TPP:5.0.0 Release Notes
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| ** '''Kojak''' for cross-linking analysis | ** '''Kojak''' for cross-linking analysis | ||
| ** '''DISCO''' for analysis of DIA data without using spectral libraries | ** '''DISCO''' for analysis of DIA data without using spectral libraries | ||
| - | ** '''StPeter''' for label-free quantitation | + | ** '''StPeter''' for label-free quantitation via MS2 normalized spectral indices |
| * Updated user interface look and feel | * Updated user interface look and feel | ||
| Line 25: | Line 25: | ||
| == New Features == | == New Features == | ||
| + | |||
| + | * ''PepxMLViewer'': | ||
| + | ** Link iProphet prob to new models page | ||
| * ''ProteinProphet:'' | * ''ProteinProphet:'' | ||
| + | |||
| * ''Petunia:'' | * ''Petunia:'' | ||
| + | |||
| * ''tpp_models:'' | * ''tpp_models:'' | ||
| + | |||
| + | * New versions of ''pepXML'' and ''protXML'' schemae. | ||
| + | |||
| == Improvements/Changes == | == Improvements/Changes == | ||
| + | |||
| + | * ''ASAPRatio'': | ||
| + | ** Write xml-compliant 'NaN' string when applicable | ||
| + | ** Removed obsolete .bof files code | ||
| + | |||
| + | * ''PTMProphet'': | ||
| + | ** auto-populate modifications not known to SpectraST Peptide library | ||
| + | |||
| + | * ''tpp_models'' | ||
| + | ** Display decoy-based ROC curves, with errorbars | ||
| + | |||
| + | * ''PeptideProphet'': | ||
| + | ** Expanded N-Glyc model | ||
| + | |||
| + | |||
| + | * ''ProteinProphet'': | ||
| + | ** More user and progress feedback | ||
| == Bug fixes == | == Bug fixes == | ||
| + | |||
| + | * Fixed definition for ''lysn_promisc'' enzyme (to [X]|[KR]) | ||
| + | |||
| + | * ''InteractParser'': | ||
| + | ** Do not crash when protein descriptions are blank | ||
| + | ** Upgrade scan numbers to ''long'' | ||
| + | |||
| + | * ''PTMProphet'' | ||
| + | ** Fixed memory leak | ||
| + | |||
| + | |||
| + | * ''PepxMLViewer'': | ||
| + | ** regenerate index when a new column is added, and keep the column always in display | ||
| + | ** corrected issue with bad byte offsets in large files | ||
| + | |||
| + | * ''ProteinProphet'': | ||
| + | ** Synced usage statement, removed obsolete XML option | ||
| + | ** Check for existence of input files before attempting to open them; provide meaningful feedback to user | ||
| Line 49: | Line 92: | ||
| * Removed no longer needed or supported components: | * Removed no longer needed or supported components: | ||
| - | ** ''refresh_interact'' | + | ** ''refresh_interact'', ''runperl'', ''run_in'' |
| ** Visual Studio project files | ** Visual Studio project files | ||
| ** Misc .bat files. | ** Misc .bat files. | ||
| ** ''fdr_plot.cpp'', ''getSpectrum.cpp'', ''mzxml2dta1.cpp'', ''plottic1.cpp'', ''prophet_png1.cpp'' | ** ''fdr_plot.cpp'', ''getSpectrum.cpp'', ''mzxml2dta1.cpp'', ''plottic1.cpp'', ''prophet_png1.cpp'' | ||
| + | ** Old help files | ||
| + | |||
| + | |||
| + | * Using ''Inno'' to produce Windows installer | ||
Revision as of 01:39, 30 August 2016
Trans-Proteomic Pipeline (TPP) software, release 5.0.0 is a major release of TPP that contains new features, improvements, and fixes to 4.8.0. The software is available for Windows as well as Linux (and unofficially) for OSX from all the usual locations (please see the section below, "Getting the software"). Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a web server). For advanced users who need to customize the TPP, or for those who run on Linux or OS X, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.
Previous release notes are available at TPP:4.8.0_Release_Notes
Contents |
Major Changes and Overview
- Heavily modified code organization, build, and installation system
- 64-bit
- Windows installer:
- includes all external dependencies, including stand-alone Apache web server (uses port 10401, user configurable) and Strawberry perl
- allows for user-configurable software and data locations
- new (optional) TPP Tray application provides convenient shortcuts to TPP, web server control, and data
- New major software components:
- Kojak for cross-linking analysis
- DISCO for analysis of DIA data without using spectral libraries
- StPeter for label-free quantitation via MS2 normalized spectral indices
- Updated user interface look and feel
More details below.
New Features
- PepxMLViewer:
- Link iProphet prob to new models page
- ProteinProphet:
- Petunia:
- tpp_models:
- New versions of pepXML and protXML schemae.
Improvements/Changes
- ASAPRatio:
- Write xml-compliant 'NaN' string when applicable
- Removed obsolete .bof files code
- PTMProphet:
- auto-populate modifications not known to SpectraST Peptide library
- tpp_models
- Display decoy-based ROC curves, with errorbars
- PeptideProphet:
- Expanded N-Glyc model
- ProteinProphet:
- More user and progress feedback
Bug fixes
- Fixed definition for lysn_promisc enzyme (to [X]|[KR])
- InteractParser:
- Do not crash when protein descriptions are blank
- Upgrade scan numbers to long
- PTMProphet
- Fixed memory leak
- PepxMLViewer:
- regenerate index when a new column is added, and keep the column always in display
- corrected issue with bad byte offsets in large files
- ProteinProphet:
- Synced usage statement, removed obsolete XML option
- Check for existence of input files before attempting to open them; provide meaningful feedback to user
Miscellaneous
- Major code reorganization and standardization:
- Updated path furnishing utilities, as some paths are user-settable post-compilation
- Renamed all ".cxx" C++ source files as ".cpp"
- Harmonize directory names
- Moved Enzyme code to Common/
- moved COVERAGE/ folder into src/Util and renamed it batchcoverage (its target name)
- Moved xtandem out of extern/ and into src/Search
- Updated boost
- Removed no longer needed or supported components:
- refresh_interact, runperl, run_in
- Visual Studio project files
- Misc .bat files.
- fdr_plot.cpp, getSpectrum.cpp, mzxml2dta1.cpp, plottic1.cpp, prophet_png1.cpp
- Old help files
- Using Inno to produce Windows installer
Known Issues
- Kojak graphical models in PeptideProphet are not displaying correctly on the MODELS page.
Getting the TPP Software
- Download the TPP version 5.0.0 native windows installer (TPP_Setup_v5_0_0.exe) from the Sashimi SourceForge project file release page:
http://sourceforge.net/projects/sashimi/files/
- Everyone is encouraged to read and contribute to our wiki, at
http://tools.proteomecenter.org/wiki/
- For guides to installing and using our software, please see our wiki:
http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
- For downloading the source code, please go to the following link:
http://sourceforge.net/projects/sashimi/files/ and find the 5.0.0 source code .tgz package;
- Or, check out the code directly from svn:
svn checkout svn://svn.code.sf.net/p/sashimi/code/tags/release_5-0-0
- For building from source, please refer to the README and INSTALL files in src/ directory of TPP as well as this wiki.
Acknowledgements
The TPP Team: David, Luis, Mike, Jimmy, and our old colleague Joe, plus all other developers who contributed to this release from the ISB. Thanks to developers and users from the TPP's user community who provided feedback and code contributions.
SVN Log
The SVN log of all changes since the previous release are available at TPP:5.0.0_SVN_Log.
