pep3D (1087 bytes)
1: ==Getting the software==
2: ...oftware is included in the current [[Software:TPP|TPP]] distribution.''' - Software:TPP (8918 bytes)
1: The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS pr...
5: [[image:TPP.jpg|1200px]]
7: image:TPP.jpg|
8: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio]]
9: ...p://tools.proteomecenter.org/wiki/index.php?title=Software:XPRESS]] - Software:Petunia (464 bytes)
1: ==Getting the software==
2: .../sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/tpp_gui/ Sashimi SVN] for source code installs.'''
5: ...I (Petunia) provides a web-based interface to the TPP.
8: See the [[TPP:Using Petunia|"using Petunia" guide]] for some sc... - 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: ... 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.
8: ... package. For convenience the latest versions of TPP contain this program.
14: ...ll only work under Windows with Thermo's XCalibur software installed.
16: ==Getting the software==
18: ... no longer included in the current [[Software:TPP|TPP]] distribution.''' - 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.)
11: The Analyst 1.1 version included since the TPP 3.0.3 distrution does not have this bug.
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... - 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 (6427 bytes)
1: ...)''' is committed to providing free, open-source, software projects in support of cutting-edge proteomics re...
5: *SPC/TPP course:
12: ...up] for important notifications of updates to our software.
17: ==The [[Software:TPP|Trans-Proteomic Pipeline (TPP)]]: MS2 proteomics validation and analysis==
18: ...ans-Proteomic Pipeline (TPP) is a completely free software - 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)
2: These instructions are meant for versions of TPP 4.8.1 and prior.
4: ...f installing TPP 5.0 or newer, please refer to: [[TPP:5.0_Installation]]
7: =TPP pre-5.0 installation=
8: Installing the Windows version of the TPP is fairly straightforward. Detailed instructions ...
9: * '''Make sure that you have rights to install software on your computer''' (i.e. Admin privileges) - TPP:Supported Search Engines (1578 bytes)
6: The TPP now officially works with these search engines:
9: ... open-source database search engine provided with TPP (as of version 4.7.1)
11: ===[[TPP:X!Tandem and the TPP|X!Tandem]]===
12: ... plugin is now distributed as part of the Windows TPP (as of version 3.2.1).
14: ===[[TPP:Sequest and the TPP|SEQUEST]]=== - 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: ...y of which are integrated into the [[Software:TPP|TPP]] project.
3: ==The Trans-Proteomic Pipeline (TPP) Project==
5: '''Please see the [[Software:TPP|TPP page]] for descriptions of the pipeline and these...
7: The TPP software distribution integrates the following programs:
9: ...mary]], [[Software:MzXML2Search|MzXML2Search]], [[Software:MsXML2Other|MsXML2Other]], - TPP:Windows Cygwin Installation (7499 bytes)
2: ...re meant for the installation of the Cygwin-based TPP, which is now obsolete.''' ===
9: ...r to installing the SPC software. By default the software installs and uses the Apache2 webserver. The Apac...
14: ....proteomecenter.org/software/TPP_Cygwin_Setup.exe TPP_Cygwin_Setup.exe installation program]. Note, yo...
17: ...uld be able to now access the [[TPP:Using Petunia|TPP web interface]]
22: ...C:, you must CHANGE the path to c:\cygwin, or the software WILL NOT work!<br/>Keep the other options set to ... - 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)
1: ==TPP Frequently Asked Questions==
3: ===What is the current version of the TPP?===
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?=== - TPP:7.0.0 Release Notes (6884 bytes)
1: = TPP 7.1.0 ALBEDO Release Notes =
2: ...p://tools.proteomecenter.org/wiki/index.php?title=TPP:7.1.0_Release_Notes
4: = TPP 7.0.0 ARAFEL Release Notes =
27: ...rters. This is potentially inefficient for legacy software that calls readHeader() and readPeaks() independe...
78: === [tpp_gui.pl (a.k.a. PETUNIA) :] === - TPP:Installing on Mac OSX (12870 bytes)
2: ''Please Note: '''The TPP is not currently officially supported on Max OSX....
8: This guide describes installation of the TPP, version v4.0 SQUALL (release candidate) rev.0, B...
13: ...nix shell commands and installing and configuring software.
18: ==Getting the TPP source==
20: *TPP source at SourceForge: [http://sourceforge.net/pr... - Software:PeptideProphet (1728 bytes)
1: ==Getting the software==
2: ...oftware 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: ...oftware 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...
46: ...developer Henry Lam had to say in May 2008 on the TPP developers' forum: - Software:XPRESS (1756 bytes)
1: ==Getting the software==
2: ...oftware 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: ...oftware 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: ...oftware is included in the current [[Software:TPP|TPP]] distribution.'''
17: ...dition file using the built-in utility within the TPP web UI (Petunia), or by using a text editor. - Software:Pep3D (1087 bytes)
1: ==Getting the software==
2: ...oftware is included in the current [[Software:TPP|TPP]] distribution.'''
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