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, one that could join the [[Worldwide ZINC]] network. | Here is how I would set up a computational lab, one that could join the [[Worldwide ZINC]] network. | ||
= Time Expectations = | |||
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, plan for a few days of work. 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. | |||
{{TOCright}} | |||
= Tier 0 - Requirements and assumptions = | = Tier 0 - Requirements and assumptions = | ||
This page describes setting up a full research lab. We describe the minimum setup, plus options for expansion. | 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. | ||
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 | |||
= Tier 1 - Physical level = | = Tier 1 - 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]]. | ||
* Hardware: We recommend Intel or AMD. [[Supported platforms for DOCK 3.7]]. | * Hardware: We recommend Intel or AMD. [[Supported platforms for DOCK 3.7]]. | ||
= Tier 2 - Operating System level = | = Tier 2 - Operating System level = | ||
* [[Centos]] 6.3. | * [[Centos]] 6.3. | ||
* | * [[Foreman]] | ||
* DNS | * DNS | ||
* | * Authentication | ||
* Perimeter security. | * Perimeter security. | ||
* | * [[SGE]] | ||
== Set up a database server == | == Set up a database server == | ||
== Add a new node to the cluster == | == Add a new node to the cluster == | ||
[[How to spin up a new virtual machine]] | [[How to spin up a new virtual machine]] | ||
== Add new disk to the cluster == | == Add new disk to the cluster == | ||
[[Configure new disk]] | [[Configure new disk]] | ||
| Line 48: | Line 34: | ||
= 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]]. | ||
= Set up psql/rdkit from scratch = | = Set up psql/rdkit from scratch = | ||
= Tier 4 - Computational Pharmacology Application Software - Server side = | = Tier 4 - Computational Pharmacology Application Software - Server side = | ||
[[ | [[Install DOCK 3.7]] | ||
[[Install SEA]] | |||
[[ | [[Install DOCK 6]] | ||
[[Install ZINC]] | |||
[[DOCK Blaster]] | [[Install DOCK Blaster]] | ||
== [[ZINC]] == | == [[ZINC]] == | ||
Revision as of 07:50, 13 March 2014
Here is how I would set up a computational lab, one that could join the Worldwide ZINC network.
Time Expectations
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, plan for a few days of work. 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.
Tier 0 - 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.
Tier 1 - 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.
Tier 2 - 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
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
Install DOCK 3.7 Install SEA Install DOCK 6 Install ZINC Install 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
Tier 6 - Operations
Monthly maintenance tasks.