So you want to set up a lab: Difference between revisions

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We describe an entry level system that can be easily expanded.
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.
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= 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 =
= Tier 2 - Operating System level =

Revision as of 07:40, 13 March 2014

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

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

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

SEA

DOCK Blaster

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

PyMol

Chimera

Knime

Marvin

InstantJChem

Tier 6 - Operations

Monthly maintenance tasks.

Backups

Security Review

Software upgrades

CCP4

Chimera

H. acquire and install docking.org software

dockenv

I. configure docking.org software

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