So you want to set up a lab: Difference between revisions

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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, 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. 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.
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 =  
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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 =
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 =
 
Each product is licensed and distributed separately.  Allow at least a day for each product, more if the previous steps above are incomplete.  
* [[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.  


* [[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 =  
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]]
[[Category:Setup]]

Latest revision as of 19:38, 10 January 2019

Here is how I would set up a computational lab, one that could join the Worldwide ZINC network.

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 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

Before starting, let's talk about what you need for a successful computational pharmacology cluster. Cluster Narrative.

Physical level

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

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

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 computational drug discovery lab. Allow one week for this step.

Our Software

Each product is licensed and distributed separately. Allow at least a day for each product, more if the previous steps above are incomplete.

Operations

Once the system is set up and running, it will need to be maintained. Please see the system administrator's guide