Overview
[ Objectives | How Does it Work? | Components | Version 1.5 (Current Version) | Version 1.4 | Bio-ClusterGrid for ROCKS 3.3.0 | Future Plans ]
The Bio-ClusterGrid is the first of many deployment architectures that realizes the benefit of the BioBox initiative.
Objectives- To enable biologists harness the power of a clustergrid through a web interface
- To simplify and speed up the installation of a cluster running bioinformatics applications
- To provide a portal interface to command line applications
- To evenly distribute jobs in a cluster
How Does it Work?
More than 20 of the most popular bioinformatics applications are made available on the Bio-ClusterGrid through the portal, which greatly enhances application usability. Biologists access the portal either through a browser in Sunray Thin Clients in the access tier or through any browser enabled device. The Grid Engine software provides the resource management mechanism to schedule all the bioinformatics applications to run on the cluster of execution servers.
Components
The core components of the Bio-ClusterGrid are:
- Operating System (Linux/Solaris)
- Job Scheduler (Sun Grid Engine)
- Grid Engine Portal running on Sun Java System Portal Server
- More than 20 pre-compiled and tested bioinformatics applications that is provided by APBioNet
Version 1.5 (Current Version)
Version 1.5 Components
- Java Enterprise System Portal Server 2005Q4
- Sun Grid Engine 6.1
- Bioinformatics application binaries
- Bioinformatics applications intergration scripts
Version 1.5 System/Platform Requirements
Bio-ClusterGrid Master Nodes
- Solaris 10 on 32-bit x86
- Solaris 10 on x64
- RHEL 3.0 AS/WS/ES update 4 (32-bit only)
- Solaris 10 on 32-bit x86
- Solaris 10 on x64
- RHEL 4.0 WS (x86_64) and similar
The list of applications are as follows. To view the complete list of applications availability of different platform and the compatibility matrix, download the BCG 1.5 Applications List.
*Portal enabled applications
Version 1.4
Version 1.4 Update 2 Components
- Java Enterprise System Portal Server 2005Q4
- N1 Grid Engine 6 Update 4
- Bioinformatics application binaries
- Bioinformatics applications intergration scripts
Version 1.4 Update 2 System/Platform Requirements
Bio-ClusterGrid Master Nodes
- Solaris 9/10 on SPARC
- Solaris 10 on 32-bit x86
- Solaris 10 on x64
- RHEL 3.0 AS/WS/ES update 4 (32-bit only)
- ROCKS 3.3.0 i386
- Solaris 9/10 on SPARC
- Solaris 10 on 32-bit x86
- Solaris 10 on x64
- RHEL 3.0 WS (x86_64) and similar
- ROCKS 3.3.0 x86_64
Version 1.4 Update 2 Applications
The list of applications are as follows. To view the complete list of applications availability of different platform and the compatibility matrix, download the BCG 1.4 Applications List.
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*Portal enabled applications
Bio-ClusterGrid for ROCKS 3.3.0
The ROCKS 3.3.0 version of Bio-ClusterGrid has been developed by South China University of Technology - Network Center (SCUT-NC) under the ChinaGrid project. The project team consisted of:
Project Director
- Dr. Dong Shoubin
- Dr. Yuan Hua
- Ning Guoning
- Yue Qiang
- Liu Pengfei
- Chen Xiaofeng
- Java Enterprise System Portal Server 2005Q4
- Sun Grid Engie 5.3
- Bioinformatics application binaries roll
- Bioinformatics applications intergration scripts
ROCKS 3.3.0 System/Platform Requirements
Bio-ClusterGrid Master Nodes
- ROCKS 3.3.0 i386
- ROCKS 3.3.0 x86_64
Please refer to the 'Guides & Documentations' link above for the installation guide. If you would like to receive a copy, please email engage-apstc@sun.com
Future Plans
- Inclusion of MPI applications