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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 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

• 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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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 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-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
• shahir_at_fbb.utm.my
• www.fbb.utm.my