MouseBIRN Site Map

Background

1. 1. MouseBIRN^?
      1. About
         1. Overview
         2. Mission Statement
         3. MouseBIRN Disease Models^?
            • MouseBIRN ASYN
            • MouseBIRN EAE
              • EAE Mouse Model, Multiple Sclerosis
            • MouseBIRN APP
              • Tet-off APP Transgenic Mouse Model, Alzheimer's Disease
            • MouseBIRN GRP
         4. Mouse Roadmap-both the general circle view and Ilya's
         5. MBAT project (Atlasing for data integration) - add the figure from the SfN poster
      2. Our Science
         1. MouseBIRN Manuscripts
            • Acknowlegments Guidelines
            • Publications
         2. MouseBIRN Presentations
            • SfN 2006
            • SfN 2007
      3. News
         1. Important Dates
         2. Software Release Announcement
         3. Wish List
         4. Progress
      4. FAQ
   2. Joining Institute
      1. Partner Institutions
      2. Individual Site Subject ID

Data Acquisitions and Processings

1. 1. MouseBIRNWorkflows
      • Work Flow Process
      • How to DF
      • Multi-scale Mouse Brain Data Collection Protocols
   2. Upload
      • BIRN Microarray Data Upload
      • CCDB data upload
      • UCSD data upload
      • AIDB

Atlasing

1. 1. Overview
      1. General Needs
      2. Goal
      3. Site Atlas
      4. Atlasing Resources
   2. Atlasing Use Case Work Page
      1. Use Cases
      2. Atlas Workshop Day
   3. Atlas Model
      1. GENSAT
      2. MAP
         • Atlasing Hierarchy
      3. ABA
   4. MouseBIRN Atlasing Workgroup
      1. Registration
   5. Technical Aspect
      • Exchange of StateBetweenAtlasesPage^?
      • To-Do List
      • Planning Phase
   6. Atlas Related Resources
      1. Links to related Programs^?

Data Federation

1. 1. Collaboration
      1. Sources
         • CCDB (+SiteSchema)
         • GeneNetwork^? (+SiteSchema)
         • BIRN Microarray (+SiteSchema)
         • ABA Neurocommon Project^?
      2. [[MouseBIRNDataManagement][Data Management Tools]
      3. SRB
         • DataMediation
      4. Mediator
      5. MouseBIRN^? Ontology
         1. Ontology Standards and Format^?
         2. Relevant Ontologies to Mouse BIRN
         3. Resources
            1. Ontology Viewers
            2. Major Biomedical Ontologies Groups
            3. Bio-Ontology Conferences
            4. Bio-Ontology References
      6. BIRN Data Sharing
   2. Integration
      1. General
         • Workflow Automation
      2. Common Data Model
         • 2D Image Data Model
         • 3D Volume Data Model^?
      3. Mapping Across Data Models
         • MetadataMapping^?
      4. GlobalConcSchema
      5. DataExchange
         1. Gene Expression
            • MAGE
            • MAGE Working Page
            • MAGE onotlogy entries
              • Term Definition
            • Recommendation for BIRNMAGE^?
            • MicroarrayMinimumMetadata
         2. 3D Volume MetaData^?
            • MosueBIRN data model mapping to XCEDE
            • fBIRN/HID
              • Modification of HID for AIDB
         3. Ontology
            • BIRNLex
            • Mapping to BIRNLex terms
      6. a. Potential Schema Items

Applications

1. 1. Webservices
   2. MBAT
      1. Overview/Planning
         1. RegWorkSpace
            • Issues
            • Meeting
         2. VisWorkSpace i [AnaForumWorkspace][Atlas]
      2. FileFormats
      3. Visualization
         1. 2D Image multi-axes comparisons
         2. 3D multi-volume comparisons
            • 2Dto3D
            • 3Dto3D
         3. BrainGraph
      4. Query
         1. Use Case/Sample Queries
         2. Prototype
      5. Analysis
         1. GeneExpression^?
         2. Registration/Wrapping
      6. Documentation
         1. Programmer's Page^?
            • Server Protocol
         2. User's manual^?
         3. MBATDesign
         4. MBAT/SHIVARepositoryCheckInPolicy
         5. MBATSearch
         6. MBATUpcomingFeatures
         7. MBATFileFormats
      7. Release
         1. MBAT_v1
         2. MBAT_v110
         3. MBAT_v150
         4. MBAT_v20
   3. SmartAtlas^?
      1. Visualization
      2. Analysis
   4. LONI Pipeline
      1. Workflow Management
   5. BIRN Microarray i GEMigrationPlan

Resources

1. 1. Useful Links
      • BIRN
      • Mouse BIRN
      • BIRN Portal
      • BIRN WIKI
      • NIH
   2. MouseBIRN^? Mouse Info
      1. CurrentMouseStrains
      2. SubjectStrainGenotypePhenotype
   3. Mouse BIRN Tools

Meetings and Events

1. 1. MouseBIRNAnnouncement^?
      1. MouseBIRNDates
      2. PreviousMeetings
   2. Annual AHM
      1. 2007BIRNAHMeeting
      2. AHM2006Presentation
      3. BIRN2005AHM
   3. Semi-annual Mouse AHM
      1. MouseBIRNMeeting2007
         • 2007MouseDay
         • MouseBIRN^? All Hands Meeting Logistics
         • MouseAHM2007Presentation^?
      2. MouseBIRNMeeting2006
         • MouseLogistics
         • MouseAHM2006Presentation^?
      3. MouseBIRNMeetings2005^?
   4. Programmer In-Person Meeting and Weekly Programmer Meetings
      1. June252007In-PersonProgrammerMeeting
      2. MBATMinutesAll
      3. MBATMinutesUCLA
   5. Ad-hoc meetings
      1. DataFedTCons
         1. MouseBIRNDataFedTcon^?_20060801
         2. MouseBIRNDataFedTcon^?_20060808
         3. MouseBIRNDataFedTcon^?_20060815
      2. GeneExpressionMeeting^?
         1. Dec1Minutes
         2. Dec8Minutes
      3. DF
         1. MouseBIRNDFMinutes2006Aug15
         2. MouseBIRNDFMinutesAug08
      4. Registration
         1. MouseRegistrationMeeting