2005 AHM Mouse BIRN

Goals Review progress on mouse BIRN milestones Update priorities and milestones for SFN, next spring, and next fall 2006 Clarify and review plans of action Identify specific manuscripts with work-to-be-done and authorship Develop action items related to combined atlas effort and name beta testers outside BIRN Foster interactions and communications between different research and technical groups within the BIRN

Foci of meeting Progress: much done since last spring! Today: Brief updates, followed by working sessions  Mouse models  Ontologies  Data Management  Atlasing Tuesday and Wednesday: Cross testbed sessions Also, working sessions on how to use available tools Thursday: Atlasing workshop

Mouse AHM Action Items (EAE) To be completed in June 2005  Ship animals to CIVM  MRH  Track down which litters these mice have come from (stock and room number) and from now on keep track of this information  Investigate and decide if the EAE animals will have the affymatrix arrays done at UCLA instead of UTHSC (although data will be sent to UTHSC for analysis)  The likelihood of amending the animal protocols of Duke and UCLA for longer-term care of the EAE mice at Duke will be determined and the process for approval will be started. Whether EAE mice will live at Caltech or be transferred there from UCLA will be decided To be completed by August 2005  MRM  UCSD and Duke will work on a perfusion protocol so the brain can be passed to UCSD after MRH at Duke and test this with the C6 normal mouse. To be completed by October 2005  Atlas Construction  Anatomical Delineations Cerebellar Cortex Cerebral Cortex Thalmus

Mouse AHM Action Items (data integration)  By July 2005 Get mouse BIRN publications on the BIRN web site Post renewal Set up resources on the internet, either on wiki or BIRN Portal  Provide a set of resources for ontology development  Available mouse BIRN tools: descriptions, links, functions, and their API’s  Available outside tools: some information, descriptions, and links Stand up a working interface to Mouse BIRN data federation  Set up meeting schedule  Conduct schema review of each database  Review the current state of imaging schemas  By October 2005 Stand up a working interface to Mouse BIRN data federation  Review existing ontologies  Work with BIRN mediation group about linking data conceptually  Work with EAE group to design workflows and integrated views  Continue to develop and map to global conceptual schema  XML standards for data exchange (using human work as guide)  A virtual BIRN Data Grid will be kept at UCSD for Tenn/Drexel

Mouse AHM Action Items (tools) By July 2005  GENSAT data Rob provided a relevent gene list Weed down list to manageable subset of genes to register  Generating a high resolution segmented mouse brain atlas Yoni’s Nissl rat brain atlas warped into the mouse brain Interpolate surfaces from this and into the SmartAtlas and LONI atlas  Test for swapping images back and forth from the 3 atlasing programs  All applications accessible through Mouse BIRN portal and mouse wiki By October 2005  Population of mouse BIRN atlases with data Registration of some of the MBL data Gensat data-Decide who will register which data sets  All applications accessible through Mouse BIRN portal Integration with portal  Develop a set of “evidence metrics” Gold standard: comparison with Nissl or equivalent?  Develop a set of requirements of data and what’s needed to get it into this common atlas space, both for current mouse BIRN and future users

Monday  9: :15: Experimental models: 9:00-9:45: EAE, Allan 9:45-10:30:  -Syn, Diana 10: :45: Coffee Break 10: :15: Alzheimer’s  11:15 – 12:15: Ontologies: Maryann and Billl.  12:15 - 1:30: Lunch  1:30 – 2:45: Data Management: Jeff, Maryann, and Vadim  2:45 – 3:15: Atlasing: Ilya  3:15 – 4:00: Experiment with the atlas interface/Coffee  4:00 – 5:30: Continuation of Atlasing  5:30 – 6:00: Wrap up, SFN, and rest of the AHM

Tuesday and Wednesday  MRI image processing sessions led by Allan MG (~3-4 hours total) will be held during lunch time.  Session I: Tuesday over working lunch 12-2 pm Starting with MRI data (Duke and CIT) Hands on preprocessing images Generating atlases from MRI images Delineation of structures  Session II: Wednesday over working lunch 12-2 pm More hands on practice

Thursday: Atlasing Workshop Clarify different terminology about atlasing Examine and discuss tools/functionality we may like to integrate into the mouse BIRN atlasing effort  Part of the BIRN  Others Learn how to use some of these tools Discuss lessons learned by participants that can help guide this effort Determine a more concrete future direction for the mouse BIRN atlasing environment