Michigan Life Sciences Corridor Michigan Life Sciences Corridor Bioinformatics, University of Bioinformatics, University of Michigan Michigan March 14, 2001 March 14, 2001 Building Analysis Building Analysis Environments Environments Beyond the Genome and the Web Beyond the Genome and the Web Bruce R. Schatz CANIS Laboratory School of Library & Information Science School of Biomedical & Health Information Sciences University of Illinois at Urbana-Champaign [email protected] , www.canis.uiuc.edu
40
Embed
Building Analysis Environments Beyond the Genome and the Web
Building Analysis Environments Beyond the Genome and the Web. Bruce R. Schatz CANIS Laboratory School of Library & Information Science School of Biomedical & Health Information Sciences University of Illinois at Urbana-Champaign [email protected] , www.canis.uiuc.edu. - PowerPoint PPT Presentation
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Michigan Life Sciences CorridorMichigan Life Sciences CorridorBioinformatics, University of MichiganBioinformatics, University of Michigan
March 14, 2001March 14, 2001
Building Analysis EnvironmentsBuilding Analysis Environments Beyond the Genome and the WebBeyond the Genome and the Web
Bruce R. SchatzCANIS Laboratory
School of Library & Information ScienceSchool of Biomedical & Health Information Sciences
In the past decade, technology has created the Genome and the Web
In 1991, these ideas were only plansIn 2001, they have already progressed from research systems to commercial products
In the next decade, the revolution will actually begin and the world will be completely
different!
Paradigm Shift (Pre)Paradigm Shift (Pre)
Towards Dry-Lab Biology, Walter Gilbert (Jan 1991)
“The new paradigm, now emerging, is that all the 'genes' will be known (in the sense of being resident in databases available electronically), and that the starting point of a biological investigation will be theoretical. An individual scientist will begin with a theoretical conjecture, only then turning to experiment to follow or test that hypothesis. ...
To use this flood of knowledge [the total sequence of the human and model organisms], which will pour across the computer networks of the world, biologists not only must become computer-literate, but also change their approach to the problem of understanding life. ...
The Coming of Informational ScienceCorrelation of Information across Sources
Paradigm Shift (Post)Paradigm Shift (Post)
Dissecting Human Disease, Victor McKusick (Feb 2001)
Structural genomics Functional genomics Genomics Proteomics Map-based gene discovery Sequence-based gene discovery Monogenic disorders Multifactorial disorders Specific DNA diagnosis Monitoring susceptibility Analysis of one gene Analysis of multi-gene
pathways Gene action Gene regulation Etiology (mutation) Pathogenesis (mechanism) One species Several species
Analysis Environments IAnalysis Environments I
The Present -- Year 2001
Search Central Archives
Locating a Generic (average) solution mining sequences from the Genome diagnosing diseases from the Clinical Trial
some Problems may have point Solutions find the cystic fibrosis gene find the diabetes treatment
Analysis Environments IIAnalysis Environments II
The Future -- Year 2011
Navigate Distributed Repositories
Locating a Specific (situational) solution correlating sequences, genes, expressions correlating diagnoses, treatments, lifestyles
most Problems have cluster Solutions find genes for Heart Disease find treatments for Arthritis
WCS -- a testbed for the world of 2001 community repositories before the Web
in 1991, a distributed analysis environment
MCS -- a testbed for the world of 2011 concept navigation before the Interspace
in 2001, a biomedical analysis environment
to enable Michigan Corridor faculty and students
to live in the world of the future (information space)
Testbeds of the FutureTestbeds of the Future
Community SystemsCommunity Systems
browse and share all the knowledge of a community
data results(database management) (electronic mail)
literature news(information retrieval) (bulletin
boards)
knowledge(hypertext annotations)
Formal Informal
Worm Community SystemWorm Community System WCS Information:Literature BIOSIS, MEDLINE, newsletters,
Databases Sequences: GENBANK, Celera Genes and Maps from Model Organisms Microarray Expressions, Protein Structures Gene Pathways, Cellular Anatomy
Ten Steps from Here to ThereTen Steps from Here to There Determine Users (range of needs) Develop Hardware (networks) Determine Collections (range of types) Develop Software (databases) Interlinks Automatic (name recognition) Interlinks Manual (distributed
annotation) Community Literature (journals, conferences) Concept Navigation (indexing, switching) Custom Databases (community datasets) Custom Software (specialized analysis)
Bioinformatics CenterBioinformatics Center Institute for Biological Information Systems
develop new information systems deploy to study biological systems integrated analysis for biological information analysis environment for community repositories
IBIS New GloryIBIS New Glory Institute for Biological Information Systems
unique facility for all Michigan laboratories interactive systems training for all levels
IBIS reborne Thoth, sacred ibis who hatched the world inventor of writing, keeper of divine archives inventor of arts & sciences, medicine & surgery First of the magicians, he was called the Elder:
His disciples claimed access to the crypt where he kept his books of magic, so they undertook to decipher and learn “these formulas which commanded all the forces of nature and subdued the very gods themselves”.