Note
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:
- PRACE – The Scientific Case for HPC in Europe 2012-2020 http://www.prace-ri.eu/PRACE-The-Scientific-Case-for-HPC
- European Exascale Software Initiative Working Group report on Life Science and Health activities http://www.eesi-project.eu/media/download_gallery/EESI_D3.6_WG3.4-Report_R2.0.pdf
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.