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National Centers for Biomedical Computing Software and Data Integration Working Group (SDIWG). Peter Lyster and Zohara Cohen NA-MIC All Hands Meeting Tuesday January 10, 2006. Brief Journey Through the Seven Centers. NIH Roadmap National Centers for Biomedical Computing (NCBC). - PowerPoint PPT Presentation
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
National Centers for Biomedical Computing
Software and Data Integration Working Group (SDIWG)
Peter Lyster and Zohara CohenNA-MIC All Hands MeetingTuesday January 10, 2006
National Alliance for Medical Image Computing http://na-mic.org
Brief Journey Through the Seven Centers
NIH Roadmap National Centers for Biomedical Computing (NCBC)
Informatics for IntegratingBiology and the Bedside (i2b2)Isaac Kohane, PI
Center for Computational Biology(CCB)Arthur Toga, PI
Multiscale Analysis of Genomicand Cellular Networks (MAGNet)Andrea Califano, PI
National Alliance for MedicalImaging Computing (NA-MIC)Ron Kikinis, PI
The National Center ForBiomedical Ontology (NCBO)Mark Musen, PI
Physics-Based Simulation ofBiological Structures (SIMBIOS)Russ Altman, PI
National Center for Integrative Biomedical Informatics (NCIBI) Brian D. Athey, PI
Physics-based Simulation of Biological Structures (SIMBIOS)PI: Russ Altman, M.D., Ph.D. PI Institution: Stanford University
This Center will develop, disseminate, and support a simulation tool kit (SimTK) that will enable biomedical scientists to develop and share accurate models and simulations of biological structures from atoms to organisms. SimTK will be an open-source, extensible, object-oriented framework for manipulating data, models, and simulations. The software will include advanced capabilities for modeling the geometry and physics of biological systems, generating the governing differential equations of these systems, integrating the equations to simulate the system dynamics, and interpreting the simulation results through comparison with experimental data. http://cbmc-web.stanford.edu/simbios/
National Alliance for Medical Imaging Computing (NAMIC)PI: Ron Kikinis, M.D.PI Institution: Brigham and Women's Hospital
The National Alliance for Medical Image Computing (NAMIC), proposed here, will integrate the efforts of leading researchers with a shared vision for development and distribution of the tools required to advance the power of imaging as a methodology for quantifying and analyzing biomedical data. This shared vision is based on a thorough composition of computational methods, from image acquisition to analysis, that builds on the best available practices in algorithm development, software engineering, and application of medical image computing for understanding and mitigating the effects of disease and disability. NAMIC’s goal is to develop, integrate, and deploy computational image analysis systems that are applicable to multiple diseases, in different organs. To provide focus for these efforts, a set of key problems in schizophrenia research has been selected as the initial Driving Biological Projects (DBPs) for NAMIC. http://www.na-mic.org/index.htm
Informatics for Integrating Biology and the Bedside (I2B2)PI: Isaac Kohane, M.D., Ph.D.PI Institution: Brigham and Women's Hospital
I2B2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The I2B2 Center is developing a scalable informatics framework that will bridge clinical research data and the vast data banks arising from basic science research in order to better understand the genetic bases of complex diseases. This knowledge will facilitate the design of targeted therapies for individual patients with diseases having genetic origins. http://www.partners.org/i2b2
Center for Computational Biology (CCB)PI: Arthur Toga, Ph.D. PI Institution: University of California at Los Angeles
The Center for Computational Biology (CCB) was established to develop, implement and test computational biology methods that are applicable across spatial scales and biological systems. Our objective is to help elucidate characteristics and relationships that would otherwise be impossible to detect and measure. The CCB employs an integrative approach, both in terms of the biology and the participating disciplines. The Center focuses on the brain, specifically on neuroimaging, and involves research in mathematics, computational methods and informatics. It also is involved in the development of a new form of software infrastructure – the computational atlas – to manage multidimensional data spanning many scales and modalities. This will be specifically applied to the study of brain structure and function in health and disease, but will have much broader applicability to both biomedical computing and computational biology. http://www.loni.ucla.edu/CCB/
Open Biomedical Ontologies
(OBO)
Open Biomedical Data (OBD)
BioPortal
Capture and index experimental results
Revise biomedicalunderstanding
Relate experimental data to results from other sources
National Center for Biomedical Ontology (NCBO)PI: Mark A. Musen M.D., Ph.D.PI Institution: Stanford University
Ontologies are essential to make sense of biomedical data
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Core 7: AdministrativeInfrastructure
National Center for Integrative Biomedical Informatics (NCIBI)
Core 4: Computing and DataInfrastructures
DiabetesGenetics
ProstateCancer
BipolarGenetics
DiabetesComplications
Core 3
Core 1:Computational
Technology
Core 2:Bioinformatics
Technology
Core 6: Outreach andDissemination
Core 5: Trainingand Education
PI: Brian D. Athey Ph.DPI Institution: University Of Michigan
SAGA: Patel Lab Feldman Lab:
Diabetes Type 1, NRF2 signalingT1DM pathways
Boehnke Lab: Diabetes Type IISNP WGA workflow Genetic Interaction linkage workflow
McInnis lab: Bipolar DisorderInteractions Between Genetic Linkage Peaks, WNT signaling
Chinnaiyan and Omenn Labs: Prostate CancerBayesian, NLP, Oncomine
Bayesian Nets: Woolf Lab
Workflows: Weymouth,
McEachin, & Programming team
MBI
MiMI
MBI: Molecular Biology Integration DB: States lab, Phillips
Natural Language Processing: States, Meng, Radev Labs
Tools for large- Scale analysis
Database Technologies for
Deep Integration of Biological
Information
MiMI: Michigan Molecular Interactions DB:
Jagadish lab, Tarcea
A B C D
MiMI
User Environment Analyses: Mirel,Ackerman labs
MiMI Onco-mine MBI
BDW
Data
BDW Client
Track useractions
workflow
Concept Mapper: Rhodes, Patel,
Woolf
BDW: Biomedical Data Workbench prototype: Weymouth
First User Environment
Driving Biological Problems
Granular Overview of NCIBI Activities Underway: Cores 1-3
Multiscale Analysis of Genomic and Cellular Networks (MAGNet)
• To study the organization of the complex networks of biochemical interactions whose concerted activity determines cellular processes at increasing levels of granularity.
• To provide an integrative computational framework to organize molecular interactions in the cell into manageable context dependent components.
• To develop interoperable computational models and tools that can leverage such cellular interaction maps to elucidate key biological processes and to dissect complex diseases.
PI: Andrea Califano Ph.D.PI Institution: Columbia University
Core 1: Computational SciencesCore 2: BioinformaticsCore 3: Cadherin binding; Cancer; Genetic determinants of common heritable disorders (Alzheimer’s, Autism)
10 U10 U
10 U
Internet
Open Science Grid
caGRID
Databases
MAGNet/C2B2
Core I, II, III
Algorithms
Data
MPI
BISON
BISON
BISON
geWorkbench
National Alliance for Medical Image Computing http://na-mic.org
Goals of Software and Data Integration Working Group (SDIWG)
The RFA states the goal of creating “the networked national effort to build the computational infrastructure for biomedical computing for the nation”. In furthering this, the goals of the SDIWG in concert with the Project Team and Centers staff are:
1. To advance the domain sciences, and promote software interoperability and data exchange.
2. To capture the collective knowledge of software engineering and practices among the Centers and publish this knowledge widely
National Alliance for Medical Image Computing http://na-mic.org
Mechanics…
• Google “SDIWG” (on NA-MIC!)
• Monthly last Friday Breeze/Tcon 2:30 – 3:30 PM ET
• Open (anyone and open minutes)
• Chair Peter Lyster [email protected]
National Alliance for Medical Image Computing http://na-mic.org
NCBC Staff serving on SDIWG
• Bill Lorensen (NA-MIC)• Mike Sherman (Simbios)• Henry Chueh (I2B2)• Ivo Dinov (CCB)• Aris Floratos (MAGNet)• Daniel Rubin (NCBO)• Brian Athey (NCIBI)• Many others—Suzi Lewis, David States,
Steve Pieper, Tina Kapur, Shawn Murphy, Center PIs…
National Alliance for Medical Image Computing http://na-mic.org
Peter Lyster (NIGMS, Chair)Michael Ackerman (NLM)Carol Bean (NCRR)Art Castle (NIDDK)German Cavelier (NIMH)Larry Clarke (NCI)Zohara Cohen (NIBIB)Elaine Collier (NCRR)Jennifer Couch (NCI)Peter Covitz (NCI)Valentina Di Francesco (NIAID)Dan Gallahan (NCI)Peter Good (NHGRI)John Haller (NIBIB)
Donald Harrington (NIBIB)Peter Highnam (NCRR)Michael Huerta (NIMH)Donald Jenkins (NLM)Jennie Larkin (NHLBI)Yuan Liu (NINDS)Michael Marron (NCRR)Richard Morris (NIAID)Bret Peterson (NCRR)Salvatore Sechi (NIDDK)Karen Skinner (NIDA)Michael Twery (NHLBI)Terry Yoo (NLM)
NIH Staff serving on SDIWG
National Alliance for Medical Image Computing http://na-mic.org
There are a number of similar efforts to SDIWG at NIH
• Integrated Cancer Biology Program (ICBP)
• NIAID (Allergy/Infectious Diseases) Bioinformatics Resource Centers (BRC)
• Clinical Research Networks (NECTAR)• Chronic Disease Outcomes (PROMIS)• BIRN/caBIG/Sysbiol/Glue/PSI/TCNP/
P41/PGA/…
National Alliance for Medical Image Computing http://na-mic.org
Discussions in the First Year
• Demonstration projects
• Collaborative software development environment (yellow pages, knowledge environment, full development environment or Framework)
• NIH-forge
• Emerging efforts in the community (Neuroscience Information Framework, Clearinghouse)
• Intangibles—pairwise interactions, consciousness raising
• Example—SimTK<->ITK
National Alliance for Medical Image Computing http://na-mic.org
What would you do?
National Alliance for Medical Image Computing http://na-mic.org
A Biomedical Software Ontology?
• ACM categorization
• Open Directory Project
• Home grown, tipping point?
Why?• To help query tools (computer-computer, human-computer)• To help describe tools (human-human)
National Alliance for Medical Image Computing http://na-mic.org
NA-MIC Software Classification
ApplicationsSlicer2LONI Pipeline
ToolkitsInsight Toolkit itk Ontology Visualization Toolkit KWWidgets
Software Engineering ToolsTesting
Dart2CTest
Cross-Platform BuildCMake
Cross-Platform DistributionCPack
Cross-Language Wrapping CableSWIG
National Alliance for Medical Imaging ComputingRon Kikinis, M.D.Brigham and Women's Hospital
National Alliance for Medical Image Computing http://na-mic.org
Simbios Software Classification
Deliverable software modules
Applications
Models
Computational components
Model-building toolsets
Application-building toolsets
User and developer documentation
Application areas
Driving Biological Problems
RNA folding
Myosin dynamics
Cardiovascular fluid dynamics
Neuromuscular biomechanics
Molecule modeling
Electrostatics
Physics-based Simulation of Biological StructuresRuss Altman, M.D., Ph.D. Stanford University
National Alliance for Medical Image Computing http://na-mic.org
Simbios Software Classification
User categories ClinicianExperimentalistApplication developerModelerAlgorithm developerSimTK software developer
Platform support Shared memory multiprocessorsClusters
Language support Scripting languages (tcl, perl, python)JavaC++, C, Fortran
National Alliance for Medical Image Computing http://na-mic.org
Simbios Software Classification
Computation components Linear Algebra (dense, sparse)Numerical Integrators (ODE, DAE, PDE, Stochastic)Monte Carlo simulationMultibody dynamicsContact modelingMeshingPDE solversControllersOptimizers/root findersMolecular force field calculationsComputational geometry
Software development tools Source control
Multiplatform build system Regression test support
Document generation
National Alliance for Medical Image Computing http://na-mic.org
Simbios Software Classification
Software dissemination tools User interaction
Bug reportingFeature requestsMailing listsNews
Software and documentation delivery supportInstallationDownloadUpgrade
EducationTutorials
Course material and software Online courses
National Alliance for Medical Image Computing http://na-mic.org
CCB Software Classification
Analysis EDA Feature Analysis
Shape Analysis Pattern Recognition
Genomic & Phenotypic Data Analysis Statistical Analysis
E.g., RIntegration
DB Efficient DB Traversal & Querying
Graphical e.g., HIVE Pipeline Grid Computing Resources Mappers e.g., BrainGraph BrainMapper Portals Resource Integration Components Web Services
Center for Computational BiologyArthur Toga, Ph.D. University of California at Los Angeles
National Alliance for Medical Image Computing http://na-mic.org
CCB Software Classification
Modeling Algorithms
Image Processing Atlas Generation Cortical Modeling Registration Segmentation
Engineering Open Source
Sequence Annotation Simulation SW Development
National Alliance for Medical Image Computing http://na-mic.org
CCB Software Classification
Pre-Processing Data Transforms
Spectral Transforms Fourier Transform Wavelet Transform
Filtering Skull Stripping
Inhomogeneity Correction Visualization
Clinical Charts e.g., Demographics Graph Viewers
Hyperbolic Graphs Hierarchical Trees
Imaging Cross-Sectional Viewers
Manifold Viewers 2D, 3D, 4D, ND Sequences
National Alliance for Medical Image Computing http://na-mic.org
I2B2 Software Classification
Computer Code Source
Application Domain(s)LicenseTested on platforms
BinariesApplication Domain(s)LicenseTested on platforms
Informatics for Integrating Biology and the BedsideIsaac Kohane, M.D., Ph.D.Brigham and Women's Hospital
National Alliance for Medical Image Computing http://na-mic.org
I2B2 Software Classification
Documentation Biological Experimentation ProtocolAlgorithm DescriptionPublication
PUBMED ID or DOIHuman Cohort DescriptionNon-Human Experiment Description
OrganismSoftware/Technology protocolsTechnology white papers
Application Domains (Software)
National Alliance for Medical Image Computing http://na-mic.org
I2B2 Software Classification
Clinical Information Systems Natural Language Processing
Predictive modeling and classificationExtract, Transform, and LoadDatabase SchemaOntology ManagementService Oriented Architecture
Biological StructureStructure:function and structure:disease predictionProtein interaction modeling
National Alliance for Medical Image Computing http://na-mic.org
I2B2 Software Classification
Clinical Information Systems (cont.)Expression studies
Disease classification/advanced histopathologyOutcome predictionPathway/gene identification for diseaseIntegration of expression w/DNA studies
DNA/Genomic studiesPopulation study type (association/linkage etc)Scoring/predicting DNA variant functional and disease
significanceComparative genomicsMotif studies (TFBS/miRNA/protein domains, etc)
National Alliance for Medical Image Computing http://na-mic.org
I2B2 Software Classification
Experimental Data Aggregate Human Data
DNARNAProteinNon-image PhenotypeImage
Individual Human DataDNA (sequence and
mapping)RNAProtein
Non-image Phenotype
ImageUsage
Non-humanDNARNAProteinNon-image PhenotypeImage
National Alliance for Medical Image Computing http://na-mic.org
I2B2 Software Classification
Equipment Genomic MeasurementImaging
Imaging ClassDNA (sequence and mapping)
Gene IDNon-standard descriptor
RNA Gene IDSplice variantNon-standard descriptor
ProteinID or AA sequence?
Non-image Phenotype UMLS or other vocabulary codedNarrative text
National Alliance for Medical Image Computing http://na-mic.org
I2B2 Software Classification
Usage Anonymity levelConsent level
Image DICOM?MIME type?
Reagents Chemical Organismal
National Alliance for Medical Image Computing http://na-mic.org
NCIBI Software Classification
Data ManagementTIMBER
Michigan Molecular Interactions (MiMI)
Biomolecular Interaction Network Database (BIND)
Human Proteome Organization Plasma Proteome Project (HUPO)
BioWarehouse
BioPAX
Community and User Interaction SystemsWorm Community System
MEDSPACE
VEHICLES
Answer Garden
NJFun
National Center for Integrative Biomedical InformaticsBrian D. Athey, Ph.D. University of Michigan
National Alliance for Medical Image Computing http://na-mic.org
NCIBI Software Classification
Database and Information Retrieval AlgorithmsPeriscopemiBLAST
Workflow ManagementGenePattern
Ontologies and Natural Language ProcessingMEADNewsInEssenseProtégé
Image ProcessingEdgewarp
National Alliance for Medical Image Computing http://na-mic.org
MAGNet Software Classification
AnalysesRegulatory/Signaling network reconstruction
ARACNE (gene expression) GeneClass (gene expression)
Network characterization NetClass/NetBoost (molecular interactions networks)InfoMod (molecular interactions networks)
Homology-based protein sequence classification Bio-Kernels (protein sequences)RankProp/MotifProp (protein sequences)
Structured-based protein classification Protein function pipeline (protein structure)
Prediction of regulatory (cis) elementsREDUCE (gene expression)MEDUSA (gene expression)
National Center for Multi-Scale Study of Cellular NetworksAndrea Califano, Ph.D. Columbia University
National Alliance for Medical Image Computing http://na-mic.org
MAGNet Software Classification
Analyses (cont.)
Protein structure prediction
Protein structure pipeline (protein sequence)
META-server (protein sequence)
Super-NEST (protein sequence)
Protein cavity and binding site prediction (protein structure)
Databases
Molecular interactions
GeneWays
Cellular Network KB
Gene-phenotype associations
PhenotypeML DB
National Alliance for Medical Image Computing http://na-mic.org
NCBO Software Classification
Ontology Management ProtégéOBO-EDIT
Ontology Diff and Alignment PROMPT
Ontology Visualization JambalayaOntoVizPromptVizTGViz
National Center for Biomedical OntologyMark A. Musen, M.D., Ph.D.
Stanford University
National Alliance for Medical Image Computing http://na-mic.org
NCBO Software Classification
Biomedical Data Annotation OBO-EDIT
Progammatic Access to Ontologies Protege Script Tab
Web Access to Ontologies WebProtege
National Alliance for Medical Image Computing http://na-mic.org
Suggestion for Next Step1. Choose one of the existing ontologies as a starting point, perhaps a
combination of the MAGNet and CCB ontologies.
2. Find one person at each NCBC who is interested in the issue of categorizing their software and who is willing to work with the SDIWG on incorporating their taxonomy into the chosen top level ontology.
3. The NCBC representatives will incorporate their software into the ontology directly or suggest changes needed in order to incorporate their software.
4. After the software are all integrated into one ontology, a set of attributes to describe the software will be developed. A format for storing the ontology will be agreed upon.
5. Each NCBC will create and host an instance of the ontology to describe their resources. OWL/Semantic Web may be used.
National Alliance for Medical Image Computing http://na-mic.org
National Alliance for Medical Image Computing http://na-mic.org
National Alliance for Medical Image Computing http://na-mic.org
Contact Peter Lyster [email protected]
301.594.3928