Difference between revisions of "So you want to set up a lab"

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{{TOCright}}
 
{{TOCright}}
  
= Tier 0 - 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. 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 initial set up, and then 1 day/month for maintenance.
 
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. 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 initial set up, and then 1 day/month for maintenance.
  
 
When you have all the software and hardware, you can get a docking lab up and running at a basic level in less than a day. If you do not have all the software and hardware, it will take longer. If you've never run a molecular docking lab, allow a week to learn the basics.  Once you have a basic installation running, plan for a few days to [[get a queuing system working]] the way you like it.  We may be able to help. Ask us, but please read this wiki first.
 
When you have all the software and hardware, you can get a docking lab up and running at a basic level in less than a day. If you do not have all the software and hardware, it will take longer. If you've never run a molecular docking lab, allow a week to learn the basics.  Once you have a basic installation running, plan for a few days to [[get a queuing system working]] the way you like it.  We may be able to help. Ask us, but please read this wiki first.
  
= Tier 1 - Physical level =
+
= Physical level =
 
We describe an entry level system that can be easily expanded.
 
We describe an entry level system that can be easily expanded.
 
* O/S: We recommend [[Centos]].  
 
* O/S: We recommend [[Centos]].  
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= Tier 2 - Operating System level =
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= Operating System level =
 
* [[Centos]] 6.3.   
 
* [[Centos]] 6.3.   
 
* [[Foreman]]
 
* [[Foreman]]
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[[Workstation Install]]
 
[[Workstation Install]]
  
= Tier 3 - "Middleware" level =
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= Middleware level =
 
Set up middleware for a [[Compbio middleware | computational drug discovery lab]].
 
Set up middleware for a [[Compbio middleware | computational drug discovery lab]].
  
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= Tier 4 - Server Application Software =
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= Server Application Software =
  
 
[[Install DOCK 3.7]]
 
[[Install DOCK 3.7]]
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== Using git and github ==
 
== Using git and github ==
  
= Tier 5 - Client Application Software =
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= Client Application Software =
  
 
[[PyMol]]
 
[[PyMol]]
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[[InstantJChem]]
 
[[InstantJChem]]
  
= Tier 6 - Operations =  
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= Operations =  
 
Monthly maintenance tasks.  
 
Monthly maintenance tasks.  
  

Revision as of 08:37, 13 March 2014

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. 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 initial set up, and then 1 day/month for maintenance.

When you have all the software and hardware, you can get a docking lab up and running at a basic level in less than a day. If you do not have all the software and hardware, it will take longer. If you've never run a molecular docking lab, allow a week to learn the basics. Once you have a basic installation running, plan for a few days to get a queuing system working the way you like it. We may be able to help. Ask us, but please read this wiki first.

Physical level

We describe an entry level system that can be easily expanded.


Operating System level

Set up a database server

Add a new node to the cluster

How to spin up a new virtual machine

Add new disk to the cluster

Configure new disk

Deploy a workstation

Workstation Install

Middleware level

Set up middleware for a computational drug discovery lab.

Set up psql/rdkit from scratch

Server Application Software

Install DOCK 3.7

Install SEA

Install DOCK 6

Install ZINC

Install DOCK Blaster

ZINC

Here is how to set up ZINC from scratch on a new cluster.

  • create database
  • install software and web interface
  • test


Using git and github

Client Application Software

PyMol

Chimera

Knime

Marvin

InstantJChem

Operations

Monthly maintenance tasks.

Backups

Security Review

Software upgrades

CCP4

Chimera

H. acquire and install docking.org software

dockenv

I. configure docking.org software