Mass Spec / Proteomics applications|_. Application |_. Version |_. Hosts deployed |_. Description |_. Application type | | APEX | 1.1.0 | all nodes | implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data | Java GUI application | | Census | 1.57 | all nodes | Proteome Quantification tool | Java GUI application | | GPM | ? | Mango (accessible via web browser http://mango.seer.harvard.edu:81/ from login nodes) | XTandem! search engine front-end | web application | | GPMAW | 8.21 | Mango | Set of tools for Mass Spec analysis of proteins and peptides | GUI application | | Insilicos Viewer | 1.54 | Login node | mzXML MS/MSMS spectra viewer | GUI application | | IP2 | current | web application, ip2.rc.fas.harvard.edu | Proteomics suite, with sequest, prolucid search engines and massspec/proteomics toolkit | Web application. NOTE: requires special group membership due to licensing | | MakeMS2 | 2009 | all nodes | RAW to MS2 converter, works with VLO | GUI tool | | Mascot | 2.2 | Mango (accessible via web browser http://mango.seer.harvard.edu/mascot/ from login node and Mascot daemon) | Proteomics search engine package| system with web interface | | Mascot Daemon| 2.2 | Mango, accessible from login nodes | Mascot search submission and automation tool| GUI application | | massWolf | 4.31 | all nodes | Waters MassLynx .raw directories to mzXML converter | cmd-line tool | | MaxQuant | 18.104.22.168 64 bit | all nodes | Quantitative proteomics package | .NET GUI application | | MSDataFileTrimmer | 1.1.2991 | all nodes | tool for filtering and trimming mzXML data files | .NET cmd-line tool | | MSQuant | 2.0a81 | all nodes | Quantitative proteomics package, MaxQuant predecessor | GUI application | | Panda | 2.0.1 | all nodes | Quantitative proteomics package | .NET GUI application | | Peaks | 5.3 | win004/ accessible from parathyro | Proteomics package for searches and DeNovo sequencing | Java GUI app. with client, server, database and compute component | | Percolator | 1.13 | all nodes | Proteomics search engine | cmd-line application | | Perseus | 22.214.171.124 | all nodes | Graphical analysis proteomics package | .NET GUI application | | Proteome Discoverer, Sequest | 1.2 | mango | Platform for the analysis of qualitative and quantitative proteomics data. Front-end to sequest (included) and mascot | .NET client/server application supporting a single host | | Raw2mzXMLComb | 20100914 | all nodes | tool for extraction, filtering and combining multiple run RAW file MSMS spectra and their precursors to a single single mzXML file | cmd-line tool | | RawXTract | 126.96.36.199 | WinXP nodes | conversion tool for Thermo RAW format to MS2 | GUI tool | | ReaDW | 4.3.1 | all nodes | conversion tool for Thermo RAW format to mzXML | cmd-line tool | | Skyline | 0.7 | all nodes | Mass Spec data analysis | .NET GUI application | | TPP (Trans-proteomic pipeline)| 4.4.0 (Vuvuzela) | Mango, accessible from login nodes browser, http://mango.seer.harvard.edu:81/tpp-bin | Suite of masspec/proteomics search and analysis tools build into a pipeline with webUI | web system with web interface | | Trapper | 4.3.1 | all nodes | conversion tool for Agilent MassHunter format to mzXML | cmd-line tool | | XCalibur | 2.1.0 | argo-VM-002 | Proteomics package from Thermo | GUI application suite with COM programming interface | | XCaliburImport | 20100914 | all nodes | tool for easy extraction of various parameters from Thermo RAW files | cmd-line tool | | XTandem! | 2010.01.01.4 | all nodes | high-performance proteomics search engine | cmd-line app |
Economics applications|_. Application |_. Version |_. Hosts deployed |_. Description |_. Application type | | SmartCom | 1161 | argo-004 | market data analysis | GUI app | | Smart Trade | 5.3 | argo-004 | market data analysis | GUI app | | SuperTrade Beta | ?.? | argo-004 | market data analysis | GUI app |
Other applications|_. Application |_. Version |_. Hosts deployed |_. Description |_. Application type | | StarDrop | current | win005 (client), stardrop.rc.fas.harvard.edu (linux server) | drug discovery / simulation suite | GUI QT Windows client, integrated with Linux compute services (python) |
Development toolsCygwin (login nodes only) LabView 2009 .NET 2, 3.5 runtimes MS Visual Studio 2010, with MPI .NET and MS MPI, AnkhSVN plugin (login nodes only) Perl 5.8 (ActivePerl) Python 2.6 (Active Python), with numpy and scipy Java 6 JRE Notepad++ (login nodes only) R 2.10.1
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