Bioinformatics is specific Computational Biology

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Bioinformatics is specific Computational Biology
Computational Biology
Bioinformatics Biological Information
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Biological Function
Understanding biological function(s) in living
organisms is the ultimate goal of the Biomedical
Sciences Understanding means gaining knowledge
about something, i.e. knowing how it works and
what it can be used for
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Knowledge

• Knowledge differs from data and information in
  the sense that
• it is directly usable (eg diagnostics, decision
  support, drug design)
• more knowledge can be derived using only existing
  knowledge and logical inference

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Acquiring knowledge

• Primary databases (EMBL Genbank SwissProt)
• Secondary databases (Prosite, Prints, Blocks)
• Integrated Databases
• (Columba proteins, structures, annotations)
• Curated Resources (Reactome) and Genome Browsers
  (Ensembl)

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Environmental genomics

• JC Venter et al, Science Apr 2004
• Environmental Genome Shotgun Sequencing of the
  Sargasso Sea
• 2 million fragments, quasi-industrial assembly
• Potential descovery of 150 new species, but
  only two complete genomes....
• Identification of 1200 new genes
• Some experts believe that there is material for
  more than 10 years of research in those 900
  liters of seawater

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Seeing is believing, not knowing
The famous Boehringer Manheim Biochemical
Pathways wallchart
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But the real problem is in ...the complexity!
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Lifes Complexity Pyramid
Oltvai-Barabasi, Science 10/25/02)
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The omics revolution

• Genomes
• Proteomes
• Transcriptomes
• Metabolomes
• Whateveromes (...?)
• the need to make sense of all of the above

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Living systems

• Research is still largely driven by reductionism
• Living systems are not sets of parts working to
  an end
• Biological complexity not a myth
• Biological complexity lies on the relationships
  amongst components and their constant interplay

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Systems Biology

• Is said to be the key to unlocking the value
  within the Omics Revolution
• Projections show that its products and services
  are growing at an annual compound rate of 66,
  reaching 785 million by 2008
• Pharmaceutical companies are looking at ways to
  overcome deficitay innovation activities

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• http//www.systemsbiology.org

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Integration of HT experiments
Integrating omic information a bridge between
genomics and systems biology Hui Ge, Albertha
J.M. Walhout and Marc Vidal, TRENDS in Genetics
Vol.19 No.10 October 2003
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Post omics

• Crete databases that are
• Following standards
• Use ontologies
• XML
• ...
• Interoperable
• Easy to integrate
• Prone to Mining

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Connection to Medical Informatics

• Integrate Clinical and Omic data
• Clinical trials, cohort, EBM
• Grab intelligent solutions from other areas
• Deliver filtered info services to
• Medical practitioners
• Decision makers
• Public

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Is Biology such a big data source?

• Data source size estimates
• There are 1011 galaxies in the observable
  Universe
• There are 4x1022 stars in the observable Universe
• The number of 1 micron grains of sand in a
  typical beach (5km x 500m x 5m) is 12.5x1025
• Projections show that there can be 1066 different
  molecular species, of which we know a little
  fraction 105

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Genome Sizes