Bioinformatics

Introduction

BioInformatics Center (BIC), the first bioinformatics core facility arising from the Bioinformatics User and Support Group in 1991, was founded in 1996 as a national Bioinformatics Centre and has since been providing core facility support and training for research and teaching in undergraduate modules.

Funding

Funded first by EDB in 1996, and hosted in NUS, the Bioinformatics Centre's cutting edge research and resources was a key factor in helping to attract pharmaceutical companies to set up research labs in Singapore then. Its funding was then transferred to the NSTB, which used it to lay the foundation for setting up the A*STAR Bioinformatics Institute BII in 2001. Bioinformatics Centre continued to exist as an NUS Bioinformatics Centre to provide computational research and teaching resources at NUS, occasionally providing friendly support and advice to GIS, IMCB and BII. From 1998 to date, it is a core facility used in teaching undergraduates in BM1106, LSM2104, LSM2241, LSM3241, MDG5101 directly and other modules informally, including the funded training of 20 Graduates in Bioinformatics from 2002 to 2008. It runs ad hoc workshops every year to researchers on how to use Bioinformatics techniques. It has leveraged on funding from the Bioinformatics Programme of the Life Science Institute LSI, space support from the Biochemistry Department where computer facilities and research labs are hosted, as well as computing power from Computer Centre's TeraCampus Grid and the Supercomputing Visualisation Lab from early 2000s to date. It is also host to the first bioinformatics node and secretariat of the APEC-TEL-endorsed Asia Pacific Bioinformatics Network (APBioNet) which has been coordinating one of Asia's most successful premier international conferences (InCoB) now in its tenth year since 2002 and internationally renowned bioinformatics outreach programmes to Asia and beyond by the S* Life Science Informatics Alliance of NUS, Stanford University, Swedish universities of Uppsala and Karolinska, University of Sydney, South Africa National Bioinformatics Institute, University of California San Diego, through an inter-university MoU in 2001. Its resources are also funded by two NIH sub-contracts and one EUAsiaGrid EC infrastructure contract.

Achievements

For the past 15 years, BIC is the only generic, non-project-based Core Facility serving the NUS community in Bioinformatics hosting databases of the international Bio-Mirrors consortium, representing Singapore, including an official mirror of the Protein DataBank PDB from 200X to 200X providing grid computing services since 2002; from 2001 to 2003, a Cray X1 supercomputing service for Bioinformatics; from 2007, a bioinformatics Linux distribution BioSLAX; a completed project endorsed by ASEAN COST; since 2010 the first cloud computing bioinformatics system for teaching and research use; and since 2011, the BioDB100 cloud reinstantiable database repository.

BioInformatics Resources

BIC consists of cross-disciplinary engineers who are highly skilled in almost all aspects of IT and yet have enough knowledge in the areas of biology to make their presence indispensable. Their mission is to design, implement and maintain the core life science/IT infrastructure that supports research that is done in the field of bioinformatics. From fixing the smallest problems in Microsoft Windows to writing complex programs to help researchers manipulate the largest databases or analyse and fix networking problems, the team lends their talents to almost anything that is within their capability.

Most important is the team's tireless effort in helping to propagate bioinformatics resources. The team participates actively as technical consultants in the Asia Pacific Bioinformatics Network (APBioNet) as well as in other Asia-Pacific Networking Group (APNG) supported organisations and has recently begun assisting several groups to set up bioinformatics resources and provide individual assistance.

Some of these groups include:
  • NUS Department of Biological Sciences Bioinformatics Node
  • NUS Bioprocessing Technology Centre Bioinformatics Node
  • The National Cancer Centre Bioinformatics Node

The team also assists serveral of scientists on their projects as well as maintain links to many well known external resources like the Protein Databank (PDB) mirrored directly from the Research Collaboratory for Structural Bioinformatics (RCSB). Their involment in APBioNet has resulted in active participation of the BioMirrors project, This project provides users with high speed access to these large databases some of which exceed 10 Gigabytes. The project sites are connected with the Internet II infrastructure of vBNS and the Asia-Pacific Advanced Network (APAN). Good planning, team cohesiveness and hard work has resulted in a cheap, highly scalable system to house the ever growing data sets with little maintainence.

With the creation of the S-Star Alliance in bioinformatics education, the team has also taken up the added responsibility of providing technical resourses and consultancy for this prestegious collaboration between some of the top univesities in the world. The links below, under Resource Categories, will pop up lists of all the resources both commercial, external and in-house that are available from the center. Update listings and descriptions will help you find the right application you require.

The unit is also starting to test several GRID enabled bio/life science applications on the Tera Campus Grid (TCG) (United Devices GRID-BLAST was a tremendous success) and will be adding them soon. Also feel free to download (when available) our BIC Resource Handbook, which will give you information on what resources are available, how to use them, what kind of regulation apply to the use of applications, the different groups of specialists (PERL programmers, database administrators, etc) who may be able to assist you in any particular area of need and much more.

Links

Resource Categories Life Science Portal Tera Campus Grid (TCG)
BioMirror Databases Life Science Database Portal GRID BLAST Submission
Local Databases/Services GRID BLAST Job Status
Resource Database GRID BLAST Results Retrieval
GRID HMMER Submission
GRID HMMER Job Status
GRID HMMER Results Retrieval

Contacts

PI-in-charge Life Science Portal Tera Campus Grid (TCG)
A/P Tan Tin Wee

+65 6516 3242
IT Architect /
Bioinformatics Manager

Mark De Silva

+65 6774 7149
Senior Systems Engineer /
Dy Bioinformatics Manager

Lim Kuan Siong

+65 6774 7149

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