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Biodiversity informatics: Uniformity in DiversityBiodiversity informatics: Uniformity in DiversityMohd Shahir Shamsir

Department of Biological Sciences, Faculty of Bioscience & Bioengineering

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Contents

• Introduction to Bioinformatics in UTM• People and Places

• Biodiversity Project• Outline

• Uniformity and diversity• Expectations and ideals• Trials and tribulations

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Peoples and Places■ The Artificial Intelligence and

Bioinformatics Laboratory (AIBIL)

■ Prof. Safaai Deris, Dr. (Director)

■ Software Engineering Department,

■ Faculty of Computer Science and Information Systems (FSKSM).

■ Bioinformatics Research Laboratory

■ Shahir Shamsir, Dr (Principle Researcher)

■ Biological Scieces Department

■ Faculty of Bioscience and Bioengineering (FBB) www.fbb.utm.my

■ UTM youngest faculty

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Lab - AIBILIBM eServer Cluster 1350

• 32 processors with: Intel Xeon DP

3.06GHz/533Mhz FSB.

1GB of ECC DDR SDRAM RDIMM.

IBM 36.4GB 10K-rpm Ultra320 SCSI Hot-Swap SL HDD.

• Connected to MyREN.

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• Bachelor of Computer Science (Bioinformatics)

• Master of Science (by Research)

• PhD (by Research)

Education

Faculty of Computer Science and Information Systemswww.fsksm.utm.my

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Biodiversity Informatics Project - Outline■ Initiated to catalogue medicinal flora in Endau Rompin

■ 2nd project for FBB

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Bodiversity

■ Biological diversity" is defined as the variability among living organisms from all sources including, inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems. Convention of Biological Diversity (CBD)

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Biodiversity Informatics

■ the application of information technologies to the management, algorithmic exploration, analysis and interpretation of primary data regarding life, particularly at the species level of organization – (Soberón & Peterson 2004)

Providing resource for policy makers and environmental managers with relevant information on biodiversity.

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Biodiversity Informatics - Database■ Biota.my

■ Typical biodiveristy database

■ Interoperability with GBIF

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Biodiversity Informatics - Database■ Online depository – user can

create their own datatypes ■ Information Catalogue - fact

sheets, species guide etc■ Bibliographical information – in-

house or third party■ A Geographic Information

System (GIS) ■ Forum – to encourage user

participation, information exchange

■ Information on depositors – profile page to determine authenticity of data

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Biodiversity Informatics - GIS

■ Tie in with ArcGIS

■ Sense of being- 3D view

■ Departure from typical biodiversity database – pseudo 3D

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STORe-BiodiSpatio-Temporal Object Relational Biodiversity

DatabaseA Biodiversity Informatics database for marine ecosystem

PresentedConference On Marine Ecosystem of Malaysia29-30 May 2007 Port Dickson, Malaysia

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Uniformity – Expectations & Ideals■ It should

– posses a global “data harmony”

– Maintain certain standard

– Strengthen the existing infrastructures

– Reinforces open scientific inquiry

– Encourages diversity of opinion and analysis; promotes new research;

– Facilitates the education of new researchers;

– Make possible the exploration of ideas not envisioned by the initial investigators;

– Allow the creation of new data when data from multiple sources are combined.

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Uniformity - Trials and tribulations■ Costs?

– fat cats and running dogs; political bureaucracy

– Business model?

– Scientific will?

■ Lack of sharing culture? – Biologist, computer scientist, geoinformaticist, botanist

– Sharing expertise

– Relied on hybrids

■ concerns about ownership and IPR – Who owns what? Access? Data deposition?

– Biopiracy and bioprospecting

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Further information and contact

■ Mohd Shahir Shamsir– shahir@fbb.utm.my

■ www.fbb.utm.my