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- TPP:V5Feedback (11460 bytes)
44: ** pvalue link to interact-pval.png is broken. (look in PValueModel.cxx)
72: * <s>Extra '/' in link for Additional Analysis Info on pepxmlviewer</s>
94: ...ctrast/OR20080317_S_SILAC-LH_1-1_01.00417.00417.2.png) Seen when clicking on a spectrum in the pepxmlv...
103: ...>legacy proteinprophet results: sensitivity/error info has broken image/page with error "The system cann...
105: * <s>legacy proteinprophet results: more analysis info reports error "The system cannot find the path sp... - TPP:Developer Documentation (23931 bytes)
24: ...forge.net/svn/?group_id=69281 our SourceForge SVN info page.]
69: *libpng www.libpng.org
303: ;ICAT: use peptide icat info in probability calculation
304: ;NOICAT: do not use peptide icat info in probability calculation
306: ;GLYC: use peptide NXS/T motif info in probability calculation - Software:Overview (3074 bytes)
18: Please see the [[Formats:mzXML|mzXML]] page for info on ReAdW (Thermo), mzStar (ABI/MDS Sciex Analyst)... - TPP:Installing on Mac OSX (12870 bytes)
191: ...ome report that it is necessary to edit the boost info file before installing with fink to disable --wit...
193: .../sw/fink/10.4/stable/main/finkinfo/libs/boost1.33.info
199: Information about 2301 packages read in 1 seconds.
325: (to get right path for png images with WEBSERVER_ROOT stripped off)
328: //printf("<img src=\"%s\"/>\n", pngFile); - Software:PeptideProphet (1728 bytes)
7: ==More info==
8: ...ic termini, number of missed cleavages, and other information, the method learns to distinguish correctl... - Software:ProteinProphet (6941 bytes)
7: ==More info==
8: ...n is present in the sample. This protein grouping information is then employed to adjust the individual ...
13: NOPLOT: do not generate plot png file
31: ... DELUDE: do NOT use peptide degeneracy information when assessing proteins - Software:TPP (8915 bytes)
32: |[[Image:Info.png|middle|left]]
42: ...ation guides, which are more detailed and contain information specific to certain distributions: [[Linux...
115: ... Engines|supported search engines]] page for more information. - Formats:mzXML (9722 bytes)
27: ...ument name is not recorded in mzXML; charge state info is not recorded in mzXML || [http://tools.proteom...
59: ...ndor formats. Follow the links for more specific information for each converter:
77: ...adata is stored in this format, so you will loose information going from raw to dta then back to mzXML.
107: ... It can also link to CID and peptide probability information.
126: ...a. For more information, visit the [http://psidev.info/index.php?q=node/257 mzML development page]. As ... - TPP:Installing on Ubuntu 7.04 (9446 bytes)
35: | libpng
36: | www.libpng.org
37: | libpng12-dev
52: | www.gnuplot.info
165: # Contact info. for when people break the machine - TPP:X!Tandem and the TPP (5454 bytes)
5: The k-score is a [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22...
29: Someone could contribute info on setting up the params file for Tandem here.. - TPP Tutorial v1 (43187 bytes)
15: ...ication of TPP and only briefly touches on the bioinformatics behind the tools which are included in TPP...
27: ... Small ''Itallics'' is use for notes that contain information that is not required to complete this tuto...
35: Information on installing and downloading the Windows ...
157: ...e proteomics pipeline GUI. The Home tab contains information about TPP and the structure of the GUI, al...
158: [[Image:login.png]] - Software:QualScore (559 bytes)
8: ==More info== - TPP:ProbID and the TPP (578 bytes)
2: ... see the [[Software:ProbID|ProbID]] page for more info.
11: Someone could contribute info on setting up the params file, or point to the [[... - Expert search and TPP usage (12929 bytes)
81: ...ntandemsearch and the like) gives a lot of useful info about how your searches and TPP went: - Terry's compbio links (11123 bytes)
89: ...://vim.wikia.com/wiki/File_format Line terminator info.]
95: [http://www.perlmonks.org/?node_id=469927 Informative discussion of test module options]
112: [http://pipe.systemsbiology.net The Pipe] Protein Information and Property Explorer, developed at ISB by...
120: ...wnload NCBI's UniGene human. Contains chromosomal information, among many other data.
127: ===ISB proteomics informatics=== - Terry's blog (18394 bytes)
128: * Incorporate PeptideProphet information (e.g. probabilities) into PeptideAtlas. Wh...
131: * Figure out how to get this info into PeptideAtlas
132: ...s info is viewable, and draw conclusions from the info. - Building Peptide Atlas (26978 bytes)
71: ...template file contains only the unadjusted pepXML info for PSMs with P>=0.4; it is cached in the same di...
83: ... peptide sequence (includes modification & charge info)
93: ...ev>_all.PAxml'''<br>These two files have the same info with different formatting. There is one record pe...
124: ...ot robust (will break if createPipelineInput.pl's informational output changes):
173: ...iosequence_set (but before load_atlas_build --protinfo). - TPP:4.2.1 Release Notes (3668 bytes)
35: *when parsing scan info from description, watch for mass spec file extens...
80: *massWolf: charge state information is not recorded in output mzXML - PABST peptide examples (6378 bytes)
30: -s, --show_builds Print info about builds in db - TPP 4.2.1: Installing on Ubuntu 9.04 (4386 bytes)
13: ...+ subversion vim apache2 libbz2-dev swig expat libpng12-dev gnuplot libperl-dev build-essential libgd2-...
103: # Possible values include: debug, info, notice, warn, error, crit,
142: AddHandler default-handler .jpg .png .css .ico .gif
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