1. Mouse BIRN AHM 2007 Mouse BIRN-related activities at NCMIR- UCSD & BIRN-CC: “What we did and what we will do. Mouse BIRN-related activities at NCMIR- UCSD & BIRN-CC: “What we did and what we will do.” Mark H. Ellisman NCMIR-UCSD & BIRN-CC

2. IT infrastructure accomplishments  Continued UCSD contributions to development and implementation of Mouse BIRN Atlasing Toolkit (MBAT).  Created a workflow for 2D images for spatial registration of images using Gridsphere to be deployed through the BIRN portal. 1) Each component in the registration workflow is a web service, so that other warping services with the same signatures can be plugged in without much work. 2) There is a public API to query spatial registry and the ArcIMs services, so that other tools like MBAT can use it by calling the webservices.  Improved the functionality of SmartAtlas and developed plans to incorporate appropriate functionality into MBAT/WOMBAT as these evolve.  Extended infrastructure to visualize and easily access external datasets (e.g. The Allan Brain Institute Reference Atlas and Gene Expression Data).  BIRNLex progressed as a “controlled vocabulary” (led by Martone, Bug & MacKenzie-Graham)  CCDB group created automatic upload and download tools that will integrate with BIRN (and these were disseminated to BIRN groups).  CCDB group developed web services for discovery and access of cell-level data  Web services API for atlas interoperability developed and demonstrated  Querying of gene expression databases from MBAT via the BIRN Mediator

3. IT infrastructure directions and challenges  Improve the Atlas Interoperability API, and test with different Atlas clients, beyond Smart Atlas-Neuroterrain integration demonstration Standardize coordinate transformation services  Incorporate appropriate functionality into MBAT/WOMBAT as the project progresses.  Publish web services API for spatial registry search, to enable MBAT/WOMBAT to find relevant images  Register more data via the Image Registration workflow  Publish web services API for ArcIMS image services  Standardize and publish web service APIs supporting communication between components of image registration workflow Standardize 3 methods: execute (e.g. do warping, or create ArcIMS service); notify the calling portlet; update spatial registry  Access to additional databases via the BIRN Mediator  Examine and assimilate infrastructure components from other testbeds Upload scripts (+ integrate spatial registration from MouseBirn) Animal imaging database Web service and XCEDE interfaces  See next slide for more 

4. Grid infrastructure BIRN Roadmap Upload FindAccessCollaborate Upload scripts Human Imaging DB Spatial registry BIRNLex Animal Imaging DB OrganizeAnalyze Provenance management Performance improvements, better error handling, utilization of authentication resources, integration of application services with ROCKS, BIRN authentication, portal via application launcher… FAQs, tutorials, API registry, collaborative programming tools. Morphometric analysis Microarray analysis Atlas Interoperability server and API status Replication services Oracle upgrade SRB upgrade Distributed MCAT Mediator WS- XCEDE WS Upload client Data Quality Assurance, specific for data classes Atlas and Query tools: Concept- based query, view-based query Global search FIPS: grid-based Annotation tools FreeSurfer, 3D Slicer LONI Pipeline integration Workflow management integration Better compute grid access Data publication standards Command- line data access Portal Databases WS- XCEDE CCDB WS Registration workflows: Clinical/behavioral MR scanner MR (FBIRN) Microarray Microscopy/atlas data (2D, 3D…) ontologies WS Registration portlets WS- XCEDE WS Subject IDs generator Project IDs generator WS ID assignment portlets Projects DB Subjects DB Subject ID mapper Project ID mapper status Global search portlet : web service interface : high priority Respective portlets Database backup Data grid: Compute grid: Integrate Data serve and download (e.g. for large images) WS Annotation interfaces Data integration services: terms mapping MBAT/WOMBAT; query interfaces Tools accessed from portal; Eclipse Workflow Client SRB URIs collection management XCEDE 2.0 Improved data security DB schemas and GUI (portal dashboard), versioning and regression tests (HID) DB dashboards and backup Image QA on grid (+curation dashboard) Microarray DB WS Other DBs Find commonalities Adjust to AIDB,MADB XNAT

5. Parkinsonian project accomplishments  Continued imaging, molecular biology, and behavioral pharmacology studies  Linked observations mouse model  human disease state  Expansion of collaborative efforts with non-BIRN entities  Renewed linked funding from Branfman Family Foundation  Publications 4 Abstracts 2 published (w/ another under review)  Provided MRI workflow for case study analysis

6. Parkinsonian project directions  Continue imaging, molecular biology, and behavioral pharmacology studies  Wrap up MRI analyses & determine whether publication of results is appropriate  Continue integration of data into project Portal and BIRN federation of databases  Publish, publish, publish!  Share, share, share!

7. Publications 2006-2007: Abstracts & Proceedings  Price DL, Rockenstein E, MacLean NAB, Phung V, Masliah E, Ellisman MH (2006) Altered dopamine receptor immunoreactivity in CNS of transgenic mice overexpressing alpha-synuclein. International Conference on Alzheimer’s Disease and Related Disorders (ICAD), Abstract, Madrid, Spain July 16 2006.  Boline JK, MacKenzie-Graham A, Shattuck D, Yuan H, Anderson S, Sforza DM, Wang J, Williams RW, Wong W, Martone ME, Zaslavsky I, Toga AW (2006) A Digital Atlas and Neuroinformatics Framework for Query and Display of Disparate Data. Society for Neuroscience, Abstract #100.12  Price DL, Rockenstein E, Phung V, MacLean NAB, Masliah E, Ellisman MH (2006) A Parkinsonian mouse model overexpressing alpha-synuclein: assessment of changes in behavior and glutamate and dopamine receptor immunoreactivity. Society for Neuroscience, Abstract #75.20.  Gupta A, C Bean, W Bug, C Fennema-Notestine, ME Martone, JA Turner, JS Grethe (2006) Creating a community-based knowledge management framework for integrating neuroscience data via ontologies. Society for Neuroscience, Abstract #XXX.XX.  Turner JA, Fennema-Notestine C, Martone ME, Laird AR, Grethe JS, Bug W, Gupta A, Bean C (2006 You say potato, I say potahto: ontological engineering applied within the Biomedical Informatics Research Network. Society for Neuroscience, Abstract #100.6  Price DL, Rockenstein E, Phung V, MacLean NAB, Masliah E, Ellisman MH (2007) mGluR5 antagonism reverses motor deficits in a transgenic mouse model of Parkinsonism. 8th International Conference on AD/PD, Abstract, Salzberg Austria March 14-18, 2007  Astakhov V, A Gupta, J Grethe, E Ross, D Little, A Yilmaz, M Martone, X Qian, S Santini, M Ellisman (In press) Semantically Based Data Integration Environment for Biomedical Research. Proceedings of the 19th IEEE International Symposium on Computer-Based Medical Systems.  Bug W, Wong WW, Gustafson C, Johnson GA, Martone ME, Price DL, Rosen GD, Williams RW, Zaslavsky I, Nissanov J. (Submitted) Brain atlasing tool interoperation: NeuroTerrain-Smart Atlas synergistic visualization and analysis environment, Proceedings, 3rd International IEEE EMBS Conference on Neural Engineering May 2-5, 2007, Kohala Coast, Hawaii, USA.

8. Publications 2006-2007: Manuscripts & Book Chapters  Price DL, Chow SK, MacLean NAB, Hakozaki H, Peltier S, Martone ME, Ellisman MH (2006) High- Resolution Large-Scale Mosaic Imaging using Multiphoton Microscopy to Characterize Transgenic Mouse Models of Human Neurological Disorders. Neuroinformatics 4(1):65-80.  Martone ME, Sargis J, Tran J, Wong WW, Jiles H, Mangir C (In Press) Database Resources for Cellular Electron Microscopy, In R. McIntosh (ed) Cellular Electron Microscopy, Methods in Cell Biology, Volume 79  Price DL, Rockenstein E, MacLean NAB, Phung V, Masliah E, Ellisman MH (Under review) Increased mGluR5 receptor immunoreactivity in CNS of Parkinsonian patients and transgenic mice overexpressing alpha-synuclein.