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Computational Biology Resource Center

Installed Software Log

CBRC Software

CBRC General Infrastructure

Intel 12 Compiler, Mpich (message passing software) R Statistical package , lam (message passing software), GlobusOnLine (software for transferring files between MUSC and national XSEDE computers),Boost (computational libraries)

Drug Discovery

MOE license multiuser, multiyear, SYBYL multiuser license,DOCK65,VMD, DOCK Compatible Drug Databases

        AMBER

Image Analysis

Epd (object-oriented language from Python package, version 7.1-2-rh3-x86_64)

QT 4.8.0, QT3,CMAKE-2.8.6,VTK-5.8.0,VTK-5.8.0.B ,VTK-5.0.4, fsl, NIPY, FreeSurf_Support, freesurfer, Slicer-4.0.1, camino, nifticlib-2.0.0, scons-2.1.0, camino-trackvis-0.2,cp2, ilastik-0.5.04, cp2B, cp2C, cp2-v171, cp2-v170

Next Generation Sequencing

Partekgs,BFAST,SAMTOOLS,CLCMainWorkbench6,SeqMonk,abin,MapSplice,Pubsw,TOPHAT141,BEDTools,IGV,CLUSTER-1.50,Cytoscape_2_8_2,AltAnalyze_v.2.0.7.1-Py, cufflinks-2.0.2, TOPHAT204, gnuplot-4.6.0, ncurses-5.9, illumina, BOWTIE, cummeRbund

Structural Biology

SNB23,SOLVER,UCSF Chimera, cyana-2.1bin-110128.tgz,Cyana-3.0demo-111125.tgz, rnamotif-3.0.7

Bioinformatics

R(2.15.2),Rmpi,Numpy,Scipy, Bioperl

CBRC Wiki Provides on-line how-to tips on usage of  CBRC cluster and software. https://wiki.musc.edu/index.php/HPCC_Application_Notes

Installed Software Log

As of April , 2013 the following software has been installed:

SoftwareDescriptionInstalledTestedBenchmarkGUIBasic Usage
BioPythonPython tools for computational molecular biologyYesNoNoNo 
BioPerlPerl tools for bioinformatics, genomics and life science researchYesYesNoNo 
CLUSTALWA multiple sequence alignment program.YesYesNo clustalw
EMBOSSTools for sequence analysisYesNoNoYes 
FASTASearching protein and DNA sequence databasesYesNoNoPlanned 
GLIMMERFinds genes in microbial DNA,YesNoNoNo 
GROMACSMolecular dynamics simulationYesYesNoNosee WIKI
HMMERA profile HMM method for sensitive database searchesYesNoNoMPI-Plannedhmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch

Intel C & FortranCompilers 

 YesYesNoNo 

Intel Math Kernal  

 YesYesNoNo 
MPI-BLAST    Parallelizes the NCBI Blast SearchYesYesNoPlanned 
MrBayes*     Bayesian inference of phylogenyYesYesYesNombpar
NCBI-BLAST   Searches for regions of local similarity between sequencesYesYesNoYesblast
T_COFFEE     A multiple sequence alignment packageYesYesNoYest_coffee
Shake-and-Bake

Direct-Methods Procedure for determining x-ray structures

YesYesNoYessnb
GAMESSQuantum ChemistryYesYesNoNo 
NAMD**Scalable Molecular DynamicsYesYesYesSort of, See VMDsee WIKI
VMDViewer/GUI for NAMDYesYesYesIt is a GUIvmd
AMBER11 AMBERTOOLS v1.2Molecular DynamicsYesParallel Vers. Being TestedParallel Vers. Being TestedSort of. VMD can visualize the trajectoriesSee WIKI
AUTODOCK/MGLToolsDockingYesNoNoYespmv, adt, vision,pythonsh
Bioconductor 2.12software for biologists and statisticians working in bioinformaticsYesNoNoNoembedded in R
SGX-ProX-rayYesYesNoYessgxpro --starts many other programs
PHENIXX-rayYesYesNoYesphenix
CCP4 Suite CCP4i, CCP4mg, COOT, CHOOCHX-rayYesYesNoYes

ccp4i,ccp4mg,

chooch, coot

SOLVE-RESOLVEX-rayYesYesNoYessgxpro
UCSF Dock 6.5***DockingYesYesYesSort of see CHIMERAsee WIKI
CHIMERAMolecule setup and viewer for UCSF DockYesYesYesIt is a GUIchimera

R-version 2.15.3, 3.0.0

R-mpi

A software environment for statistical computing and graphicsYesYesNoNoR
IGVAGenome Alignment ViewerYes

SeqMonk

version 0.24.0

A software tool to visualize and analyze high throughput mapped sequence dataYesYesNoYesseqmonk
MaNORMYesNo
SICERYesNo
FastQCYesNo
TrimmomaticYesNo
MACS-1.4.2, 2.0YesNo
SICERYesNo
GATKYesNo

CuffLinks v 2.02

CuffLinks, CuffCompare

Cuffmerge, CuffDiff

Transcript DiscoveryYesNo
 cummeRbundRsql Tool for CuffDiffYesNo
BEDToolsYesNo
Picard-ToolsYesNo
SamToolsSAMTOOLS "provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format."YesNo

TopHat, Bowtie

Versions

2.0.8,2.10

respectively

TopHat "is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. " Bowtie "is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end)." YesYesNoNotophat, bowtie or samtools
XPLOR

A System for X-ray Crystallography and NMR

Planned    

**The NAMD benchmark, APOA1 (protein in lipid bilayer with some water) is too large to run on a LINUX PC but 10000 steps ran in 65 minutes on the cluster.

*The parallel version of MrBayes finished a 1.2 million generation run in about 12 hours. This compares to over 4 weeks on a single CPU Linux workstation to complete the same 1.2 million generation run.

*** DOCK.mpi running on 80 of the CBRC's 132 cores docked and scored 1019 ligands in approximately an hour April 11, 2008.

 

The CBRC oversight committee encourages MUSC researchers to submit requests for additional software to be installed on the cluster. Requests should be sent to Starr Hazard (hazards@musc.edu)

 
 
 

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