Compbio middleware: Difference between revisions

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(Created page with "= Essential = * Computer and operating system. We recommend Centos on either Intel or AMD. Supported platforms for DOCK 3.7. * Python - 2.7 series * AMSOL - at...")
 
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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.
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= Essential =
= Essential =
* Computer and operating system. We recommend [[Centos]] on either Intel or AMD. [[Supported platforms for DOCK 3.7]].
* [[Installing AMSOL]] [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building.
* [[Python]] - 2.7 series
* [[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.
* 3D modeling - [[PyMol]] or [[Chimera]]
* [[Matplotlib]] - currently only needed for analysis plots (enrichment)
* [[Matplotlib]] - currently only needed for analysis plots (enrichment)
* [[MSMS]] - currently only needed by [[be_blasti]]
* [[MSMS]] - currently only needed by [[be_blasti]]


= Recommended =
= Recommended =
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* [[OGS/GE]] - queuing system.  OpenGridEngine is included in [[Centos]] and you do not need to install it separately.
* [[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.
* [[PyMol]]
* [[Chimera]]
* [[Knime]]
* [[Marvin]]  and [[InstantJChem]] from [[ChemAxon]]
* [[OpenBabel]]
* [[rdkit]]
* [[psql]] and [[MySQL]]
== Feeware ==
* [[pgf]]
* [[CSD]]
* [[Chemaxon]]
* [[OpenEye]]
* [[AMSOL]]
* [[Epik]] and [[ligprep]] from Schrodinger
* [[OpenEye]]
Chemaxon.
mysql.
openbabel.
wiki
Return to [[So you want to set up a lab]].


[[Category:Internal]]
[[Category:Internal]]
[[Category:Sysadmin]]
[[Category:Sysadmin]]
[[Category:Docking]]
[[Category:Docking]]
[[Category:Software]]

Latest revision as of 21:08, 23 May 2024

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

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.