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HPC Software - Data Mining and Analysis Applications

NCL - (NCAR Command Language)

NCL is an interpreted language designed specifically for scientific data analysis and visualization. [NCL Website - November 2012]

Available versions and module name

5.1.1 (ncl-5.1.1 or ncl)

Default version available

5.1.1

Website

http://www.ncl.ucar.edu/

Ncview

Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change colour maps, invert the data, etc. [Ncview Website - June 2014]

Available versions and module name

2.1.2 (ncview-2.1.2 or ncview)

Default version available

2.1.2

Website

http://meteora.ucsd.edu/~pierce/ncview_home_page.html

NetCDF

NetCDF (Network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. It is also a community standard for sharing scientific data. [NetCDF Website - June2020]

Please note that from version 4.7.4, the C version is a seperate mode to the frontran version.

Available versions and module name

4.7.4 (netcdf-4.7.4)

4.4.0 (netcdf-4.4.0)

4.3.2 (netcdf-4.3.2 or netcdf)

4.1.1 (netcdf-4.1.1)

Default version available

4.7.4

Website

http://www.unidata.ucar.edu/software/netcdf/

NetCDF-Fortran

NetCDF (Network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. It is also a community standard for sharing scientific data. [NetCDF Website - June2020]

Available versions and module name

4.5.3 (netcdf-fortran-4.5.3 or netcdf-fortran)

Default version available

4.5.3

Website

http://www.unidata.ucar.edu/software/netcdf/

RapidMiner

Using RapidMiner's modern enterprise platform, you can quickly and easily create analytic workflows called processes to determine who to target. In these processes you transform data by connecting the building blocks or operators that will eventually result in a model that helps predict the future. Sounds like fantasy or science fiction? It's not, it's predictive analytics reimagined. It allows you to operationalize predictive decisions closing the loop between insight and action.[RapidMiner Website - December 2015]

Available versions and module name

6.5.002 (rapidminer-6.5.002 or rapidminer)

Default version available

6.5.00

Website

https://rapidminer.com/products/studio/

Getting Startedhttp://docs.rapidminer.com/studio/getting-started/

STIR - (Tomographic Imaging)

STIR is Open Source software for use in tomographic imaging. Its aim is to provide a Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging. Currently, the emphasis is on (iterative) image reconstruction in PET, but other application areas and imaging modalities can and might be added.

STIR is the successor of the PARAPET software library which was the result of a (European Union funded) collaboration between 6 different partners (see Credits). [STIR Website - November 2012]

Available versions and module name

2.2 (STIR-2.2 or STIR)

Default version available

2.2

Official Website

http://stir.sourceforge.net/

Weka

Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes. 
[Weka Website - November 2012]

Available versions and module name

3.6.4 (weka-3-6-4 or weka)

3.6.1 (weka-3-6-1)

Default version available

3.6.4

Official Website

http://www.cs.waikato.ac.nz/ml/weka/

If, for whatever reason, you would like to use the older versions of the compilers, or other available software, you can simply "unload" the current module and load the older version. See Software Module Information webpage.

Software list

Bioinformatics
  • AmpliconNoise
  • ARB
  • BLAST (Legacy BLAST- Not BLAST+)
  • BLAST+
  • Bowtie2
  • CD-HIT
  • cdbtools
  • ChimeraSlayer
  • clearcut
  • Cufflinks
  • Cytoscape
  • FastQC
  • FastTree
  • Fastx-Toolkit
  • Gepard
  • HMMER
  • IGV
  • infernal
  • Kraken
  • metavelvet
  • mothur
  • MUSCLE
  • Ngopt
  • ParsInsert
  • Pear
  • Pplacer
  • QIIME
  • RAxML
  • rRNASelector
  • RSEM
  • RTAX
  • SAM Tools
  • SAMStat
  • SourceTracker
  • TopHat
  • Trimmomatic
  • Trinityrnaseq
  • UCLUST
  • UProC
  • USEARCH
  • Velvet
  • Velvet Optmiser
Compilers
  • Glasgow Haskell Compiler
  • GNU Bison
  • GNU Compiler
  • GNU Fortran Compiler
  • Go Compiler
  • Intel C and C++ Compiler
  • Intel Fortran Compiler
  • Mono C# Compiler and associated libraries
Data Mining and Analysis Applications
  • NCL (NCAR Command Language)
  • Ncview
  • NetCDF
  • NetCDF-Fortran
  • RapidMiner
  • STIR (Tomographic Imaging)
  • Weka
Development tools
  • Apache Maven
  • GNU Emacs
  • IntelliJ IDEA
  • RStudio
Documentation Tools
  • Tex Live
  • Tex Info
Engineering Applications
  • ANSYS (Fluent and Mechanical)
  • ABAQUS
  • AVL Fire
  • Comsol Multiphysics
Geospatial Tools
  • GDAL
  • GEOS
  • Panoply
Graphics Applications
  • Circos
  • ImageJ
  • ImageMagick
  • PLPlot
  • Xfig
Interpreters
  • Perl
  • Python (with many Modules Installed)
Mathematics and Statics
  • Mathematica
  • Grid Mathematica
  • Matlab
  • Matlab-Simulink
  • Octave
  • OpenBUGS
  • R
  • SPSS (by IBM)
Run Time Environments
  • Java
Simulation Software
  • APSIM
Software Libraries
  • Boost C++ Libraries
  • Expat XML Parser
  • FFTW
  • GMP (GNU Multiple Precision Arithmetic Library)
  • GNU Scientific Library (GSL)
  • HDF5
  • HDF-EOS5
  • Intel Math Kernel Libraries (Intel® MKL)
  • libbz2
  • libcurl
  • libjpeg
  • libpng
  • MPI
  • OpenBLAS
  • PCRE (Perl Compatible Regular Expressions)
  • szip
  • tcl
  • tk
  • UDUNITS
Text Tools and Software
  • Flex