So you want to set up a lab
Here is how I would set up a computational lab, one that could join the Worldwide ZINC network.
- DRAFT IN PROGRESS***
Tier 0 - Requirements and assumptions
This page describes setting up a full 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 need someone with system administration experience for 100 hours (3 weeks) for the initial set up, and then 1 day a month for maintenance.
Tier 1 - Physical level
We describe an entry level system that can be easily expanded.
Once you have all the software and hardware, you can get up and running at a basic level in less than a day. If you do not have all the software, plan for a few days of work. If you've never had your own molecular docking lab, plan for at least a week to learn the basics (and a lifetime to master). 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.
Hardware and Operating System
Compbio middleware needed to support our software and a computational pharmacology lab.
Tier 2 - Operating System level
- Centos 6.3.
- configure network
- Perimeter security.
Set up a database server
Add a new node to the cluster
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 - Computational Pharmacology Application Software - Server side
Here is how to set up ZINC from scratch on a new cluster.
- create database
- install software and web interface
Using git and github
Tier 5 - Compuational Pharmacology Application Software - Client side
Tier 6 - Operations
Monthly maintenance tasks.