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
As of April , 2013 the following software has been installed:
| Software | Description | Installed | Tested | Benchmark | GUI | Basic Usage |
| BioPython | Python tools for computational molecular biology | Yes | No | No | No | |
| BioPerl | Perl tools for bioinformatics, genomics and life science research | Yes | Yes | No | No | |
| CLUSTALW | A multiple sequence alignment program. | Yes | Yes | No | clustalw | |
| EMBOSS | Tools for sequence analysis | Yes | No | No | Yes | |
| FASTA | Searching protein and DNA sequence databases | Yes | No | No | Planned | |
| GLIMMER | Finds genes in microbial DNA, | Yes | No | No | No | |
| GROMACS | Molecular dynamics simulation | Yes | Yes | No | No | see WIKI |
| HMMER | A profile HMM method for sensitive database searches | Yes | No | No | MPI-Planned | hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch |
Intel C & FortranCompilers | Yes | Yes | No | No | ||
Intel Math Kernal | Yes | Yes | No | No | ||
| MPI-BLAST | Parallelizes the NCBI Blast Search | Yes | Yes | No | Planned | |
| MrBayes* | Bayesian inference of phylogeny | Yes | Yes | Yes | No | mbpar |
| NCBI-BLAST | Searches for regions of local similarity between sequences | Yes | Yes | No | Yes | blast |
| T_COFFEE | A multiple sequence alignment package | Yes | Yes | No | Yes | t_coffee |
| Shake-and-Bake | Direct-Methods Procedure for determining x-ray structures | Yes | Yes | No | Yes | snb |
| GAMESS | Quantum Chemistry | Yes | Yes | No | No | |
| NAMD** | Scalable Molecular Dynamics | Yes | Yes | Yes | Sort of, See VMD | see WIKI |
| VMD | Viewer/GUI for NAMD | Yes | Yes | Yes | It is a GUI | vmd |
| AMBER11 AMBERTOOLS v1.2 | Molecular Dynamics | Yes | Parallel Vers. Being Tested | Parallel Vers. Being Tested | Sort of. VMD can visualize the trajectories | See WIKI |
| AUTODOCK/MGLTools | Docking | Yes | No | No | Yes | pmv, adt, vision,pythonsh |
| Bioconductor 2.12 | software for biologists and statisticians working in bioinformatics | Yes | No | No | No | embedded in R |
| SGX-Pro | X-ray | Yes | Yes | No | Yes | sgxpro --starts many other programs |
| PHENIX | X-ray | Yes | Yes | No | Yes | phenix |
| CCP4 Suite CCP4i, CCP4mg, COOT, CHOOCH | X-ray | Yes | Yes | No | Yes | ccp4i,ccp4mg, chooch, coot |
| SOLVE-RESOLVE | X-ray | Yes | Yes | No | Yes | sgxpro |
| UCSF Dock 6.5*** | Docking | Yes | Yes | Yes | Sort of see CHIMERA | see WIKI |
| CHIMERA | Molecule setup and viewer for UCSF Dock | Yes | Yes | Yes | It is a GUI | chimera |
R-version 2.15.3, 3.0.0 R-mpi | A software environment for statistical computing and graphics | Yes | Yes | No | No | R |
| IGV | AGenome Alignment Viewer | Yes | ||||
SeqMonk version 0.24.0 | A software tool to visualize and analyze high throughput mapped sequence data | Yes | Yes | No | Yes | seqmonk |
| MaNORM | Yes | No | ||||
| SICER | Yes | No | ||||
| FastQC | Yes | No | ||||
| Trimmomatic | Yes | No | ||||
| MACS-1.4.2, 2.0 | Yes | No | ||||
| SICER | Yes | No | ||||
| GATK | Yes | No | ||||
CuffLinks v 2.02 CuffLinks, CuffCompare Cuffmerge, CuffDiff | Transcript Discovery | Yes | No | |||
| cummeRbund | Rsql Tool for CuffDiff | Yes | No | |||
| BEDTools | Yes | No | ||||
| Picard-Tools | Yes | No | ||||
| SamTools | SAMTOOLS "provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format." | Yes | No | |||
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)." | Yes | Yes | No | No | tophat, 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)