So you want to set up a lab - Revision history

Khtang at 19:38, 10 January 2019

2019-01-10T19:38:34Z

← Older revision		Revision as of 19:38, 10 January 2019
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	[[Category:Sysadmin]]		[[Category:Sysadmin]]
	[[Category:Tutorials]]		[[Category:Tutorials]]
			[[Category:Setup]]

Frodo: /* Requirements and assumptions */

2014-05-01T17:31:06Z

Requirements and assumptions

← Older revision		Revision as of 17:31, 1 May 2014
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	= Requirements and assumptions =		= Requirements and assumptions =
	This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend $20K on servers and $2K on a workstation, or you already own equivalent or better hardware. You'll need an acoustically insulated air conditioned room. Expect to spend a month to specify, order and deploy hardware, a week to install operating system level, a week to install middleware, and a week to install our software. Times will be longer if ~~you don't have experience~~. Once running, expect 1 day/month/cluster ~~and~~ 1 day/month/rack of sysadmin time to maintain your system.		This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend $20K on servers and $2K on a workstation, or you already own equivalent or better hardware. You'll need an acoustically insulated air conditioned room. Expect to spend a month to specify, order and deploy hardware, a week to install operating system level, a week to install middleware, and a week to install our software. Times will be longer if it is your first time. Once running, expect 1 day/month/cluster plus 1 day/month/rack of sysadmin time to maintain your system.

	= Narrative =		= Narrative =

Frodo: /* Operations */

2014-03-20T11:52:46Z

Operations

← Older revision		Revision as of 11:52, 20 March 2014
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	= Operations =		= Operations =
	Once the system is set up and running, it will need to be maintained. Please see the [[Category:Sysadmin \| system administrator's guide]]		Once the system is set up and running, it will need to be maintained. Please see the [[:Category:Sysadmin \| system administrator's guide]]

	[[Category:Sysadmin]]		[[Category:Sysadmin]]
	[[Category:Tutorials]]		[[Category:Tutorials]]

Frodo: /* Operations */

2014-03-20T11:52:25Z

Operations

← Older revision		Revision as of 11:52, 20 March 2014
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	= Operations =		= Operations =
	Once the system is set up and running, it will need to be maintained. Please see the [[~~System~~ administrator's guide]]		Once the system is set up and running, it will need to be maintained. Please see the [[Category:Sysadmin \| system administrator's guide]]

	[[Category:Sysadmin]]		[[Category:Sysadmin]]
	[[Category:Tutorials]]		[[Category:Tutorials]]

Frodo: /* Our Software */

2014-03-20T11:48:04Z

Our Software

← Older revision		Revision as of 11:48, 20 March 2014
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	= Our Software =		= Our Software =
	Each product is licensed and distributed separately.		Each product is licensed and distributed separately. Allow at least a day for each product, more if the previous steps above are incomplete.

	* [[Install DOCK 3.7]]		* [[Install DOCK 3.7]]
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	* [[Install ZINC]]		* [[Install ZINC]]
	* [[Install DOCK Blaster]]		* [[Install DOCK Blaster]]

	* [[AMSOL]]
	* [[Epik]] and [[ligprep]] from Schrodinger
	* [[OpenEye]]

	= Operations =		= Operations =

Frodo at 11:46, 20 March 2014

2014-03-20T11:46:46Z

← Older revision		Revision as of 11:46, 20 March 2014
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	= Physical level =		= Physical level =
	We discuss options for acquiring various sizes of hardware in [[Cluster Theory]]. More thoughts: [[Acquire and deploy hardware]]		We discuss options for acquiring various sizes of hardware in [[Cluster Theory]]. More thoughts: [[Acquire and deploy hardware]]. Allow a month to obtain and deploy hardware.

	= Operating System level =		= Operating System level =
	~~here~~ we use Operating system to describe all software components that are not particular to our field. Thus for the purposes of this discussion, python and a queuing system are considered part of the operating system level. [[Install operating system]]		Here we use Operating system to describe all software components that are not particular to our field. Thus for the purposes of this discussion, python and a queuing system are considered part of the operating system level. [[Install operating system]]. Allow one week for this step.

	= Middleware level =		= Middleware level =
	We use middleware to mean 3rd party software required by our software that is specific to our field and that you would not normally expect to find installed on a new computer.		We use middleware to mean 3rd party software required by our software that is specific to our field and that you would not normally expect to find installed on a new computer.
	Set up middleware for a [[Compbio middleware \| computational drug discovery lab]].		Set up middleware for a [[Compbio middleware \| computational drug discovery lab]]. Allow one week for this step.

	= ~~Client Application Software =~~		= Our Software =

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

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

	~~= Server Application~~ Software =
	Each product is licensed and distributed separately.		Each product is licensed and distributed separately.

Frodo: /* Requirements and assumptions */

2014-03-20T11:45:03Z

Requirements and assumptions

← Older revision		Revision as of 11:45, 20 March 2014
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	= Requirements and assumptions =		= Requirements and assumptions =
	This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend $20K on servers and $2K on a workstation, or you already own equivalent or better hardware. You'll need an acoustically insulated air conditioned room. ~~It would help~~ to ~~have someone with system administration experience for 100 hours (3 weeks) for the purchase~~, ~~acquisition~~ and ~~deployment of the~~ hardware ~~and installation of the~~ operating system and software ~~components~~. Once running, expect 1 day/month/cluster ~~plus~~ 1 day/month/rack of ~~expert~~ sysadmin to ~~keep~~ your ~~cluster running smoothly. Once you have all the software and hardware ready, you can get a cluster up and running in a day, and another day to get our software running on it~~.		This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend $20K on servers and $2K on a workstation, or you already own equivalent or better hardware. You'll need an acoustically insulated air conditioned room. Expect to spend a month to specify, order and deploy hardware, a week to install operating system level, a week to install middleware, and a week to install our software. Times will be longer if you don't have experience. Once running, expect 1 day/month/cluster and 1 day/month/rack of sysadmin time to maintain your system.

	= Narrative =		= Narrative =

Frodo: /* Operating System level */

2014-03-19T17:25:49Z

Operating System level

← Older revision		Revision as of 17:25, 19 March 2014
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	= Operating System level =		= Operating System level =
	We use Operating system to describe all software components that are not particular to our field. Thus for the purposes of this discussion, python and a queuing system are considered part of the operating system level. [[Install operating system]]		here we use Operating system to describe all software components that are not particular to our field. Thus for the purposes of this discussion, python and a queuing system are considered part of the operating system level. [[Install operating system]]

	= Middleware level =		= Middleware level =

Frodo: /* Requirements and assumptions */

2014-03-19T17:25:35Z

Requirements and assumptions

← Older revision		Revision as of 17:25, 19 March 2014
Line 4:		Line 4:

	= Requirements and assumptions =		= Requirements and assumptions =
	This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend $20K on servers and $2K on a workstation, or you already own equivalent or better hardware. You'll need an acoustically insulated air conditioned room. It would help to have someone with system administration experience for 100 hours (3 weeks) for the purchase, acquisition and deployment of the hardware and installation of the operating system and software components. Once running, ~~as a guideline you should plan for the equivalent of~~ 1 day/month of expert sysadmin ~~time for each 10 computer enclosures~~ to keep your cluster running smoothly.		This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend $20K on servers and $2K on a workstation, or you already own equivalent or better hardware. You'll need an acoustically insulated air conditioned room. It would help to have someone with system administration experience for 100 hours (3 weeks) for the purchase, acquisition and deployment of the hardware and installation of the operating system and software components. Once running, expect 1 day/month/cluster plus 1 day/month/rack of expert sysadmin to keep your cluster running smoothly. Once you have all the software and hardware ready, you can get a cluster up and running in a day, and another day to get our software running on it.
	Once you have all the software and hardware ready, you can get a ~~docking lab~~ up and running in ~~less than~~ a day~~. If you have not administered a molecular docking lab before~~, ~~allow a few months~~ to ~~learn how to care for~~ it.

	= Narrative =		= Narrative =

Frodo: /* Operations */

2014-03-19T13:08:43Z

Operations

← Older revision		Revision as of 13:08, 19 March 2014
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	= Operations =		= Operations =
	* [[Periodic system ~~maintenance]]~~		Once the system is set up and running, it will need to be maintained. Please see the [[System administrator's guide]]
	* [[Backups]]
	* [[Security review]]
	* [[~~Software upgrades~~]]

	[[Category:Sysadmin]]		[[Category:Sysadmin]]
	[[Category:Tutorials]]		[[Category:Tutorials]]