Compbio middleware: Difference between revisions
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Drupal. | Drupal. | ||
* [[PyMol]] | |||
* [[Chimera]] | |||
* [[Knime]] | |||
* [[Marvin]] and [[InstantJChem]] from [[ChemAxon]] | |||
* [[OpenBabel]] | |||
* [[rdkit]] | |||
* [[psql]] and [[MySQL]] | |||
== Feeware == | |||
* [[pgf]] | |||
* [[CSD]] | |||
* [[Chemaxon]] | |||
* [[OpenEye]] | |||
Revision as of 11:47, 20 March 2014
We define middleware here to mean whatever comes between your application and the operating system. If you have a better name for it, tell us.
Essential
- Installing AMSOL AMSOL - atomic charge and desolvation penalty calculations required for database building.
- Omega by OpenEye - conformation generation required for database building.
- Matplotlib - currently only needed for analysis plots (enrichment)
- MSMS - currently only needed by be_blasti
Recommended
- rdkit - recommended and soon to be essential for the DOCK 3.7 pipeline.
- OGS/GE - queuing system. OpenGridEngine is included in Centos and you do not need to install it separately.
Set up psql/rdkit from scratch
Psql.
rdkit.
Drupal.
Feeware
Chemaxon.
mysql.
openbabel.
wiki
Return to So you want to set up a lab.