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.
Timeline
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
- O/S: We recommend Centos.
- Hardware: We recommend Intel or AMD. Supported platforms for DOCK 3.7.
Middleware
Compbio middleware needed to support our software and a computational pharmacology lab.
Tier 2 - Operating System level
- Centos 6.3.
- configure network
- DNS
- Foreman
- Perimeter security.
- Passwords.
- SGE
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 - Computational Pharmacology Application Software - Server side
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 - Compuational Pharmacology Application Software - Client side
Tier 6 - Operations
Monthly maintenance tasks.