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.

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

• Centos 6.3.
• Foreman
• DNS
• Authentication
• Perimeter security.
• SGE

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.

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

Tier 5 - Client Application Software

PyMol

Chimera

Knime

Marvin

InstantJChem

Tier 6 - Operations

Monthly maintenance tasks.

Backups

Security Review

Software upgrades