Applications
Software that can be categorized as ‘Applications’, i.e., not compilers, tools etc. For a full list see the AZ list.
Instructions shown only to loggedintowordpress users
The tables of apps for each category are now autogenerated. You should add two custom fields to each software app page: RI_Summary
giving the summary description of the app, and RI_Cat
which can be a commaseparated list of one or more of: bioinf, chemistry, cfd, fea, gpu, maths, physics, ml, prog, viz
. Categories tool, compiler, library
can also be used but these will be displayed in tables on the appropriate page (see menu on left), not here. To add these custom fields you will need to click on ‘Screen Options’ (topright when in the page editor) and tick ‘Custom Fields’ and then the boxes you need to fill in appear at the bottom of the page editor.
Available application categories: Bioinf Chemistry CFD FEA Mathematics Physics Machinelearning Programming GPUcapable Visualization Pythonpackages
Bioinformatics
Please note: More bioinf apps are available than listed here by first running:module load apps/bioinf (then use module avail to list all modules)

PACKAGE  NOTES 

Affymetrix Power Tools (APT)  Algorithms for analyzing and working with GeneChip™ arrays 
Alphafold  application for predicting models of protein structures 
AMICO  Diffusion magnetic resonance data processing in python 
Aspera  ascp fast downloader 
BBTools  Suite of tools designed for analysis of DNA and RNA sequence data. 
Bioinformatics Helper Modulefile  Modulefile to make more Bioinformatics apps available 
BLAST  suite of tools for comparing primary biological sequence information 
Bowtie2  tool for aligning sequencing reads to long reference sequences. 
bwamem2  BurrowWheeler Aligner 
Canu  Hierarchical assembly pipeline for highnoise singlemolecule sequencing. 
CheckM  Quality assessment of genomes recovered from isolates, single cells, or metagenomes. 
Compucell3d  Virtual Tissue in silico simulation modelling environment. 
Diamond  Sequence aligner for protein and translated DNA searches 
eggNOG mapper  Fast functional annotation of novel sequences. 
Fasta_number  Replace FASTA labels with xxx1, xxx2, xxx3 etc, where xxx is a prefix provided as a commendline argument. Used e.g. to label OTUs as OTU_1, OTU_2 etc. 
FastANI  Fast alignmentfree computation of wholegenome Average Nucleotide Identity 
FastTree  Infer approximatelymaximumlikelihood phylogenetic trees from alignments of nucleotide or protein sequences. 
FeGenie  Identify potential homologs and operons that may be linked to the microbial iron cycle 
GTDBtk  Toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy. 
Guppy  GPU enabled basecaller 
HMMRATAC  HMMRATAC peak caller for ATACseq data 
HOMER  Software for motif discovery and next generation sequencing analysis 
InterProScan  Scan sequences against InterPro's member database signatures 
JAGS  Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. 
Kaiju  Taxonomic classification of highthroughput sequencing reads. 
MACS  Modelbased Analysis of ChIPSeq (MACS) 
MaxBin  Binning assembled metagenomic sequences 
Medaka  Create a consensus sequence from nanopore sequencing data 
MEGAHIT  Fast metagenomics assembly tool 
MemeSuite  Motifbased sequence analysis tools 
Microsoft R Open (MRO)  Statistical computing and graphics. Includes bioconductor. 
Minimap2  Sequence alignment 
miRDeep2  Discovers active known or novel miRNAs from deep sequencing data 
Mothur  Tool for processing data generated from several DNA sequencing methods 
MrBayes  Bayesian Inference of Phylogeny 
MRIcron  NIfTI format image viewer 
PBMPI  Bayesian phylogenetic reconstruction 
Prodigal  Proteincoding gene prediction. 
Prokka  Annotate bacterial, archaeal and viral genomes 
R & bioconductor  Statistical computing and graphics. Includes bioconductor. 
RAxML  Maximum Likelihood based inference of large phylogenetic trees 
Relion  Statistical CryoEM reconstruction 
RepeatMasker  screens DNA sequences for interspersed repeats and low complexity DNA sequences 
Rosetta Commons  Algorithms for computational modeling and analysis of protein structures 
RSEM  Software package for estimating gene and isoform expression levels from RNASeq data 
Salmon  Transcript quantification from RNAseq data 
SNPTest  Program for the analysis of single SNP association in genomewide studies. 
SPAdes  Genome assembler toolkit 
STAR  Spliced Transcripts Alignment to a Reference 
Structure  Software package for using multilocus genotype data to investigate population structure. 
subread  a tool kit for processing nextgen sequencing data 
TEtranscripts  Including transposable elements in differential enrichment analysis of sequencing datasets. 
Trimmomatic  Program to perform a variety of useful trimming tasks for Illumina pairedend and single ended data. 
UKBioBank Helper Modulefile  Environment variables to help access UK BioBank fullrelease datasets. 
USEARCH  Sequence analysis tool 
VSEARCH  Sequence analysis tool 
Computational Chemistry and Molecular Dynamics
PACKAGE  NOTES 

acpype  Generate topologies for chemical compounds 
ADF  Amsterdam Modeling Suite (DFT, semiempirical, reactive force fields and fluid thermodynamics) 
AIMall  Software for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems. 
AMBER  A general purpose molecular mechanics/dynamics suite 
Autodock4 and Vina  Autodock4 and Vina – Molecular docking tools 
CASTEP  CASTEP is a leading code for calculating the properties of materials from first principles 
CASTEPconv  Script to automate CASTEP convergence calculations 
CHARMM  Macromolecular mechanics 
ChemShell  Interactive shell for computational chemistry calculations 
Chimera  UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures. 
CP2K  Atomistic and molecular simulations 
CRYSTAL  Ab initio simulations of periodic systems 
Crystal Analysis Tool (draft)  Code for analysing output of atomistic simulations 
DL_MESO  General purpose mesoscale simulation package. LBE and DPD. 
DL_MONTE2  Monte Carlo simulation of condensed phases. 
DL_POLY  General purpose classical molecular dynamics 
Gaussian 09  Performs semiempirical and abinitio molecular orbital calculations 
Gaussian 16  Performs semiempirical and abinitio molecular orbital calculations 
Geant 4  Geant4 is a toolkit for the simulation of the passage of particles through matter. 
Gold suite  Protein Docking 
gpyro  Open source computer model that describes the thermal response of solid materials exposed to radiative or convective heating, including thermooxidative pyrolysis of the condensed phase. 
GROMACS  Molecular Dynamics simulation package. 
HOOMDblue  Hardparticle Monte Carlo simulations toolkit 
LAMMPS  Classical molecular dynamics code. 
Materials Studio  Materials modelling and simulation application (chemical, materials, pharmaceutical) 
MOLCAS@UU  Ab initio quantum chemistry software 
MOLDEN  Molecular Graphics Visualisation Tool 
Molpro  Ab initio quantum chemistry software 
NAMD  21.02.2019  This application is being installed. Docs will be updated when it is available. 
NBO  Natural Bond Orbital program (Electron analysis) 
NWChem  ab initio quantum chemistry 
ONETEP  Linearscaling code for quantummechanical calculations based on densityfunctional theory. 
Openbabel  Open Babel is a chemical toolbox designed to search, convert, analyze, or store data from molecular modelling, chemistry, solidstate materials, biochemistry, or related areas. 
OpenMolcas  Quantum chemistry software package using a multiconfigurational approach to the electronic structure. 
ORCA  Ab initio, DFT and semiempirical SCFMO package for quantum chemistry 
Packmol  Initial configurations for Molecular Dynamics Simulations by packing optimization 
Phenix and Rosetta Commons  Pythonbased Hierarchical ENvironment for Integrated Xtallography 
PubChemPy  PubChem interaction in Python 
Quantum Espresso  Ab initio simulations of periodic systems 
Rosetta Commons  Algorithms for computational modeling and analysis of protein structures 
Towhee  Towhee is a Monte Carlo molecular simulation code. 
TURBOMOLE  Quantum chemistry – electronic structure calculations 
UMMAP  UMMAP is a trajectory analysis package for molecular dynamics type simulations. 
VASP  The Vienna Ab initio Simulation Package 
Visual Colloids  Visual Colloids is used to produce images of colloidal systems. 
Votca  VOTCA is a software package which focuses on the analysis of molecular dynamics data. 
WPS  Weather Research and Forecasting Preprocessors 
WRF  Weather Research and Forecasting 
WRFChem  21.02.2019  This application is being installed. Docs will be updated when it is available. 
Computational Fluid Dynamics
PACKAGE  NOTES 

CFX  CFX is a general purpose fluid dynamics product from ANSYS 
Code_Saturne  21.02.2019  This application is being installed. Docs will be updated when it is available. 
FDS  Largeeddy simulation (LES) code for lowspeed flows, with an emphasis on smoke and heat transport from fires. 
Fluent  A computational fluid dynamics package 
GeoChemFoam  An open source porescale numerical simulator based on OpenFOAM 
LSDYNA  A general purpose explicit solver from ANSYS 
OpenFOAM  Fluid dynamics platform 
StarCCM+  A computation continuum mechanics application 
Telemac  Freesurface flow solvers. 
Finite Element Analysis
PACKAGE  NOTES 

ABAQUS  Finite Element Analysis package 
Ansys Mechanical  Ansys finite element analysis application 
Code_Aster  21.02.2019  This application is being installed. Docs will be updated when it is available. 
DAMASK  DAMASK is used for the simulation of crystal plasticity within a finitestrain continuum mechanical framework. 
PRISMSPF  Parallel finite element code for microstructural evolution 
Mathematics
PACKAGE  NOTES 

Dakota  A Multilevel Parallel ObjectOriented Optimization Framework 
Julia  Power mathematical programming and scripting language with native parallel capability 
Jupyter Notebook  Webbased python notebook 
Keras  Neural Network python API using Tensorflow 
Mathematica  Numeric and symbolic computing and programming 
MATLAB  Numerical computation, visualization and programming 
Microsoft R Open (MRO)  Statistical computing and graphics. Includes bioconductor. 
MKL  Intel Math Kernel Library of optimized maths routines 
NAG Libraries  User callable routines for mathematical and statistical computation 
PRISMSPF  Parallel finite element code for microstructural evolution 
PyTorch  Deep learning framework in python 
R & bioconductor  Statistical computing and graphics. Includes bioconductor. 
RStudio  GUIbased development environment for R 
Multiphysics and solvers
PACKAGE  NOTES 

ANSWERS  A suite of montecarlo nuclear simulation tools 
COMSOL  Multiphysics solver 
Dakota  A Multilevel Parallel ObjectOriented Optimization Framework 
EMsoft  Computation and visualization of scanning electron microscopy diffraction patterns. 
Geant 4  Geant4 is a toolkit for the simulation of the passage of particles through matter. 
gprMax  Electromagnetic wave propagation simulation 
HOOMDblue  Hardparticle Monte Carlo simulations toolkit 
mumax  GPUaccelerated micromagnetic simulation 
PRISMSPF  Parallel finite element code for microstructural evolution 
Serpent  Montecarlo Nuclear reactor physics 
Neural Networks and Machine Learning
PACKAGE  NOTES 

Chainer  Deeplearning GPUcapable framework in python 
cudatorch  GPU enabled machine learning framework 
DeepLabCut  Tensorflow based markerless pose estimation of animals performing various tasks. 
Keras  Neural Network python API using Tensorflow 
lens (Light Efficient Network Simulator)  Lens is an efficient, yet flexible, neural network simulator that runs on a variety of platforms, is able to handle large, complex simulations 
Monai  Framework for deep learning in healthcare imaging 
PyTorch  Deep learning framework in python 
Tensorflow  Data flow graph processing on GPUs and CPUs 
Programming and Development
PACKAGE  NOTES 

Anaconda Python  A scientific python distribution 
Apache Spark  Cluster computing with Hadoop 
Boost  C++ library. 
Chainer  Deeplearning GPUcapable framework in python 
cmake  Crossplatform, opensource build system 
Flame  Agentbased modelling system 
git & gitlfs  Version Control 
GNU Compilers  gcc, g++ and gfortran 
HOOMDblue  Hardparticle Monte Carlo simulations toolkit 
Java Compilers  Java compiler 
Julia  Power mathematical programming and scripting language with native parallel capability 
Jupyter Notebook  Webbased python notebook 
Keras  Neural Network python API using Tensorflow 
MATLAB  Numerical computation, visualization and programming 
Microsoft R Open (MRO)  Statistical computing and graphics. Includes bioconductor. 
MKL  Intel Math Kernel Library of optimized maths routines 
MPI (OpenMPI)  Message Passing Interface library 
NAG Libraries  User callable routines for mathematical and statistical computation 
OpenMP  Open MultiProcessing library 
PRISMSPF  Parallel finite element code for microstructural evolution 
PyTorch  Deep learning framework in python 
R & bioconductor  Statistical computing and graphics. Includes bioconductor. 
RStudio  GUIbased development environment for R 
Singularity  Container execution 
SQLite browser (DB4S)  Graphical browser for sqlite files 
Subversion (svn)  Version Control 
TBB  Intel Thread Building Blocks for parallel software development. 
Tensorflow  Data flow graph processing on GPUs and CPUs 
GPU capable
PACKAGE  NOTES 

ABAQUS  Finite Element Analysis package 
AMBER  A general purpose molecular mechanics/dynamics suite 
Chainer  Deeplearning GPUcapable framework in python 
CP2K  Atomistic and molecular simulations 
cudatorch  GPU enabled machine learning framework 
DeepLabCut  Tensorflow based markerless pose estimation of animals performing various tasks. 
EMsoft  Computation and visualization of scanning electron microscopy diffraction patterns. 
FSL  Library of analysis tools for FMRI, MRI and DTI brain imaging data 
gprMax  Electromagnetic wave propagation simulation 
GROMACS  Molecular Dynamics simulation package. 
Guppy  GPU enabled basecaller 
HOOMDblue  Hardparticle Monte Carlo simulations toolkit 
Keras  Neural Network python API using Tensorflow 
LAMMPS  Classical molecular dynamics code. 
Medaka  Create a consensus sequence from nanopore sequencing data 
MEGAHIT  Fast metagenomics assembly tool 
mumax  GPUaccelerated micromagnetic simulation 
PyTorch  Deep learning framework in python 
Relion  Statistical CryoEM reconstruction 
Tensorflow  Data flow graph processing on GPUs and CPUs 
Visualization
PACKAGE  NOTES 

ANSWERS  A suite of montecarlo nuclear simulation tools 
Compucell3d  Virtual Tissue in silico simulation modelling environment. 
Dakota  A Multilevel Parallel ObjectOriented Optimization Framework 
FEPX  Polycrystal Generation and Meshing 
Freesurfer  Visualisation of structural and functional brain imaging data 
FSL  Library of analysis tools for FMRI, MRI and DTI brain imaging data 
Gold suite  Protein Docking 
Grace / xmgrace  2D interactive plotting tool 
Jupyter Notebook  Webbased python notebook 
Mathematica  Numeric and symbolic computing and programming 
MATLAB  Numerical computation, visualization and programming 
Microsoft R Open (MRO)  Statistical computing and graphics. Includes bioconductor. 
MOLDEN  Molecular Graphics Visualisation Tool 
MRIcron  NIfTI format image viewer 
mumax  GPUaccelerated micromagnetic simulation 
Neper  Polycrystal Generation and Meshing 
ovito  Scientific visualization and analysis of atomistic simulation data 
ParaView  Scientific data visualization using parallel software rendering. 
Pymol  Pymol is a molecular visualisation tool. 
R & bioconductor  Statistical computing and graphics. Includes bioconductor. 
RStudio  GUIbased development environment for R 
Visual Colloids  Visual Colloids is used to produce images of colloidal systems. 
VMD  Molecular Graphics Visualisation Tool 
Python Packages
PACKAGE  NOTES 

acpype  Generate topologies for chemical compounds 
AMICO  Diffusion magnetic resonance data processing in python 
DeepLabCut  Tensorflow based markerless pose estimation of animals performing various tasks. 
eggNOG mapper  Fast functional annotation of novel sequences. 
Fasta_number  Replace FASTA labels with xxx1, xxx2, xxx3 etc, where xxx is a prefix provided as a commendline argument. Used e.g. to label OTUs as OTU_1, OTU_2 etc. 
FeGenie  Identify potential homologs and operons that may be linked to the microbial iron cycle 
GenX  Refine xray, neutron reflectivity data and surface xray diffraction data 
gprMax  Electromagnetic wave propagation simulation 
GTDBtk  Toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy. 
HOOMDblue  Hardparticle Monte Carlo simulations toolkit 
MACS  Modelbased Analysis of ChIPSeq (MACS) 
Medaka  Create a consensus sequence from nanopore sequencing data 
Monai  Framework for deep learning in healthcare imaging 
PubChemPy  PubChem interaction in Python 
pyroppl  Universal probabilistic programming language (PPL) written in Python and supported by PyTorch on the backend 
PyTorch  Deep learning framework in python 
scikitcuda  Python interfaces to many of the functions in the CUDA device/runtime libraries. 
Tensorflow  Data flow graph processing on GPUs and CPUs 
TEtranscripts  Including transposable elements in differential enrichment analysis of sequencing datasets. 