Difference between revisions of "UFRC Help and Documentation"

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The following is a list of the installed software at the UF HPC Center.
 
The following is a list of the installed software at the UF HPC Center.
  
−
List updated '''07 October 2011'''.
+
List updated '''11 October 2011'''.
 
==Software==
 
==Software==
 
{| border="1"
 
{| border="1"
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| [[Crystal]] || 1.0.2 || || || Will be removed on 2011-10-30
 
| [[Crystal]] || 1.0.2 || || || Will be removed on 2011-10-30
 
|-
 
|-
−
| [[tuxedo|Cufflinks]] || 1.0.3 || [http://cufflinks.cbcb.umd.edu/ http://cufflinks.cbcb.umd.edu/] || Biology, NGS ||  
+
| [[tuxedo|Cufflinks]] || 1.0.3 || [http://cufflinks.cbcb.umd.edu/ Cufflinks] || Biology, NGS ||  
 
|-
 
|-
 
| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ SF.net] || Backup ||  
 
| [[dar]] || 2.3.9 || [http://sourceforge.net/projects/dar/ SF.net] || Backup ||  
 
|-
 
|-
−
| [[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 Desmond] || Simulation, Biology, Chemistry ||
 
|-
 
|-
 
| [[dlpoly]] || 3.0.9 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml www.cse.clrc.ac.uk]  || Simulation, Biology, Chemistry ||
 
| [[dlpoly]] || 3.0.9 || [http://www.cse.clrc.ac.uk/ccg/software/DL_POLY/index.shtml www.cse.clrc.ac.uk]  || Simulation, Biology, Chemistry ||
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| [[gadget]] || 2.0.4, 2.0.5 || [http://confluence.atlassian.com/display/GADGETS/Atlassian+Gadgets+2.0.5+Release+Notes Atlassian Gadgets] || Software Development ||
 
| [[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]|| Quantum Chemistry||
+
| [[gamess]] || 11-Aug11 || [http://www.msg.ameslab.gov/gamess/ GAMESS]|| Quantum Chemistry||
 
|-
 
|-
 
| [[gaussian]] || 03,09 || [http://www.gaussian.com/ Gaussian]||Modeling, Physics||
 
| [[gaussian]] || 03,09 || [http://www.gaussian.com/ Gaussian]||Modeling, Physics||
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| [[lammps]] || 17-Sept11 || [http://lammps.sandia.gov/ LAMPPS]||Simulation||
 
| [[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]||Math, DIff. Equation solving||
+
| [[madness]] || 0.9 || [http://code.google.com/p/m-a-d-n-e-s-s/ MADNESS]||Math, DIff. Equation solving||
 
|-
 
|-
 
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT]||Biology, Multiple sequence alignment||
 
| [[mafft]] || 6.859 || [http://mafft.cbrc.jp/alignment/software/ MAFFT]||Biology, Multiple sequence alignment||
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| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ NAMD]||Simulation, Chemistry, Biology||
 
| [[NAMD]] || 2.7b2 || [http://www.ks.uiuc.edu/Research/namd/ NAMD]||Simulation, Chemistry, Biology||
 
|-
 
|-
−
| [[netcdf]] || 3.6.3, 4.1.2 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF|| Data exchange, Tools ||
+
| [[netcdf]] || 3.6.3, 4.1.2 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF]|| Data exchange, Tools ||
 
|-
 
|-
 
| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
 
| [[Newbler]] || 2.5.3, 2.6 || [http://my454.com/products/analysis-software/index.asp Newbler] || Biology, NGS ||
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| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html PeakSplitter]||Biology, Chip-Seq||
 
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html PeakSplitter]||Biology, Chip-Seq||
 
|-
 
|-
−
| [[pdt]] || 3.16 ||
+
| [[pdt]] || 3.16 || [http://www.cs.uoregon.edu/Research/tau/home.php PDT]||Programming, Profiler||
 
|-
 
|-
−
| [[petsc]] || 2.3.3-p8, 3.0.0-p12 ||  
+
| [[petsc]] || 2.3.3-p8, 3.0.0-p12 || [http://www.mcs.anl.gov/petsc/petsc-as/ PETSc]||MPI toolkit||
 
|-
 
|-
−
| [[pqs]] || 3.3-19 ||
+
| [[pqs]] || 3.3-19 ||[http://www.pqs-chem.com/software.php PQS]||Modeling, Chemistry||
 
|-
 
|-
−
| [[pyopencl]] || 0.92 ||
+
| [[pyopencl]] || 0.92 || [http://mathema.tician.de/software/pyopencl PyOpenCL]||python, parallel programming||
 
|-
 
|-
−
| [[python]] || 2.5.1, 2.6.4, 2.6.5 ||
+
| [[python]] || 2.5.1, 2.6.4, 2.6.5 || [http://python.org Python]||Programming, scripting, language||
 
|-
 
|-
−
| [[RAxML]] || 7.3.0 || [http://wwwkramer.in.tum.de/exelixis/software.html RAxML]
+
| [[RAxML]] || 7.3.0 || [http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
 
|-
 
|-
−
| [[RAxML-Light]] || 1.0.5 || [http://wwwkramer.in.tum.de/exelixis/software.html RAxML]
+
| [[RAxML-Light]]|| 1.0.5 ||[http://sco.h-its.org/exelixis/software.html RAxML]||Biology, Phylogenetics||
 
|-
 
|-
−
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]
+
| [[RepeatMasker]] || 3.3.0 || [http://www.repeatmasker.org/ Repeat Masker]||Biology, Genomics||
 
|-
 
|-
−
| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ www.rosettacommons.org]
+
| [[Rosetta]] || 2.1.1, 2.1.2 || [https://www.rosettacommons.org/ Rosetta]||Biology, Structural, Modeling||
 
|-
 
|-
−
| [[rsm]] || 2961 ||
+
| [[rsm]] || 2961 || [http://www.adoptech.com/software/RSMToolkit.htm RSM]||Math, Modeling, Geometry||
 
|-
 
|-
−
| [[samtools]] || 0.1.16 || [http://samtools.sourceforge.net/ http://samtools.sourceforge.net/]  
+
| [[samtools]] || 0.1.16 || [http://samtools.sourceforge.net/ Samtools]||Biology, NGS||
 
|-
 
|-
−
| [[SAS]] || 9.2, 9.3 || [http://www.sas.com SAS]
+
| [[SAS]] || 9.2, 9.3 || [http://www.sas.com SAS]||Statistics, Graphing||
 
|-
 
|-
−
| [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ www.uam.es]
+
| [[Siesta]] || 2.0, 2.0.2, 3.0b || [http://www.icmab.es/siesta/ Siesta]||Simulation, physics, ab-initio||
 
|-
 
|-
−
| [[Stata]] || 10 || [http://www.stata.com/ Stata]
+
| [[Stata]] || 10 || [http://www.stata.com/ Stata]||Statistics, Data analysis||
 
|-
 
|-
−
| [[tau]] || 2.20.1 ||
+
| [[tau]] || 2.20.1 ||[http://www.cs.uoregon.edu/Research/tau/home.php TAU]||Profiling, Tracing, Programming, Toolkit||
 
|-
 
|-
−
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html Tandem Repeats Finder]
+
| [[TRF]] || 4.04 || [http://tandem.bu.edu/trf/trf.html TRF]||Biology, Genomics||
 
|-
 
|-
−
| [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ http://tophat.cbcb.umd.edu/]
+
| [[tuxedo|Tophat]] || 1.3.0 || [http://tophat.cbcb.umd.edu/ Tophat]||Biology, NGS||
 
|-
 
|-
−
| [[tuxedo]] ||  || The "tuxedo suite," Bowtie, Tophat, and Cufflinks
+
| [[tuxedo]] || ||  || The "tuxedo suite," Bowtie, Tophat, and Cufflinks
 
|-
 
|-
−
| [[VASP]] || 4.6.34,5.2.0 || [http://cms.mpi.univie.ac.at/vasp/ cms.mpi.univie.ac.at]
+
| [[VASP]] || 4.6.34,5.2.0 || [http://cms.mpi.univie.ac.at/vasp/ VASP]||Quantum Chemistry, ab initio||
 
|-
 
|-
−
| [[velvet]] || 1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ www.ebi.ac.uk/~zerbino/velvet/]
+
| [[velvet]] || 1.1.05 || [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet]||Biology, NGS||
 
|-
 
|-
−
| [[vmd]] || 1.9 ||
+
| [[vmd]] || 1.9 ||[http://ftp.ks.uiuc.edu/Research/vmd/ VMD]||Biology, Visualization||
 
|-
 
|-
−
| [[weka]] || 3.6.2 ||
+
| [[weka]] || 3.6.2 ||[http://www.cs.waikato.ac.nz/ml/weka/ WEKA]||Data mining algorithms||
 
|-
 
|-
−
| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast] [[WUBLAST|WU-BLAST Readme file]]
+
| [[wublast]] || 2.0 || [http://blast.wustl.edu/ WU-Blast]||Biology, Sequence Alignment||
 
|}
 
|}
  

Revision as of 16:05, 11 October 2011

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

List updated 11 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 Cufflinks Biology, NGS
dar 2.3.9 SF.net Backup
Desmond 2.4.2.1 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 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 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 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 PDT Programming, Profiler
petsc 2.3.3-p8, 3.0.0-p12 PETSc MPI toolkit
pqs 3.3-19 PQS Modeling, Chemistry
pyopencl 0.92 PyOpenCL python, parallel programming
python 2.5.1, 2.6.4, 2.6.5 Python Programming, scripting, language
RAxML 7.3.0 RAxML Biology, Phylogenetics
RAxML-Light 1.0.5 RAxML Biology, Phylogenetics
RepeatMasker 3.3.0 Repeat Masker Biology, Genomics
Rosetta 2.1.1, 2.1.2 Rosetta Biology, Structural, Modeling
rsm 2961 RSM Math, Modeling, Geometry
samtools 0.1.16 Samtools Biology, NGS
SAS 9.2, 9.3 SAS Statistics, Graphing
Siesta 2.0, 2.0.2, 3.0b Siesta Simulation, physics, ab-initio
Stata 10 Stata Statistics, Data analysis
tau 2.20.1 TAU Profiling, Tracing, Programming, Toolkit
TRF 4.04 TRF Biology, Genomics
Tophat 1.3.0 Tophat Biology, NGS
tuxedo The "tuxedo suite," Bowtie, Tophat, and Cufflinks
VASP 4.6.34,5.2.0 VASP Quantum Chemistry, ab initio
velvet 1.1.05 Velvet Biology, NGS
vmd 1.9 VMD Biology, Visualization
weka 3.6.2 WEKA Data mining algorithms
wublast 2.0 WU-Blast Biology, Sequence Alignment
  • 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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