So you want to set up a lab: Difference between revisions
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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.
- O/S: We recommend Centos.
- Hardware: We recommend Intel or AMD. Supported platforms for DOCK 3.7.
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
Deploy a workstation
Tier 3 - "Middleware" level
Set up middleware for a computational drug discovery lab.
Set up psql/rdkit from scratch
Tier 4 - Server Application Software
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
Tier 6 - Operations
Monthly maintenance tasks.