Difference between revisions of "So you want to set up a lab"

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= Middleware level =
 
= Middleware level =
 +
We use middleware to mean 3rd party software required by our software, specific to our field.
 
Set up middleware for a [[Compbio middleware | computational drug discovery lab]].
 
Set up middleware for a [[Compbio middleware | computational drug discovery lab]].
  

Revision as of 00:42, 14 March 2014

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

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.

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.

Physical level

We discuss options for acquiring hardware in Cluster Theory. More thoughts: Acquire and deploy hardware

Operating System level

We use Operating system to describe all software components that are not particular to our field. Install operating system

Middleware level

We use middleware to mean 3rd party software required by our software, specific to our field. Set up middleware for a computational drug discovery lab.

Server Application Software

Install DOCK 3.7

Install SEA

Install DOCK 6

Install ZINC

Install DOCK Blaster

Client Application Software

PyMol

Chimera

Knime

Marvin

InstantJChem

Operations

Monthly maintenance tasks.

Backups

Security review

Software upgrades