The Burnham Institute

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The Burnham Institute
Cancer, Neuroscience, and Aging Research
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The BURNHAM INSTITUTE

• 61 Faculty Members (51 full-time 10 adjunct)
• 575 Employees
• 300 M.D. and/or Ph.D.
• gt330 Publications Annually

• 2003/2004 Budget in excess of 53 Million
• 250 Patents
• National Cancer Institute-designated Cancer
  Center

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Multi- Disciplinary Approach to Science
Computational Biology
Cell Biology
Molecular Biology
Research Programs
Genetics
Bio- Chemistry
Structural Biology
Chemistry
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Informatics and Data Management (IDM) Cancer
Center Shared Resources
MISSION SUPPORT THE CANCER RESEARCH BY
ESTABLISHING A USER-FRIENDLY ACCESS TO THE
INTEGRATED FRAMEWORK FOR DATA SHARING,
COMPARATIVE ANALYSIS AND INTERPRETATION
Resource Director Adam Godzik, Ph.D. Resource
Manager Andrei Osterman, Ph.D. Resource
Specialists Darek Kedra, M.D., Ph.D.,
Kutbuddin Doctor, Ph.D.
Bridging The Gap Between Experimental Biology And
Informatics
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VISION
IDM
IDM
IDM
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SUPPORT OF ON-GOING PROJECTS
EXAMPLE GENOMICS OF COLON CANCER
AP-PCR
Clones
Spotting
Sequencing
Tumor DNA amplification, labeling, hybridization
1,920 sequences
Redundantclusters
Insert sizes
Redundantclones
Genomic mapping
Intensity files
POSTGRESSQLDATABASE
Mappingclone IDs on the array
Recalculatingintensityratios
Plotting results
Evaluatingchromosomal gains/losses
Arbitrarily Primed PCR Array, Comparative
Hybridization
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SUPPORT OF DATA SHARING
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INTEROPERABILITY PROBLEM
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FIRST YEAR PLAN
I. Integration layer (components of caBIG
infrastructure) - a local instance of gene
expression and drug activity database -
integrated data sets on gene expression and drug
activity in 60 NCI cell lines - toolkit for
statistical analysis, clustering, searches and
comparative analysis - connection of identified
characteristic gene sets to external archives
and ontologies and to TBI Cancer Molecule Pages
Interface. II. Interpretation layer (Burnham
development) - Interface interactive access to a
confederated database and specialized tools
automatic extraction and updates of protein
portraits (Cancer Molecule Pages) user input,
curation, virtual collaborations - Cancer
Molecule Pages a first set of Cancer Molecule
Pages for 300 genes (proteins) of primary
research interest for investigators at TBI cancer
center.
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INTEGRATION
EXAMPLE DRUG DISCOVERY DATABASE
Other Cancer Centers

• SHARED DATABASE
• in-house and external data
• query by compounds
• query by target
• query by cell lines

Target-based screening
Virtual Docking
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FIRST YEAR PLAN
I. Integration layer (components of caBIG
infrastructure) - a local instance of gene
expression and drug activity database -
integrated data sets on gene expression and drug
activity in 60 NCI cell lines - toolkit for
statistical analysis, clustering, searches and
comparative analysis - connection of identified
characteristic gene sets to external archives
and ontologies and to TBI Cancer Molecule Pages
Interface. II. Interpretation layer (Burnham
development) - Interface interactive access to a
confederated database and specialized tools
automatic extraction and updates of protein
portraits (Cancer Molecule Pages) user input,
curation, virtual collaborations - Cancer
Molecule Pages a first set of Cancer Molecule
Pages for 300 genes (proteins) of primary
research interest for investigators at TBI cancer
center.
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INTERPRETATION
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EXPERTISE IN PLACE
Cell Death Differ., Vol 10, 2003, pp 621-633.
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EXPERTISE IN PLACE
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Each step in the pipeline has a unique interface
and does a double job - accepts data from the
experiments and provides information to the
experimental cores
Target Selection
Peak Max from Ni Column, Soluble (YorN), Volume
of Sample Post Concentration
Automated Primer Generation, Target Activation
PCR, Amplification
Protein Purification Expression
Primers, Na concentration, Temp
PCR Observed Size
Crystallization, Coarse and Fine Screening
Setup Temp Crystal Conditions Screen
Conditions Drop Size
Shipping Screening Results via Excel
Cryo-Protectant, Crystal Quality, Diffraction
(YorN), Resoultion
Data Collection Integration Scaling Phasing Refine
ment
Structure Validation Deposition
Space Group Resolution of Molecules per ASU
Autosubmission of electronic publication
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public tracking interface
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Target history available for viewing and data
mining
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Cancer Molecular Pages
CANCER CENTER MOLECULE PAGES

• Automated annotations
• Tracking genes in HTP experiment
• Highlighting outliers
• Connection between Genes / Compounds / Pathways /
  HTP experiments
• Messages discussions on genes
• virtual collaborations