Transcript PPT 4.8Mb

Biodiversity informatics: Uniformity in Diversity
Mohd 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
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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 - AIBIL
IBM eServer Cluster 1350
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32 processors with:
 Intel Xeon DP
3.06GHz/533Mhz
FSB.
 1GB of ECC DDR
SDRAM RDIMM.
 IBM 36.4GB 10K-rpm
Ultra320 SCSI HotSwap SL HDD.
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Connected to MyREN.
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Education
• Bachelor of Computer Science (Bioinformatics)
• Master of Science (by Research)
• PhD (by Research)
Faculty of Computer Science and
Information Systems
www.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
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database
Interoperability with
GBIF
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Biodiversity Informatics - Database
■ Online depository – user can
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create their own datatypes
Information Catalogue - fact
sheets, species guide etc
Bibliographical information – inhouse 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-
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3D view
Departure from
typical biodiversity
database – pseudo
3D
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STORe-Biodi
Spatio-Temporal Object Relational Biodiversity
Database
A Biodiversity Informatics database for marine ecosystem
PresentedConference On Marine Ecosystem of Malaysia
29-30 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
– [email protected]
■ www.fbb.utm.my
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