So you want to set up a lab: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
{{TOCright}} | {{TOCright}} | ||
= | = 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. | 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. 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. | 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. 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. | ||
= | = Physical level = | ||
We describe an entry level system that can be easily expanded. | We describe an entry level system that can be easily expanded. | ||
* O/S: We recommend [[Centos]]. | * O/S: We recommend [[Centos]]. | ||
| Line 14: | Line 14: | ||
= | = Operating System level = | ||
* [[Centos]] 6.3. | * [[Centos]] 6.3. | ||
* [[Foreman]] | * [[Foreman]] | ||
| Line 33: | Line 33: | ||
[[Workstation Install]] | [[Workstation Install]] | ||
= | = Middleware level = | ||
Set up middleware for a [[Compbio middleware | computational drug discovery lab]]. | Set up middleware for a [[Compbio middleware | computational drug discovery lab]]. | ||
| Line 39: | Line 39: | ||
= | = Server Application Software = | ||
[[Install DOCK 3.7]] | [[Install DOCK 3.7]] | ||
| Line 61: | Line 61: | ||
== Using git and github == | == Using git and github == | ||
= | = Client Application Software = | ||
[[PyMol]] | [[PyMol]] | ||
| Line 73: | Line 73: | ||
[[InstantJChem]] | [[InstantJChem]] | ||
= | = Operations = | ||
Monthly maintenance tasks. | Monthly maintenance tasks. | ||
Revision as of 08:37, 13 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. 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.
Physical level
We describe an entry level system that can be easily expanded.
- O/S: We recommend Centos.
- Hardware: We recommend Intel or AMD. Supported platforms for DOCK 3.7.
Operating System level
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
Deploy a workstation
Middleware level
Set up middleware for a computational drug discovery lab.
Set up psql/rdkit from scratch
Server Application Software
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
Client Application Software
Operations
Monthly maintenance tasks.