Compbio middleware: Difference between revisions
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= Essential = | = Essential = | ||
* [[Python]] - 2.7 series | * [[Python]] - 2.7 series | ||
* [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building. | * [[Install AMSOL]] [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building. | ||
* [[Omega]] by [[OpenEye]] - [[conformation generation]] required for database building. | * [[Omega]] by [[OpenEye]] - [[conformation generation]] required for database building. | ||
* [[Matplotlib]] - currently only needed for analysis plots (enrichment) | * [[Matplotlib]] - currently only needed for analysis plots (enrichment) | ||
Revision as of 15:36, 13 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
- Python - 2.7 series
- Install 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.
Chemaxon.
mysql.
openbabel.
wiki
Return to So you want to set up a lab.