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

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Here is how I would set up a computational lab. ***DRAFT IN PROGRESS***
Here is how I would set up a computational lab, one that could join the worldwide [[docking.org network]].
 
***DRAFT IN PROGRESS***


= Tier 0 - Requirements and assumptions =
= Tier 0 - Requirements and assumptions =
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= Tier 2 - Operating System level =
= Tier 2 - Operating System level =
* [[Centos]] 6.3. Foreman.  VM. 
* [[Centos]] 6.3.   
 
* configure network
Perimeter security. Passwords. Networking.
* DNS
* Foreman
* Perimeter security.
* Passwords.  
* SGE


= Tier 3 - "Middleware" level =
= Tier 3 - "Middleware" level =
Set up middleware for a [[Compbio middleware | computational drug discovery lab]].
Set up middleware for a [[Compbio middleware | computational drug discovery lab]].
 
*SGE
*CCP4
*Chimera and PyMol




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[[Software upgrades]]
[[Software upgrades]]
=== CCP4 ===
=== Chimera ===
== H. acquire and install docking.org software ==
=== dockenv ===
== I. configure docking.org software ==
[[Category:Sysadmin]]
[[Category:Tutorial]]


[[Category:Tutorial]]
[[Category:Tutorial]]

Revision as of 18:24, 12 March 2014

Here is how I would set up a computational lab, one that could join the worldwide docking.org 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

Tier 3 - "Middleware" level

Set up middleware for a computational drug discovery lab.

  • SGE
  • CCP4
  • Chimera and PyMol


Tier 4 - Computational Pharmacology Application Software - Server side

DOCK 3.7

SEA

DOCK Blaster

ZINC

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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