HPCBIOS_2012-93: Life Sciences Productivity Environment


Life Sciences Productivity Environment includes a set of HPC tools which are needed for scientific computing and visualization in the respective domain. The following is an attempt to define which ones are relevant for the HPCBIOS communities and set an action plan.

  • BC Policy: HPCBIOS_2012-93
  • Date of Policy: 2012-12-15

The main objective of this policy is to provide the following common productivity environment across any HPCBIOS resources:

Name Category version(s) Compliance level Reference URL
CPMD Quantum Chemistry x SHOULD http://www.cpmd.org/
Dalton Quantum Chemistry x SHOULD http://dirac.chem.sdu.dk/daltonprogram.org/
GAMESS-US Quantum Chemistry x SHOULD http://www.msg.ameslab.gov/gamess/
Gaussian Quantum Chemistry x MAY http://www.gaussian.com/
OpenEye Chemical Informatics x SHOULD http://www.eyesopen.com/
BLAST/mpiBLAST Sequence Analysis x MUST http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
BWA Sequence Analysis x MUST http://bio-bwa.sourceforge.net/
CLUSTALW Sequence Analysis x MUST http://www.ebi.ac.uk/Tools/msa/clustalw2/
HMMER Sequence Analysis x MUST http://hmmer.janelia.org/
MrBayes Sequence Analysis x MUST http://mrbayes.sourceforge.net/
GROMACS Molecular Modeling x MUST http://www.gromacs.org/
NAMD Molecular Modeling x SHOULD http://www.ks.uiuc.edu/Research/namd/
AMBER Molecular Modeling x SHOULD http://ambermd.org/
AutoDock /Vina Molecular Modeling x SHOULD http://autodock.scripps.edu/ / http://vina.scripps.edu/
Glide Molecular Modeling x SHOULD http://www.schrodinger.com/
Dock Molecular Modeling x SHOULD http://dock.compbio.ucsf.edu/
Flexx Molecular Modeling x SHOULD http://www.biosolveit.de/FlexX/
FTDock Molecular Modeling x SHOULD http://www.sbg.bio.ic.ac.uk/docking/ftdock.html
LigandFit Molecular Modeling x SHOULD http://www.accelrys.com
Rosetta Molecular Modeling 3.5 SHOULD http://www.rosettacommons.org/

Reference documents:

This productivity environment may be supplemented with other related productivity tools as they become available on allocated systems.

Kindly notify -if this policy is inadequate for your work- both your local site technical representative & HPCBIOS maintainers.