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

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[[Install DOCK 3.7]]
 
[[Install DOCK 3.7]]
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[[Install SEA]]
 
[[Install SEA]]
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[[Install DOCK 6]]
 
[[Install DOCK 6]]
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[[Install ZINC]]
 
[[Install ZINC]]
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[[Install DOCK Blaster]]
 
[[Install DOCK Blaster]]
  

Revision as of 08:00, 13 March 2014

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

Time Expectations

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 0 - 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.

Tier 1 - Physical level

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


Tier 2 - 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

Tier 3 - "Middleware" level

Set up middleware for a computational drug discovery lab.

Set up psql/rdkit from scratch

Tier 4 - 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

Tier 5 - Client Application Software

PyMol

Chimera

Knime

Marvin

InstantJChem

Tier 6 - Operations

Monthly maintenance tasks.

Backups

Security Review

Software upgrades

CCP4

Chimera

H. acquire and install docking.org software

dockenv

I. configure docking.org software