Asia Pacific BioGRID Initiative

Background

1998 – APBioNet project created a distributed database mirror which was to evolve into the basis for a prototypic DataGrid. Progress was slow – until Oct 2001, the first BioGRID meeting was organised in Singapore by BIC-NUS and APBioNet. In Dec 2001, Cray Inc was involved in partnering us in setting up a SuperBioGRID’02 symposium Momentum was set and first GRID was created before Christmas 2001!

APBioGrid 2002

In June 2002, APBioNet launched APBioGrid as a collaboration among Cray Inc, KOOPrime Pte Ltd, Lion Bioscience and APBioNet towards an integrated data-compute-workflow platform. The first BioGrid platform included a pentium cluster, a Cray SV1 and Sun servers in the National University of Singapore, Cray machines in Australia and Japan integrated via the Globus Grid Toolkit (version 1.1.3/4). The front end interface would be the Workflow Integration System from KOOPrime. This project was codenamed BioWorldWideWorkflow (BioWWWF).

APBioBox 2003

In Jan 2003, APBioNet received a research grant from the Pan Asia Networking (PAN) Programme of IDRC (Canada) to build an APBioBox of commonly used bioinformatics applications and packages with grid-computing software as part of its effort to build an APBioGrid. The platform chosen was the then ubiquitous Redhat Linux.

In March 2003, APBioNet launched an industry partnership scheme (AIPS) and partnered with Sun Microsystems to build BioBox for the Solaris platform.

In Nov 2003, beta versions of APBioBox and Sun’s biobox, now called Bio-Cluster Grid were released for beta testing among selected parties. The packages included Globus Grid Toolkit Version 2.0 and Sun Grid Engine respectively.

APBioBox and Bio-ClusterGrid 2003/2004

On 4th Dec 2003, the biobox software packages now named APBioBox (Redhat Linux) and BioCluster Grid (Sun Solaris) were field-tested at a Bioinformatics Workshop was conducted at the Advanced Science and Technology Institute (ASTI), Department of Science and Technology (DOST), Philippines on the occasion of the 70th Anniversary of the National Research Council of the Philippines (NRCP). Ten pentium machines and a couple of Sun servers were successfully inducted into the APBioGrid. This Workshop and the software tested were sponsored by Sun Microsystems and partially funded by IDRC.

In April 2004, APBioNet in collaboration with the organisers of the Life Sciences Virtual Grid Community Symposium, namely, the Singapore Ministry of Health (MOH), Singapore National Grid Office (NGO), and Singapore Agency for Science, Technology and Research (A*STAR) at a pre-symposium Workshop for the life sciences and biomedical communities on “Grid Research & Information Driven Biomedical Applications”, presented a hands-on and demonstration of APBioBox.

As a result of the heightened awareness of the data-intensive nature of bioinformatics application, an effort was made to set up a biodatagrid, starting with the NUS BioDataGrid registry of mirrored archival public domain databases, research pre- and post-publication databases, and web database and computational services in July 2004. This was part of the larger effort at the Singapore national level to establish a registry of databases hosted in Singapore. Work is in progress to extend this to the Asia Pacific region by coordinating with the network of Bio-Mirror nodes by the end of 2004.

BioWorldWideWorkflow 2004/2005

In July 2004, in collaboration with the National University of Singapore and its spin-off company, KOOPrime Pte Ltd, the construction of the BioWorldWideWorkFlow of the World Wide WorkFlow (W3F) proceeded into the construction phase of the production W3F using
KOOPLite for the graphical user interface for workflow browsing and editing – the W3F browser,
KOOPServer for the workflow management, staging and execution – the W3F orchestrator or enactor
KOOPDaemon for the workflow execution – the W3F service,
the APBioBox as the shrink-wrapped pre-configured package for rapid replication of KOOPLite, KOOPDaemon and the bioinformatics applications on RedHat Linux platforms,
the Bio-Cluster Grid package for Solaris platforms,
the Globus Grid Toolkit for interfacing with grid-enabled applications