Towards An Integrated NCBC Computational Tools and Services Framework

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Towards An Integrated NCBC Computational Tools
and Services Framework

• Ivo.Dinov_at_loni.ucla.edu
• http//www.ccb.ucla.edu

2
Low Hanging Fruit?

• Whos picking the Fruits?
• How are the fruits picked?
• Where/When the fruits are picked?

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Ontologies?

• Ontology
• 
  
• XMLtology A Flexible, Inclusive, Scalable,
  Decentralized, Adaptable Framework for management
  of CompBio Tools and Services
• Not necessarily a fixed, robust or formal (ala
  http//genomebiology.com/2005/6/5/R46)

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SW Tool Yellow-Pages XMLtologies

• There is a clear distinction between these
  efforts
• A Yellow-Page Approach makes sense when
• We talk about SW packages!
• Flexible, scalable and decentralized design.
• E.g., An NCBC Wiki resource with dynamic pages
  linked directly to the Center's SW download
  utilities (Databased)
• Adopt some sort of a clever search utility (ala
  IATR, 03/17/2006 TCon)

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SW Tool Yellow-Pages XMLtologies

• Adopt some sort of a clever search utility (ala
  03/17/2006 TCon)
• E.g., IATR, XML schema shown by Valentina Di
  Francesco
• A Template for an NCBC SW Repository
• SimBiome
• IATR
• CCB Software Download
• Others

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IATR Internet Analysis Tools Registry

• http//na-mic.org/Wiki/images/0/08/The_Internet_An
  alysis_Tools_Registry_revised.doc
• http//na-mic.org/Wiki/index.php/SDIWGMeeting_Min
  utes_20060317

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SW Tool XMLtologies

• Finding SW tools is different from tool
  integration.
• XMLtological Description may be achieved via a
  well-thought of formalization description of
  the components of different SW libs, part of
  larger SW packages. For example, at the CCB we
  have developed pipelines that integrate CCB, ITK,
  FSL, AfNI and other tools from completely
  independent toolkits. Our approach is XML-based
  ontological description of each library which is
  to be available for integration.
• We can start with the top-level ontology here
  http//bioontology.org/ontologies/SoftwareOntology
  /
• Then go into describing each library/function/tool
  /routine/filter/process/etc. by carefully
  describing each I/O parameter (type, specs, etc.)
  and all the logistics about where is it available
  for execution and other info. Here are two
  examples of such library XML descriptions
  http//www.loni.ucla.edu/twiki/pub/Pipeline/Freesu
  rferTutorialModule/FreesurferTutorial.module
  http//www.loni.ucla.edu/twiki/pub/Pipeline/ITKMul
  tiModalityRigidRegistrationModule/MultiModalityRig
  idRegistration.module
• http//na-mic.org/Wiki/index.php/SDIWGNCBC_Softwa
  re_Classification

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NCBCs
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CCB SW Integration with other NCBCs

• NAMIC, http//www.na-mic.org
• SLIPIE (Slicer-LONI Pipeline Integration
  Environment)
• Java ? JNI mediation ? C/C tools
• Level-set segmentation techniques
• I2B2, http//www.i2b2.org
• HIVE cells ? Neuroscience Pipelines
• Pipeline modules ? HIVE Objects
• Neurogenetics (e.g., Huntingtons), DB and
  biosequence analysis
• SimBios, http//simbios.stanford.edu
• Structure Modeling Tools ? Pipeline Modules
• CCB Compute/Viz Libs ? SimTK
• Simulating Temporal Brain Changes
• Simulating Kinetics using Random Distribution
  Sampling
• NCBO, http//bioontology.org
• DBPs, Anatomy and Imaging ontologies
• NCIBI, http//www.ncibi.org
• Databasing
• C2B2, http//magnet.c2b2.columbia.edu
• Molecular data integration

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Common NCBC DBP Research Efforts
Commonalitythe Biology of Neurological Disorders

• CCB - http//www.ccb.ucla.edu
• Development, Aging, Dementia
• Schizophrenia and Multiple Sclerosis
• I2B2 - http//www.i2b2.org
• Huntington's Disease
• SimBios - http//simbios.stanford.edu
• Neuromuscular disorders, Cerebral Palsy,
• Stoke and Parkinson's disease
• NA-MIC - http//www.na-mic.org
• Schizophrenia, Multiple sclerosis
• Alzheimers disease, Epilepsy, Prenatal Alcohol
  Syndrome
• NCBO - http//bioontology.org
• HIV/AIDS and Neuroscience correlates
• NCIBI - http//www.ncibi.org
• Bipolar Disorder
• C2B2 - http//magnet.c2b2.columbia.edu
• Alzheimers disease
• Autism Spectrum Disorders

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A Schematic of an Integrated NCBC Data Protocol

• CCB - http//www.ccb.ucla.edu
• Shape Modeling (e.g., 3D Cortical surface
  analysis)
• CCB IDA (imaging data archive)
• I2B2 - http//www.i2b2.org
• GO Browser (gene expression maps, at specific
  Brain regions)
• Relnet map relevance networks gene expression
  data
• SimBios - http//simbios.stanford.edu
• LAPACK linear algebra library
• Finite element method for nonlinear solid
  mechanics with discontinuous Galerkin (viscous
  warping)
• NA-MIC - http//www.na-mic.org
• Image processing (e.g., 3D brain registration)
• NCBO - http//bioontology.org
• Brain Structural Labeling Ontologies
  (nomenclatures)
• NCIBI - http//www.ncibi.org
• Timber/MiMI XML databases
• Oncomine analysis of tumor gene expression maps
• C2B2 - http//magnet.c2b2.columbia.edu
• geWorkbench tools (e.g., molecular classification
  of brain tumors)

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An Integrated NCBC Data Protocol
Population/Patient
Imaging Acquisition CCB IDA
Genetic Data I2B2/NCIBI
Invert Linear Warping Fields SimBios
3D Image Alignment NA-MIC
Patient-Specific Pheno- Geno-type Analysis
Mapping I2B2/NCIBI
Shape Analysis CCB
Integrating Imaging Genotypic Info (Anat.
Ontology) CCB/NCBO
Patient Molecular Tumor Classification C2B2
Findings, Viz Interpretation CCB/NA-MIC
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An Integrated NCBC Data Protocol
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CVS? Linux?

• These are easy and need no management these are
  HOMOGENEOUS!
• How about taking a dive to reality!
• Linux, Solaris, IRIX, Win,
• Java, C, C, C, Perl, Python,
• We are not necessarily fishing for ontology
  solution we are going for a solution that will
  allow efficient integration of INDEPENDENT tools,
  available on specific architecture, and requiring
  specific environment (XMLtology).
• Interface Alone?
• Incompatible Algorithms? Look at BEMA!

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Completeness Consistency of Ontologies

• Kurt Gödel's paper On Formally Undecidable
  Propositions, 1931.
• No system/model can be consistent and complete at
  the same time, if it obeys some simple,
  reasonable and logical laws for arithmetic!
• So, we need to decide are we going for
• Complete ontological system, or
• Consistent ontological system
• I think we should go for completeness, but be
  prepared to deal with the uncertainty, variation
  and adaptability/scalability.

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Completeness Consistency of Ontologies

• If (current) ontologies cannot deal with
  variation and inconsistencies we either fix this
  problem or think of an alternate route to the
  problem of SW tool integration (XMLtology)!
• http//www.itee.uq.edu.au/colomb/Papers/Ontology.
  html

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Completeness, Consistency, Arithmetic on
Ontologies?

• Examples
• Dx Attribute1 Annotation2 Finding3
• General linear models (even for categorical vars)
• Meta-tools (meta-algorithms), e.g., BEMA/IRMA

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Example of SW Tool XMLtology

• http//pipeline.loni.ucla.edu
• http//www.loni.ucla.edu/twiki/bin/view/Pipeline/F
  ormatModuleForPipelineOntology
• http//www.loni.ucla.edu/twiki/bin/view/Pipeline/O
  ntologyDocuments
• Image TBI

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Example of SW Tool XMLtology

• http//pipeline.loni.ucla.edu
• http//www.loni.ucla.edu/twiki/bin/view/Pipeline/F
  ormatModuleForPipelineOntology
• http//www.loni.ucla.edu/twiki/bin/view/Pipeline/O
  ntologyDocuments

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Example of SW Tool XMLtology
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Example of SW Tool XMLtology
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Example of a CCB Pipeline
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Pipeline Grid Engine Integration