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This page lists software in use at various SNIC centres.
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This page lists software in use at various SNIC centres. Note that the centres can in most cases install additional software if there is need for it, and if so, please contact centre support directly through the standard [[Support|support channels]].
  
 
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Latest revision as of 13:59, 12 September 2011

This page lists software in use at various SNIC centres. Note that the centres can in most cases install additional software if there is need for it, and if so, please contact centre support directly through the standard support channels.

 FieldDescription
ABINITComputational chemistry
Computational materials science
density-functional theory code
ABySSBioinformaticsA parallel assembler for short read sequence data
ACMLSystem tool
Numerical library
efficient mathematics library
ANFOBioinformaticsA parallel assembler for short read sequence data
ANNOVARBioinformaticsFunctional annotation of genetic variants from high-throughput sequencing data
ANSYSComputational fluid dynamicslarge modeling suite
ARC clientSwestore
Grid computing
tool for accessing the Grid resources
ASEComputational materials scienceframework for setting up and analyzing atomistic simulations
Ab wtpBioinformaticsAlignment tool for SOLiD transcript reads
AbaqusSolid mechanicsfinite-element package
AmberComputational chemistry
Molecular dynamics
molecular dynamics
BEDToolsBioinformaticsBEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format
BLASTBioinformaticspackage for aligning nucleotide or amino acid sequences
BLATBioinformaticsan alignment tool like BLAST, but it is structured differently.
BWABioinformaticsA fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target).
BclConverterBioinformaticsConverts bcl files to Qseq files.
BioPerlBioinformaticsA community effort to produce Perl code which is useful in biology.
BioPythonBioinformaticsA set of freely available tools for biological computation written in Python by an international team of developers.
BioscopeBioinformaticsthe pipeline stack that comes with the solid sequence platform
BowtieBioinformaticsBowtie is an ultrafast, memory-efficient short read aligner.
CASAVABioinformaticsIllumina's Consensus Assessment of Sequence and Variation (CASAVA) software
CASTEPComputational chemistry
Computational materials science
electronic structure calculation
CDOClimate researchdata analysis
CESM1Climate researchglobal climate model
CP2KComputational chemistry
Computational materials science
atomistic and molecular simulations code
CPMDComputational chemistry
Computational materials science
plane-wave DFT
CS-RosettaBioinformaticsde novo protein structure generation
CSABioinformaticsPython implementation of the Connection-set Algebra (Djurfeldt 2012)
Ccp4Visualisation
Structural biology
determining macromolecular structures by X-ray crystallography
CharmmComputational chemistryatomistic and molecular simulations code
ClustalWBioinformaticspopular multiple sequence aligner
ComsolComputational materials science
Computational fluid dynamics
Commercial Mulitphysics Similation software
ConcaterpillarBioinformaticsA hierarchical likelihood ratio test for phylogenetic congruence.
CootVisualisation
Structural biology
software for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data
CufflinksBioinformaticsAssembles transcripts in RNA-Seq samples and calculates their abundances
CyanaBioinformatics
Structural biology
biological macromolecule structure calculation based on NMR conformational constraints
DDTSystem toolDebugger
DIANASolid mechanicscommercial FEM package
DacapoComputational chemistry
Computational materials science
plane-wave DFT
DaltonComputational chemistrypowerful molecular electronic structure program.
DesmondComputational chemistry
Molecular dynamics
molecular dynamics package
EC-EarthClimate researchglobal climate model
EMBOSSBioinformaticsA free Open Source software analysis package developed for the molecular biology.
EMMAXBioinformaticsA statistical test for large scale human or model organism association mapping accounting for the sample structure.
EMTOComputational materials scienceExact Muffin-Tin Orbitals method, an electronic structure code based on the Green's function technique
EMTOxComputational materials scienceExact Muffin-Tin Orbitals method (x), an electronic structure code based on the Green's function technique
ESPResSoComputational chemistry
Computational materials science
molecular dynamics of soft matter systems
EdgeComputational fluid dynamicsunstructured CFD solver
EfieldComputational electromagneticssimulation environment for electromagnetic simulations
ElkComputational chemistry
Computational materials science
all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features
... further results

See also