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. | 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 = | ||
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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]]. 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. | ||
= | = 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. | |||
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]] | ||
= 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]] | |||
[[ | |||
[[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