Difference between revisions of "UFRC Help and Documentation"

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! Software !! Version !! Home Website !! Category !! Notes
 
! Software !! Version !! Home Website !! Category !! Notes
 
|-
 
|-
−
| [[Abaqus]] || 6.6-1, 6.9-2 || || Simulation||
+
| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html Abaqus] || Simulation||
 
|-
 
|-
 
| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ admb-project.org] || Modeling, math ||
 
| [[ADMB]] || 9.1, 10.0 || [http://admb-project.org/ admb-project.org] || Modeling, math ||
Line 40: Line 40:
 
|-
 
|-
 
| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ SF.net] || Backup ||  
 
| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ SF.net] || Backup ||  
−
|-
 
−
| [[Newbler|denovo]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
 
 
|-
 
|-
 
| [[Desmond]] || 2.4.2.1 || [http://www.deshawresearch.com/resources_desmond.html www.deshawresearch.com/resources_desmond.html Desmond] || Simulation, Biology, Chemistry ||
 
| [[Desmond]] || 2.4.2.1 || [http://www.deshawresearch.com/resources_desmond.html www.deshawresearch.com/resources_desmond.html Desmond] || Simulation, Biology, Chemistry ||
Line 51: Line 49:
 
| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ emboss.sourceforge.net] || Biology, multi-tool suite ||
 
| [[emboss]] || 6.4.0 || [http://emboss.sourceforge.net/ emboss.sourceforge.net] || Biology, multi-tool suite ||
 
|-
 
|-
−
| [[espresso]] || 3.0, 3.2.2, 4.0.4 || [http://www.quantum-espresso.org/ quantum-espresso.org]
+
| [[espresso]] || 3.0, 3.2.2, 4.0.4 || [http://www.quantum-espresso.org/ quantum-espresso.org] || Modeling, Physics ||
 
|-
 
|-
−
| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC website]
+
| [[fastqc]] || 0.10.0 || [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ FastQC website] || Biology, NGS ||
 
|-
 
|-
−
| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ www.gaussian.com]
+
| [[fftw]] || 2.1.5, 3.1.2 || [http://www.fftw.org/ FFTW Gaussian] || Math, Library, C++ ||
 
|-
 
|-
−
| [[fluent]] || 6.3.26 ||
+
| [[fluent]] || 6.3.26 || [http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/ANSYS+FLUENT ANSYS FLUENT] || Simulation ||
 
|-
 
|-
−
| [[gadget]] || 2.0.4, 2.0.5 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes Atlassian Gadgets website]
+
| [[gadget]] || 2.0.4, 2.0.5 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes Atlassian Gadgets] || Software Development ||
 
|-
 
|-
−
| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ www.msg.ameslab.gov/gamess]
+
| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ www.msg.ameslab.gov/gamess GAMESS]|| Quantum Chemistry||
 
|-
 
|-
−
| [[gaussian]] || 03,09 || [http://www.gaussian.com/ www.gaussian.com]
+
| [[gaussian]] || 03,09 || [http://www.gaussian.com/ Gaussian]||Modeling, Physics||
 
|-
 
|-
−
| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ www.gromacs.org]
+
| [[Gromacs]] || 4.0.4, 4.0.7 || [http://www.gromacs.org/ www.gromacs.org]||Physics, Modeling||
 
|-
 
|-
−
| [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html Lawrence Livermore National Labs]
+
| [[hypre]] || 2.0.0 || [http://www.llnl.gov/casc/hypre/software.html HYPRE]||Library, Math, Physics||
 
|-
 
|-
−
| [[Inelastica]] || 1.1 ||
+
| [[Inelastica]] || 1.1 || [http://sourceforge.net/projects/inelastica/ Inelastica]||Quantum Chemistry||
 
|-
 
|-
−
| [[IE3D]] || 15.1 ||
+
| [[IE3D]] || 15.1 || [http://www.mentor.com/electromagnetic-simulation/ IE3D]||Simulation, Design||
 
|-
 
|-
−
| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS Home Page]
+
| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS]||Simulation||
 
|-
 
|-
−
| [[madness]] || 0.9 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS Home Page]
+
| [[madness]] || 0.9 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS Home Page]||Math, DIff. Equation solving||
 
|-
 
|-
−
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT Home Page]
+
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT]||Biology, Multiple sequence alignment||
 
|-
 
|-
−
| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS Home Page]
+
| [[MACS]] || 1.4.1 || [http://liulab.dfci.harvard.edu/MACS/ MACS]||Biology, ChIP-Seq||
 
|-
 
|-
−
| [[Matlab]] || 2009b || [http://www.mathworks.com www.mathworks.com]
+
| [[Matlab]] || 2009b || [http://www.mathworks.com MathWorks]||Math, Simulation, Programming||
 
|-
 
|-
−
| [[meep]] || 0.10.0, 0.20.3 ||
+
| [[meep]] || 0.10.0, 0.20.3 || || Will be removed on 2011-10-30
 
|-
 
|-
−
| [[meme]] || 3.0.13, 4.3.0 ||
+
| [[meme]] || 3.0.13, 4.3.0 || [http://meme.nbcr.net/meme/intro.html MEME]||Biology, Motifs, Sequence analysis||
 
|-
 
|-
−
| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis glaros.dtc.umn.edu]
+
| [[metis]] || 4.0 || [http://glaros.dtc.umn.edu/gkhome/views/metis Metis]||Math, Graph partitioning||
 
|-
 
|-
−
| [[mira]] || 3.2.0 ||
+
| [[mira]] || 3.2.0 || [http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html#sect_intro_whatismira MIRA Guide]||Biology, NGS||
 
|-
 
|-
−
| [[MrBayes]] || 3.1.2 || [http://mrbayes.scs.fsu.edu/ mrbayes.scs.fsu.edu]
+
| [[MrBayes]] || 3.1.2 || [http://mrbayes.scs.fsu.edu/ MrBayes]||Biology, Phylogenetics||
 
|-
 
|-
−
| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ www.ks.uiuc.edu]
+
| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ NAMD]||Simulation, Chemistry, Biology||
 
|-
 
|-
−
| [[netcdf]] || 3.6.3, 4.1.2 ||
+
| [[netcdf]] || 3.6.3, 4.1.2 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF|| Data exchange, Tools ||
 
|-
 
|-
−
| [[Newbler]] || 2.5.3, 2.6 ||
+
| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
 
|-
 
|-
−
| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page http://www.nwchem-sw.org]
+
| [[NWChem]] || 6.0 || [http://www.nwchem-sw.org/index.php/Main_Page NWChem]||Simulation, Chemistry||
 
|-
 
|-
−
| [[OpenFOAM]] || 1.7.1 ||  
+
| [[OpenFOAM]] || 1.7.1 || [http://www.openfoam.com/ OpenFoam]||Molecular Dynamics||
 
|-
 
|-
−
| [[papi]] || 4.1.2.1 ||  
+
| [[papi]] || 4.1.2.1 || [http://icl.cs.utk.edu/papi/software/index.html PAPI]||CPU API||
 
|-
 
|-
−
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html Upstream sofware page]
+
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html PeakSplitter]||Biology, Chip-Seq||
 
|-
 
|-
 
| [[pdt]] || 3.16 ||
 
| [[pdt]] || 3.16 ||

Revision as of 15:44, 11 October 2011

The following is a list of the installed software at the UF HPC Center.

List updated 07 October 2011.

Software

Software Version Home Website Category Notes
Abaqus 6.6-1, 6.9-2 Abaqus Simulation
ADMB 9.1, 10.0 admb-project.org Modeling, math
Amber 10,11.old, 11 amber.scripps.edu Simulation, chemistry
Amos 3.0.0 AMOS SourceForge Biology, Genomics
Ansys 10.0 www.ansys.com Simulation, Engineering
antlr 3.1.3 http://www.antlr.org/ Linguistics, Parser
arachne 37618 Broadinstitute page Biology, Genomics
bioscope 1.0.1, 1.2.1 ABI BioScope Biology, NGS
Blast 2.2.24, 2.2.25 NCBI page Biology, Sequence alignment
Boost 1.37.0, 1.46.1 Boost.org C++, Library
Bowtie 0.12.7 http://bowtie-bio.sourceforge.net/ Biology, NGS
Charmm 35b2 [1] Simulation, Chemistry
Circuit   circuitscape.org GIS
CPMD 3.11.1 www.cpmd.org Simulation, Chemistry
Crystal 1.0.2 Will be removed on 2011-10-30
Cufflinks 1.0.3 http://cufflinks.cbcb.umd.edu/ Biology, NGS
dar 2.3.9 SF.net Backup
Desmond 2.4.2.1 www.deshawresearch.com/resources_desmond.html Desmond Simulation, Biology, Chemistry
dlpoly 3.0.9 www.cse.clrc.ac.uk Simulation, Biology, Chemistry
dock 6.3, 6.4 dock.compbio.ucsf.edu Chemistry, ligand binding prediction
emboss 6.4.0 emboss.sourceforge.net Biology, multi-tool suite
espresso 3.0, 3.2.2, 4.0.4 quantum-espresso.org Modeling, Physics
fastqc 0.10.0 FastQC website Biology, NGS
fftw 2.1.5, 3.1.2 FFTW Gaussian Math, Library, C++
fluent 6.3.26 ANSYS FLUENT Simulation
gadget 2.0.4, 2.0.5 Atlassian Gadgets Software Development
gamess 11-Aug11 www.msg.ameslab.gov/gamess GAMESS Quantum Chemistry
gaussian 03,09 Gaussian Modeling, Physics
Gromacs 4.0.4, 4.0.7 www.gromacs.org Physics, Modeling
hypre 2.0.0 HYPRE Library, Math, Physics
Inelastica 1.1 Inelastica Quantum Chemistry
IE3D 15.1 IE3D Simulation, Design
lammps 17-Sept11 LAMPPS Simulation
madness 0.9 MADNESS Home Page Math, DIff. Equation solving
mafft 6.859 MAFFT Biology, Multiple sequence alignment
MACS 1.4.1 MACS Biology, ChIP-Seq
Matlab 2009b MathWorks Math, Simulation, Programming
meep 0.10.0, 0.20.3 Will be removed on 2011-10-30
meme 3.0.13, 4.3.0 MEME Biology, Motifs, Sequence analysis
metis 4.0 Metis Math, Graph partitioning
mira 3.2.0 MIRA Guide Biology, NGS
MrBayes 3.1.2 MrBayes Biology, Phylogenetics
NAMD 2.7b2 NAMD Simulation, Chemistry, Biology
netcdf 3.6.3, 4.1.2 [http://www.unidata.ucar.edu/software/netcdf/ NetCDF Data exchange, Tools
Newbler 2.5.3, 2.6 Newbler Biology, NGS
NWChem 6.0 NWChem Simulation, Chemistry
OpenFOAM 1.7.1 OpenFoam Molecular Dynamics
papi 4.1.2.1 PAPI CPU API
PeakSplitter 1.0 PeakSplitter Biology, Chip-Seq
pdt 3.16
petsc 2.3.3-p8, 3.0.0-p12
pqs 3.3-19
pyopencl 0.92
python 2.5.1, 2.6.4, 2.6.5
RAxML 7.3.0 RAxML
RAxML-Light 1.0.5 RAxML
RepeatMasker 3.3.0 Repeat Masker
Rosetta 2.1.1, 2.1.2 www.rosettacommons.org
rsm 2961
samtools 0.1.16 http://samtools.sourceforge.net/
SAS 9.2, 9.3 SAS
Siesta 2.0, 2.0.2, 3.0b www.uam.es
Stata 10 Stata
tau 2.20.1
TRF 4.04 Tandem Repeats Finder
Tophat 1.3.0 http://tophat.cbcb.umd.edu/
tuxedo The "tuxedo suite," Bowtie, Tophat, and Cufflinks
VASP 4.6.34,5.2.0 cms.mpi.univie.ac.at
velvet 1.1.05 www.ebi.ac.uk/~zerbino/velvet/
vmd 1.9
weka 3.6.2
wublast 2.0 WU-Blast WU-BLAST Readme file
  • Many versions available. /scratch/hpc/osg/app/etc/grid3-locations.txt may have an up-to-date list. Or look underneath /scratch/hpc/osg/app/cmssoft.


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