Difference between revisions of "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 [[docking.org network]].
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Here is how I would set up a computational lab, one that could join the [[Worldwide ZINC]] network.
  
 
***DRAFT IN PROGRESS***
 
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= Tier 4 - Computational Pharmacology Application Software - Server side =
 
= Tier 4 - Computational Pharmacology Application Software - Server side =
  
 
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[[Getting started with DOCK 3.7]]
[[DOCK 3.7]]
 
  
 
[[SEA]]
 
[[SEA]]

Revision as of 07:34, 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.


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