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

From DISI
Jump to navigation Jump to search
Line 18: Line 18:
 
We use middleware to mean 3rd party software required by our software, specific to our field.
 
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]].
 +
 +
= Client Application Software =
 +
 +
* [[PyMol]]
 +
* [[Chimera]]
 +
* [[Knime]]
 +
* [[Marvin]]
 +
* [[InstantJChem]]
 +
* [[OpenBabel]]
 +
* [[rdkit]]
 +
 +
 +
 +
== Feeware ==
 +
* [[pgf]]
 +
* [[CSD]]
 +
* [[Chemaxon]]
 +
* [[OpenEye]]
 +
  
 
= Server Application Software =
 
= Server Application Software =
Line 28: Line 47:
 
* [[Install DOCK Blaster]]
 
* [[Install DOCK Blaster]]
  
= Client Application Software =
 
 
[[PyMol]]
 
 
[[Chimera]]
 
 
[[Knime]]
 
  
[[Marvin]]
+
* [[AMSOL]]
  
[[InstantJChem]]
 
  
 
= Operations =  
 
= Operations =  

Revision as of 16:01, 18 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, or you already own equivalent or better hardware. 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 purchase, acquisition and deployment of the hardware and installation of the operating system and software components. Once running, as a guideline plan for the equivalent of 1 day/month of expert sysadmin time for each 10 computer enclosures to keep your cluster running smoothly.

When you have all the software and hardware, you can get a docking lab up and running in less than a day. If you have not administered a molecular docking lab before, allow a few months to learn how to take care of it.

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.

Client Application Software


Feeware


Server Application Software

Each product is licensed and distributed separately.



Operations

Monthly maintenance tasks.

Backups

Security review

Software upgrades