So you want to set up a lab

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


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
  • 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

Configure new disk

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

Getting started with DOCK 3.7


DOCK Blaster


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.


Security Review

Software upgrades



H. acquire and install software


I. configure software