Development tools and libraries
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devx - Development tools for fatdog64-701 (C/C++, fortran compiler, ..)
jdk - Java Development Toolkit
java version "1.7.0_65"
Java(TM) SE Runtime Environment (build 1.7.0_65-b17)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
Python 2 (#python) and Python 3 (#python3)
Multiple libraries and development files

Workflow management
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taverna - Java-based workflow management with additional functions (condition, iteration)
OpenMS/TOPPAS - Framework for mass spectrometry data processing and GUI supported design of pipelines

Data conversion and trimming
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ProteoWizard tools - MS data conversion and tools, see /usr/local/massypup64/proteowizard-tools.txt; without vendor libraries
transpose - Transposing matrix data from commandline, sourcecode in /usr/local/bin/transpose.c. Currently compiled for maximum matrix size of 10,000 x 10,000
teapot/fteapot - Spreadsheet program supporting three dimensional data sets. The manual "teapot.pdf" is located in /usr/local/doc

MS data processing suites
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MZmine - Java-based MS analysis program, focused on metabolomics
OpenMS - MS data analysis programs, with TOPPView and TOPPAS (pipelines)

Proteomics search engines and hit validation
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Comet - MS/MS peptide/protein search algorithm
OMSSA - MS/MS peptide/protein search algorithm
X!Tandem - MS/MS peptide/protein search algorithm
TPP 4.8 - Trans-Proteomic-Pipeline

R statistics language
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with MS data analysis related libraries, packages and scripts, e.g.:
XCMS/metaXCMS - Metabolomics
Metab.R - Statistical analysis of metabolomics results
Rattle - Data Mining

Compound identification
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massXpert - Analysis of polymer spectra
SpiderMass - Target DB creation/ matching, Online searches and formula generation

Mass Spectrometry Imaging (MSI)
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HelloPhidget - Test tool for detection of connected Phidgets (prototyping of MSI)
OpenMZxy - Control of Phidget imaging robot
MSI.R - MSI analysis with R	scripts

Data visualization
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GGobi