Compbio middleware - Revision history

Frodo: asdf

2024-05-23T21:08:30Z

asdf

← Older revision		Revision as of 21:08, 23 May 2024
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	wiki		wiki



	Return to [[So you want to set up a lab]].		Return to [[So you want to set up a lab]].


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

2014-03-20T11:48:13Z

← Older revision		Revision as of 11:48, 20 March 2014
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			* [[AMSOL]]
			* [[Epik]] and [[ligprep]] from Schrodinger
			* [[OpenEye]]

	Chemaxon.		Chemaxon.

2014-03-20T11:47:01Z

← Older revision		Revision as of 11:47, 20 March 2014
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	Drupal.		Drupal.

			* [[PyMol]]
			* [[Chimera]]
			* [[Knime]]
			* [[Marvin]] and [[InstantJChem]] from [[ChemAxon]]
			* [[OpenBabel]]
			* [[rdkit]]
			* [[psql]] and [[MySQL]]

			== Feeware ==
			* [[pgf]]
			* [[CSD]]
			* [[Chemaxon]]
			* [[OpenEye]]

2014-03-13T15:36:27Z

Essential

← Older revision		Revision as of 15:36, 13 March 2014
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	= Essential =		= Essential =
	* [[Python]] - 2.7 series
	* [[Installing AMSOL]] [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building.		* [[Installing 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.

2014-03-13T15:36:13Z

Essential

← Older revision		Revision as of 15:36, 13 March 2014
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	= Essential =		= Essential =
	* [[Python]] - 2.7 series		* [[Python]] - 2.7 series
	* [[~~Install~~ AMSOL]] [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building.		* [[Installing 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)

2014-03-13T15:36:03Z

Essential

← Older revision		Revision as of 15:36, 13 March 2014
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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)

2014-03-13T09:14:21Z

← Older revision		Revision as of 09:14, 13 March 2014
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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.		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.

			{{TOCright}}

	= Essential =		= Essential =

2014-03-13T09:00:39Z

← Older revision	Revision as of 09:00, 13 March 2014
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		Return to [[So you want to set up a lab]].

2014-03-13T08:01:41Z

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 * [[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.
 [[Category:Internal]]
 [[Category:Sysadmin]]
 [[Category:Docking]]

2014-03-12T18:16:32Z

Essential

← Older revision		Revision as of 18:16, 12 March 2014
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	* [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building.		* [[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 =