The Computational Shared Facility 3

Applications

Software that can be categorized as ‘Applications’, i.e., not compilers, tools etc. For a full list see the A-Z list.

Available application categories: Bio-inf Chemistry CFD FEA Mathematics Physics Machine-learning Programming GPU-capable Visualization Python-packages

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)

PACKAGENOTES
Affymetrix Power Tools (APT)Algorithms for analyzing and working with GeneChip™ arrays
Alphafoldapplication for predicting models of protein structures
AMICODiffusion magnetic resonance data processing in python
Asperaascp fast downloader
BBToolsSuite of tools designed for analysis of DNA and RNA sequence data.
Bio-informatics Helper ModulefileModulefile to make more Bio-informatics apps available
BLASTsuite of tools for comparing primary biological sequence information
Bowtie2tool for aligning sequencing reads to long reference sequences.
bwa-mem2Burrow-Wheeler Aligner
CanuHierarchical assembly pipeline for high-noise single-molecule sequencing.
CheckMQuality assessment of genomes recovered from isolates, single cells, or metagenomes.
Compucell3dVirtual Tissue in silico simulation modelling environment.
DiamondSequence aligner for protein and translated DNA searches
eggNOG mapperFast functional annotation of novel sequences.
Fasta_numberReplace FASTA labels with xxx1, xxx2, xxx3 etc, where xxx is a prefix provided as a commend-line argument. Used e.g. to label OTUs as OTU_1, OTU_2 etc.
FastANIFast alignment-free computation of whole-genome Average Nucleotide Identity
FastTreeInfer approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
FeGenieIdentify potential homologs and operons that may be linked to the microbial iron cycle
GTDB-tkToolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy.
GuppyGPU enabled basecaller
HMMRATACHMMRATAC peak caller for ATAC-seq data
HOMERSoftware for motif discovery and next generation sequencing analysis
InterProScanScan sequences against InterPro's member database signatures
JAGSProgram for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.
KaijuTaxonomic classification of high-throughput sequencing reads.
MACSModel-based Analysis of ChIP-Seq (MACS)
MaxBinBinning assembled metagenomic sequences
MedakaCreate a consensus sequence from nanopore sequencing data
MEGAHITFast metagenomics assembly tool
MemeSuiteMotif-based sequence analysis tools
Microsoft R Open (MRO)Statistical computing and graphics. Includes bioconductor.
Minimap2Sequence alignment
miRDeep2Discovers active known or novel miRNAs from deep sequencing data
MothurTool for processing data generated from several DNA sequencing methods
MrBayesBayesian Inference of Phylogeny
MRIcronNIfTI format image viewer
PBMPIBayesian phylogenetic reconstruction
ProdigalProtein-coding gene prediction.
ProkkaAnnotate bacterial, archaeal and viral genomes
R & bioconductorStatistical computing and graphics. Includes bioconductor.
RAxMLMaximum Likelihood based inference of large phylogenetic trees
RelionStatistical Cryo-EM reconstruction
RepeatMasker screens DNA sequences for interspersed repeats and low complexity DNA sequences
Rosetta CommonsAlgorithms for computational modeling and analysis of protein structures
RSEMSoftware package for estimating gene and isoform expression levels from RNA-Seq data
SalmonTranscript quantification from RNA-seq data
SNPTestProgram for the analysis of single SNP association in genome-wide studies.
SPAdesGenome assembler toolkit
STARSpliced Transcripts Alignment to a Reference
StructureSoftware package for using multi-locus genotype data to investigate population structure.
subreada tool kit for processing next-gen sequencing data
TEtranscriptsIncluding transposable elements in differential enrichment analysis of sequencing datasets.
TrimmomaticProgram to perform a variety of useful trimming tasks for Illumina paired-end and single ended data.
UKBioBank Helper ModulefileEnvironment variables to help access UK BioBank full-release datasets.
USEARCHSequence analysis tool
VSEARCHSequence analysis tool

Computational Chemistry and Molecular Dynamics

PACKAGENOTES
acpypeGenerate topologies for chemical compounds
ADFAmsterdam Modeling Suite (DFT, semi-empirical, reactive force fields and fluid thermodynamics)
AIMallSoftware for performing quantitative and visual QTAIM (Quantum Theory of Atoms in Molecules) analyses of molecular systems.
AMBERA general purpose molecular mechanics/dynamics suite
Autodock4 and VinaAutodock4 and Vina – Molecular docking tools
CASTEPCASTEP is a leading code for calculating the properties of materials from first principles
CASTEPconvScript to automate CASTEP convergence calculations
CHARMMMacromolecular mechanics
ChemShellInteractive shell for computational chemistry calculations
ChimeraUCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures.
CP2KAtomistic and molecular simulations
CRYSTALAb initio simulations of periodic systems
Crystal Analysis Tool (draft)Code for analysing output of atomistic simulations
DL_MESOGeneral purpose mesoscale simulation package. LBE and DPD.
DL_MONTE2Monte Carlo simulation of condensed phases.
DL_POLYGeneral purpose classical molecular dynamics
Gaussian 09Performs semi-empirical and ab-initio molecular orbital calculations
Gaussian 16Performs semi-empirical and ab-initio molecular orbital calculations
Geant 4Geant4 is a toolkit for the simulation of the passage of particles through matter.
Gold suiteProtein Docking
gpyroOpen source computer model that describes the thermal response of solid materials exposed to radiative or convective heating, including thermo-oxidative pyrolysis of the condensed phase.
GROMACSMolecular Dynamics simulation package.
HOOMD-blueHard-particle Monte Carlo simulations toolkit
LAMMPSClassical molecular dynamics code.
Materials StudioMaterials modelling and simulation application (chemical, materials, pharmaceutical)
MOLCAS@UUAb initio quantum chemistry software
MOLDENMolecular Graphics Visualisation Tool
MolproAb initio quantum chemistry software
NAMD21.02.2019 - This application is being installed. Docs will be updated when it is available.
NBONatural Bond Orbital program (Electron analysis)
NWChemab initio quantum chemistry
ONETEPLinear-scaling code for quantum-mechanical calculations based on density-functional theory.
OpenbabelOpen Babel is a chemical toolbox designed to search, convert, analyze, or store data from molecular modelling, chemistry, solid-state materials, biochemistry, or related areas.
OpenMolcasQuantum chemistry software package using a multiconfigurational approach to the electronic structure.
ORCAAb initio, DFT and semiempirical SCF-MO package for quantum chemistry
PackmolInitial configurations for Molecular Dynamics Simulations by packing optimization
Phenix and Rosetta CommonsPython-based Hierarchical ENvironment for Integrated Xtallography
PubChemPyPubChem interaction in Python
Quantum EspressoAb initio simulations of periodic systems
Rosetta CommonsAlgorithms for computational modeling and analysis of protein structures
TowheeTowhee is a Monte Carlo molecular simulation code.
TURBOMOLEQuantum chemistry – electronic structure calculations
UMMAPUMMAP is a trajectory analysis package for molecular dynamics type simulations.
VASPThe Vienna Ab initio Simulation Package
Visual ColloidsVisual Colloids is used to produce images of colloidal systems.
VotcaVOTCA is a software package which focuses on the analysis of molecular dynamics data.
WPSWeather Research and Forecasting Preprocessors
WRFWeather Research and Forecasting
WRF-Chem21.02.2019 - This application is being installed. Docs will be updated when it is available.

Computational Fluid Dynamics

PACKAGENOTES
CFXCFX is a general purpose fluid dynamics product from ANSYS
Code_Saturne21.02.2019 - This application is being installed. Docs will be updated when it is available.
FDSLarge-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires.
FluentA computational fluid dynamics package
GeoChemFoamAn open source pore-scale numerical simulator based on OpenFOAM
LS-DYNAA general purpose explicit solver from ANSYS
OpenFOAMFluid dynamics platform
StarCCM+A computation continuum mechanics application
TelemacFree-surface flow solvers.

Finite Element Analysis

PACKAGENOTES
ABAQUSFinite Element Analysis package
Ansys MechanicalAnsys finite element analysis application
Code_Aster21.02.2019 - This application is being installed. Docs will be updated when it is available.
DAMASKDAMASK is used for the simulation of crystal plasticity within a finite-strain continuum mechanical framework.
PRISMS-PFParallel finite element code for microstructural evolution

Mathematics

PACKAGENOTES
DakotaA Multilevel Parallel Object-Oriented Optimization Framework
JuliaPower mathematical programming and scripting language with native parallel capability
Jupyter NotebookWeb-based python notebook
KerasNeural Network python API using Tensorflow
MathematicaNumeric and symbolic computing and programming
MATLABNumerical computation, visualization and programming
Microsoft R Open (MRO)Statistical computing and graphics. Includes bioconductor.
MKLIntel Math Kernel Library of optimized maths routines
NAG LibrariesUser callable routines for mathematical and statistical computation
PRISMS-PFParallel finite element code for microstructural evolution
PyTorchDeep learning framework in python
R & bioconductorStatistical computing and graphics. Includes bioconductor.
RStudioGUI-based development environment for R

Multi-physics and solvers

PACKAGENOTES
ANSWERSA suite of monte-carlo nuclear simulation tools
COMSOLMultiphysics solver
DakotaA Multilevel Parallel Object-Oriented Optimization Framework
EMsoftComputation and visualization of scanning electron microscopy diffraction patterns.
Geant 4Geant4 is a toolkit for the simulation of the passage of particles through matter.
gprMaxElectromagnetic wave propagation simulation
HOOMD-blueHard-particle Monte Carlo simulations toolkit
mumaxGPU-accelerated micromagnetic simulation
PRISMS-PFParallel finite element code for microstructural evolution
SerpentMonte-carlo Nuclear reactor physics

Neural Networks and Machine Learning

PACKAGENOTES
ChainerDeep-learning GPU-capable framework in python
cuda-torchGPU enabled machine learning framework
DeepLabCutTensorflow based markerless pose estimation of animals performing various tasks.
KerasNeural 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
MonaiFramework for deep learning in healthcare imaging
PyTorchDeep learning framework in python
TensorflowData flow graph processing on GPUs and CPUs

Programming and Development

PACKAGENOTES
Anaconda PythonA scientific python distribution
Apache SparkCluster computing with Hadoop
BoostC++ library.
ChainerDeep-learning GPU-capable framework in python
cmakeCross-platform, open-source build system
FlameAgent-based modelling system
git & git-lfsVersion Control
GNU Compilersgcc, g++ and gfortran
HOOMD-blueHard-particle Monte Carlo simulations toolkit
Java CompilersJava compiler
JuliaPower mathematical programming and scripting language with native parallel capability
Jupyter NotebookWeb-based python notebook
KerasNeural Network python API using Tensorflow
MATLABNumerical computation, visualization and programming
Microsoft R Open (MRO)Statistical computing and graphics. Includes bioconductor.
MKLIntel Math Kernel Library of optimized maths routines
MPI (OpenMPI)Message Passing Interface library
NAG LibrariesUser callable routines for mathematical and statistical computation
OpenMPOpen Multi-Processing library
PRISMS-PFParallel finite element code for microstructural evolution
PyTorchDeep learning framework in python
R & bioconductorStatistical computing and graphics. Includes bioconductor.
RStudioGUI-based development environment for R
SingularityContainer execution
SQLite browser (DB4S)Graphical browser for sqlite files
Subversion (svn)Version Control
TBBIntel Thread Building Blocks for parallel software development.
TensorflowData flow graph processing on GPUs and CPUs

GPU capable

PACKAGENOTES
ABAQUSFinite Element Analysis package
AMBERA general purpose molecular mechanics/dynamics suite
ChainerDeep-learning GPU-capable framework in python
CP2KAtomistic and molecular simulations
cuda-torchGPU enabled machine learning framework
DeepLabCutTensorflow based markerless pose estimation of animals performing various tasks.
EMsoftComputation and visualization of scanning electron microscopy diffraction patterns.
FSLLibrary of analysis tools for FMRI, MRI and DTI brain imaging data
gprMaxElectromagnetic wave propagation simulation
GROMACSMolecular Dynamics simulation package.
GuppyGPU enabled basecaller
HOOMD-blueHard-particle Monte Carlo simulations toolkit
KerasNeural Network python API using Tensorflow
LAMMPSClassical molecular dynamics code.
MedakaCreate a consensus sequence from nanopore sequencing data
MEGAHITFast metagenomics assembly tool
mumaxGPU-accelerated micromagnetic simulation
PyTorchDeep learning framework in python
RelionStatistical Cryo-EM reconstruction
TensorflowData flow graph processing on GPUs and CPUs

Visualization

PACKAGENOTES
ANSWERSA suite of monte-carlo nuclear simulation tools
Compucell3dVirtual Tissue in silico simulation modelling environment.
DakotaA Multilevel Parallel Object-Oriented Optimization Framework
FEPXPolycrystal Generation and Meshing
FreesurferVisualisation of structural and functional brain imaging data
FSLLibrary of analysis tools for FMRI, MRI and DTI brain imaging data
Gold suiteProtein Docking
Grace / xmgrace2D interactive plotting tool
Jupyter NotebookWeb-based python notebook
MathematicaNumeric and symbolic computing and programming
MATLABNumerical computation, visualization and programming
Microsoft R Open (MRO)Statistical computing and graphics. Includes bioconductor.
MOLDENMolecular Graphics Visualisation Tool
MRIcronNIfTI format image viewer
mumaxGPU-accelerated micromagnetic simulation
NeperPolycrystal Generation and Meshing
ovitoScientific visualization and analysis of atomistic simulation data
ParaViewScientific data visualization using parallel software rendering.
PymolPymol is a molecular visualisation tool.
R & bioconductorStatistical computing and graphics. Includes bioconductor.
RStudioGUI-based development environment for R
Visual ColloidsVisual Colloids is used to produce images of colloidal systems.
VMDMolecular Graphics Visualisation Tool

Python Packages

PACKAGENOTES
acpypeGenerate topologies for chemical compounds
AMICODiffusion magnetic resonance data processing in python
DeepLabCutTensorflow based markerless pose estimation of animals performing various tasks.
eggNOG mapperFast functional annotation of novel sequences.
Fasta_numberReplace FASTA labels with xxx1, xxx2, xxx3 etc, where xxx is a prefix provided as a commend-line argument. Used e.g. to label OTUs as OTU_1, OTU_2 etc.
FeGenieIdentify potential homologs and operons that may be linked to the microbial iron cycle
GenXRefine x-ray, neutron reflectivity data and surface x-ray diffraction data
gprMaxElectromagnetic wave propagation simulation
GTDB-tkToolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy.
HOOMD-blueHard-particle Monte Carlo simulations toolkit
MACSModel-based Analysis of ChIP-Seq (MACS)
MedakaCreate a consensus sequence from nanopore sequencing data
MonaiFramework for deep learning in healthcare imaging
PubChemPyPubChem interaction in Python
pyro-pplUniversal probabilistic programming language (PPL) written in Python and supported by PyTorch on the backend
PyTorchDeep learning framework in python
scikit-cudaPython interfaces to many of the functions in the CUDA device/runtime libraries.
TensorflowData flow graph processing on GPUs and CPUs
TEtranscriptsIncluding transposable elements in differential enrichment analysis of sequencing datasets.

Last modified on March 19, 2021 at 10:15 am by George Leaver