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HPC Software - Graphics Applications

Circos

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive.

Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience.[Circos Website - Janurary 2015]

Available versions and module name

0.67-4 (circos-0.67-4 or circos)

Default version available

0.67-4

Website

http://circos.ca/

ImageJ

ImageJ is a public domainJava-based image processing program developed at the National Institutes of Health.[1] ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros.[2] Custom acquisition, analysis and processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging,[3] to radiological image processing,[4] multiple imaging system data comparisons[5] to automated hematology systems.[6] ImageJ's plugin architecture and built in development environment has made it a popular platform for teaching image processing.[7][8][Wikipedia ImageJ - http://en.wikipedia.org/wiki/ImageJ]

Available versions and module name

1.47 (imagej-1.47 or imagej)

Default version available

1.47

Website

http://rsb.info.nih.gov/ij/index.html

http://rsb.info.nih.gov/ij/developer/index.html

http://rsb.info.nih.gov/ij/links.html

ImageMagick

ImageMagick  is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 100) including DPXEXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colours, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.  [ImageMagick Website - November 2012]

Available versions and module name

6.8.0-8 (imagemagick-6.8.0-8 or imagemagick)

Default version available

6.8.0-8

Website

http://www.imagemagick.org/script/index.php

PLPlot

PLplot is a cross-platform software package for creating scientific plots. To help accomplish that task it is organized as a core C library, language bindings for that library, and device drivers which control how the plots are presented in non-interactive and interactive plotting contexts.

The PLplot core library can be used to create standard x-y plots, semi-log plots, log-log plots, contour plots, 3D surface plots, mesh plots, bar charts and pie charts. Multiple graphs (of the same or different sizes) may be placed on a single page, and multiple pages are allowed for those device formats that support them.

[PLPlot Website - November 2012]

Available versions and module name

5.9.9 (plplot-5.9.9 or plplot)
Default version available

5.9.9

Website

http://plplot.sourceforge.net/

Xfig

Xfig is a free and open source vector graphics editor which runs under the X Window System on most UNIX-compatible platforms.

In Xfig, figures may be drawn using objects such as circles, boxes, lines, spline curves, text, etc. It is also possible to import images in formats such as GIFJPEGEPSPostScript, etc. Those objects can be created, deleted, moved or modified. Attributes such as colours or line styles can be selected in various ways. For text, 35 fonts are available.

Xfig saves figures in its native text-only "Fig" format. Xfig has a facility to print figures to a PostScript printer too. A convenient feature is the PSTEX or PDFTEX export format that allows a smooth integration of Xfig-generated images into LaTeX documents.

[PLPlot Website - November 2012]

Available versions and module name

3.2.5b (xfig-3.2.5b or xfig)

Default version available

3.2.5b

Website

http://en.wikipedia.org/wiki/Xfig

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