Applications

Usage:

or:

We do not have user documentation pages for all software, any software in the table that has a link will connect to our documentation. If you want to contribute towards documentation for any software, please contact us.

We do not deal with software licenses as we do not hold the budget for them; it is the PI of the research project responsibility to have the right budget for the software that is needed. Any unusual information about licenses or how to set up a license on the ARC system is in a web page linked to from this table. Information on open source licenses and their conditions of use are available from http://opensource.org/licenses.

 

Module version(s) 1 2 M1 Description
A
abaqus 6.9EF Y Unified finite element analysis
6.10 Y
6.12 Y
6.13 Y
adams 2013.2 Y Multibody dynamics simulation software
aimpro 2.3.11b2 Y DFT electronic structure and energy calculations
amber 9 Y Molecular modelling and simulation
10 Y
12 Y Y
14 Y
ampl 12.6.1.0 Y Sophisticated modelling tool that supports the entire optimization modeling lifecycle
ansys 17.1 Y Engineering simulation software (Fluent and CFX)
17.0 Y
16.2 Y Y
16.1.1 Y
15.0.5 Y
14.5.7 Y Y
14.0 Y
13.0sp2 Y
13.0 Y
12.1 Y
12.0 Y
ansysEM 15.0 Y Y Electromagnetics simulation software (HFSS)
aten 1.3 Y Tool for the creation and editing of atomic coordinates
B
bfast 0.7.0a Y Sequencing tool
blast 2.2.25 Y Sequencing tool
bowtie 0.12.7 Y Sequencing tool
bwa 0.7.6a Y Y Sequencing tool
0.6.1 Y
C
castep 4.4.6 Y Materials modelling using density functional theory
5.0.1 Y
5.0.2 Y
5.5 Y
5.5.1 Y
6.0p3 Y
6.1.1 Y Y
7.0.1 Y
cdo 1.6.1 Y command line operators to manipulate and analyse climate and NWP model data
comsol 4.1 Y Multiphysics simulation software environment
4.2 Y
4.2a Y
4.3 Y
4.3a Y
4.3b Y
4.4 Y
5.1 Y
cufflinks 1.3.0 Y Sequencing tool for RNA-Seq samples
2.2.1 Y
D
desmond 2.2.9.1 Y Molecular dynamics simulation software
dl_poly 2.20 Y Polymer dynamics simulation
4.05 Y Y
E
ehits 2009.1 Y Molecular docking and virtual screening (Simbiosys developed this product and were brought out by John Wiley & Sons in 2014: there is no current links for this product)
12.0 Y Y
13.0 Y
14.0.3 Y Y
espresso 4.1.2 Y Electronic structure calculations
F
ferret 6.8.5 Y Y Data visualisation and analysis package for gridded data sets
fusionmap 1.42 Y DNA sequence fusion junction detection
G
gate 6.2 Y Simulations of Preclinical and Clinical Scans in Emission Tomography; Transmission Tomography and Radiation Therapy
gaussian G03.D02 Y Electronic structure modelling
G09 Y Y
G09.D01 Y Y
geant4 9.5 Y Toolkit for the simulation of the passage of particles through matter
9.6 Y
10.0 Y
glpk 4.55 Y Solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems
gmt 4.5.2 Y Manipulation of geographic and Cartesian datasets
gnuplot 4.2.3 Y Graphical plotting
4.6.4 Y
grace 5.1.22 Y Graphical plotting
5.1.23 Y
gpaw 0.10.0.11364 Y Density-functional theory (DFT) Python code
gromacs 4.5.1 Y molecular dynamics package
4.5.3 Y
4.5.5 Y
4.5.6 Y
4.6.3 Y
4.6.5 Y
5.0.2 Y
gulp 3.4 Y simulation of materials using boundary conditions for molecules and clusters; polymers, surfaces, slabs and grain boundaries; and periodic solids
H
hyperworks 10 Y CAE simulation software platform
I
idl 7.0 Y Y Data analysis language
8.4 Y
iris-explorer 5.2 Y NAG IRIS Explorer – visualisation software
J
joint-snv-mix 0.7.3 Analyse sequence data from tumour/normal pairs
L
lammps 1Feb14 Y Large-scale Atomic/Molecular Massively Parallel Simulator
ls-dyna 971r4.2.1 Y General purpose finite element program
M
macs 1.4.1 Y Sequencing tool
1.3.7 Y
materialsstudio 5.5.3 Y Materials modelling and simulation
matlab 7.9 Y Numeric computation, high level programming, graphics & visualisation
R2012a Y Y
meep 1.1.1 Y FDTD simulation package for em systems
mesmer 4.0 Y Y Master Equation Solver for Multi-Energy well Reactions
molpro 2006.1.148 Y molecular dynamics package
2010.1.23 Y
2010.1.24 Y
2010.1.34 Y
mpb 1.4.2 Y MIT Photonic Bands. Band structures of periodic dielectrics
N
namd 2.7b4 Y Molecular dynamics code for large biomolecular systems
2.8 Y
2.9 Y Y
nbo 6 Y Y Natural Bond Orbital
ncl 6.0.0-beta Y NCAR Command Language. Scientific data analysis and visualisation language.
6.1.2 Y
nco 4.0.8 Y netCDF Operator, tools to manipulate netCDF files.( Note: netCDF4 files are not supported)
4.3.7 Y Y
ncview 1.93g Y Visual browser for netCDF files
2.1.2 Y
nwchem 6.5 Y Computational chemistry tools
O
octave 3.8.2 Y Numerical solution of linear and nonlinear problems, data visualization and manipulation
onetep 3.0.0 Y Quantum mechanical calcs using density functional theory
opendx 4.4.4 Y Open source visualization software package
openeye 3.0.1 Y Y OpenEye provides software to the pharmaceutical industry for molecular modeling and cheminformatics
openfoam 1.7.1 Y CFD software package
2.1.1 Y Y
2.3.0 Y
P
paraview 3.8.1 Y Data analysis and visualisation
4.0.1 Y
4.3.1 Y
pari 2.5.0 Y Computer algebra system for fast computations in number theory
ploticus 2.41 Y Software utility that can produce various types of plots and graphs
Q
qhull 2012.1 Y Computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram
qiime 1.8.0 Y Quantitative Insights Into Microbial Ecology
R
R 2.10.1 Y Statistical computing and graphics
2.13.0 Y
2.15.0 Y
2.15.3 Y Y
3.0.2 Y Y
3.1.0 Y Y
3.2.0 Y Y
relion 1.2 Y Y cryo-EM refinement tool
1.3 Y
1.4 Y
S
samtools 0.1.18 Y Sequence Alignment/Map – sequence alignment format
1.1 Y
sas 9.2.2 Y Business Analytics
schrodinger 2014-3 Y Schrödinger is a scientific leader in computational chemistry, providing software solutions and services for life sciences and materials research. Docking tool.
starccm 9.06 Y General purpose Computational Fluid Dynamics (CFD) software
stata 12 Y Data Analysis and Statistical Software
13 Y
13.1 Y Y
stir 2.4 Y Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging
T
tophat 1.3.3 Y !TopHat is a fast splice junction mapper for RNA-Seq reads. Requires Bowtie
V
visit 2.6.3 Y Parallel visualisation and graphical analysis tool
2.9.2 Y Y
vmd 1.8.7 Y Visual molecular dynamics package
1.9.1 Y
W
weka 3.6.7 Y A collection of machine learning algorithms for data mining tasks
wien2k 09.2 Y DFT electronic structure calculations
11.1 Y
X
xmipp 2.4 Y Image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens