2006

2005

Deutsch A, Ludäscher B, Nash A (2005) Rewriting Queries Using Views with Access Patterns Under Integrity Constraints. In: Intl. Conference on Database Theory (ICDT). Edinburgh, Scotland.

Ludäscher B, Lin K, Bowers S, Jaeger-Frank E, Brodaric B, Baru C (2005) Managing Scientific Data: From Data Integration to Scientific Workflows.

2004

Ozyurt BI, Wei D, Keator DB, Potkin SG, Brown GG, Grethe JS (2004) "Web-accessible Clinical Data Management Within an Extensible Neuroimaging Database". In: SFN (Society for Neurosciences). (PDF Abstract)

2006

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, in press.

2005

Astakhov, V, A Gupta, S Santini and JS Grethe (2005) Data Integration in the Biomedical Informatics Research Network (BIRN), In: (B.Ludäscher, and L Raschid eds.) Second International Workshop, Data Integration in Life Sciences, San Diego, CA, USA, July 20-22, 2005. Proceedings. Lecture Notes in Computer Science: 3615:317

Grethe JS, Baru C, Gupta A, James M, Ludaescher B, Martone ME, Papadopoulos PM, Peltier ST, Tajasekar A, Santini S, Zaslavsky IN, and Ellisman MH (2005) Biomedical Informatics Research Network: Building a National Collaboratory to Hasten the Derivation of New Understanding and Treatment of Disease, Stud Health Technol Inform. 2005;112:100-9

Ludäscher B, Altintas I, Berkley C, Higgins D, Jaeger-Frank E, Jones M, Lee E, Tao J, Zhao Y (2005) Scientific Workflow Management and the Kepler System. Concurrency and Computation: Practice & Experience.

2004

Ellisman M, Brady M, Hart D, Lin F, Miller M, Smarr L. (2004) The emerging role of biogrids. Communications of the ACM. 47 (11):52-57.

Ellisman M, Peltier S. (2004) Medical data federation: the biomedical informatics research network. In: Foster I, Kesselman C, (eds). The Grid: Blueprint for a New Computing Infrastructure. San Francisco: Morgon Kaufmann Publishers.

Martone ME, Gupta A, Ellisman MH (2004) E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nature Neuroscience 7:467-472. (PDF)

Nash A and Ludäscher B (2004) "Processing Unions of Conjunctive Queries with Negation under Limited Access Patterns", 9th Intl. Conference on Extending Database Technology (EDBT) Heraklion, Crete, Greece, March 2004, to appear in LNCS. (PDF)

2003

Gupta A, Ludäscher B, Grethe JS, and Martone ME (2003) "Towards a Formalization of Disease-Specific Ontologies for Neuroinformatics." Special Issue on Neuroinformatics Neural Networks. (PDF)

Gupta A, Ludascher B, Martone M, Rajasekar A, Ross E, Qian X, Santini S, He H, Zaslavsky I (2003) "BIRN-M: A Semantic Mediator for Solving Real-World Neuroscience Problems." Proceedings of SIGMOD. (PDF)

Ludäscher B, A. Gupta, and M. E. Martone. (2003) "A Model-Based Mediator System for Scientific Data Management." In T. Critchlow and Z. Lacroix, editors, Bioinformatics: Managing Scientific Data. Morgan Kaufmann. (PDF)

Martone ME, Zhang S, Gupta A, Qian X, He H, Price D, Wong M, Santini S, and Ellisman MH (2003) "The Cell-Centered Database: A database for multiscale structural and protein localization data from light and electron microscopy." Neuroinformatics, 1(3): 379-396.

Peltier ST, Ellisman MH (2003) "The Biomedical Informatics Research Network, The Grid, Blueprint for a New Computing Infrastructure". 2nd edition: Elsevier (in press).

Santini S, Gupta A. (2003) "The role of Internet Imaging in the Biomedical Informatics Research Network." In: Proceedings of SPIE, Vol. 5018 (S. Santini, R. Schettini eds.) San Jose: Internet Imaging IV, January (PDF)

Wang T, Santini S, Amarnath Gupta (2003) "An Interpolated Volume Data Model." VLDB 2002: Oct. (in press)

2002

Gupta A, Ludäscher B, Martone ME (2002) Registering Scientific Information Sources for Semantic Mediation. In: Proc. 21st International Conference on Conceptual Modeling, (ER). Tampere, Finland. (PDF)

Gupta A, Ludäscher B, Martone ME, Qian X, Ross E, Tran J, Zaslavsky I (2002) A System for Managing Alternate Models in Model-based Mediation. In: British Natl. Conf. on Databases (BNCOD). Sheffield, UK. (PDF)

Gupta A, Ludascher B, Martone ME, Qian X, Ross E, Tran J, Zaslavsky I. (2002) "KIND-2: A System for Managing Alternate Models in Integrated Views". In: 19th British National Conference on Databases (BNCOD). Sheffield, UK.

Ludäscher B, Altintas I, Gupta A (2002) Time to Leave the Trees: From Syntactic to Conceptual Querying of XML. In: Proc. Intl. Workshop on XML Data Management, in conjunction with Intl. Conf. on Extending Database Technology. Prague, Czech Republic. (PDF)

Martone ME, Gupta A, Wong M, Qian X, Sosinsky G, Lamont S, Ludäscher B, Ellisman MH (2002) A Cell-Centered Database for Electron Tomographic Data. Journal of Structural Biology 138:145-155. (PDF)

Martone ME, Gupta A, Ludäscher B, Zaslavsky I, Ellisman MH (2002) Federation of Brain Data through Knowledge-Guided Mediation: Kluwer Academic Publishers. (PDF)

Qian X, Ludäscher B, Martone ME, Gupta A (2002) Navigating Virtual Information Sources with Know-ME. In: Intl. Conference on Extending Database Technology, demonstration track. Prague, Czech Republic. (PDF)

Rajasekar AK, Wan M (2002) SRB & SRB Rack - Components of a Virtual Data Grid Architecture. In: Advanced Simulation Technologies Conference (ASTC02). San Diego, CA. (PDF)

Santini S, Gupta A (2002) GeMBASE: A Geometric Mediator for Brain Analysis with Surface Ensembles. In: 28th Int'l Conference on Very Large Databases. Hong Kong, China.(PDF)

Santini S, Gupta A (2002) Conceptual Integration of Multiple Partial Geometric Models. In: 21st International Conference on Conceptual Modeling. Tampere, Finland. (PDF)

Santini S, Gupta A (2002) Principles of schema design for multimedia databases. IEEE Transactions on Multimedia. (PDF)

2001

Gupta A, Ludäscher B, Martone ME (2001) An Extensible Model-Based Mediator System with Domain Maps. In: 17th Intl. Conference on Data Engineering (ICDE), demonstration track. Heidelberg, Germany. (PDF)

Ludäscher B, Gupta A, Martone ME (2001) Model-Based Mediation with Domain Maps. In: 17th Intl. Conference on Data Engineering (ICDE). Heidelberg, Germany. (PDF)

2000

Gupta A, Ludäscher B, Martone ME (2000) Knowledge-Based Integration of Neuroscience Data Sources. In: 12th Intl. Conference on Scientific and Statistical Database Management (SSDBM). Berlin, Germany. (PDF)

Ludäscher B, Gupta A, Martone ME (2000) Model-Based Information Integration in a Neuroscience Mediator System. In: 26th Intl. Conference on Very Large Databases (VLDB) demo track. Cairo, Egypt.(PDF)

2006

BIRN Coordinating Center principal investigator Mark Ellisman (PDF) presented at the annual spring meeting of the Human Brain Project (HBP) on April 24, 2006.

BIRN principal investigators Mark Ellisman (Coordinating Center PDF), Bruce Rosen (Overview PDF, Morphometry PDF), Steven Potkin (Function PDF) and Arthur Toga (Mouse PDF) gave the National Advisory Research Resources Council (NARRC) a detailed update on BIRN's progress Jan. 19 in Bethesda, MD. The presentation was well-received by council members.

2005

Yamini S, Gupta A (2005) "STAG: Spatio-Temporal Annotation Graphs." In: ICDE 2005. San Diego Supercomputer Center University of California, San Diego. (PDF) (Powerpoint)

2004

(2004) "Building on the BIRN". In: 2004 NIH Workshop. Bethesda, MD.

Brown GG, Pieper S, Martone M, Aucoin N, Joyner A, Bischoff-Grethe A, Torvik V (2004) "The Query Atlas: A Brain Referenced Knowledge Discovery Tool." Oct 2004.

Lin AW, Maas P, Peltier S, Ellisman M (2004) "Harnessing the Power of the Globus Toolkit", ClusterWorld: Redefining High Performance Computing. Jan 2004, Vol 2 No 1.

Martone ME, Zaslavsky I, He H, Tran J, Wang Y, Sun L, Price D, Ellisman MH, Gupta A (2004) "The Smart Atlas: A Web-based Spatial Data Management and Data Mining Tool For the Mouse Brain." Oct 2004.

Ozyurt IB, Wei D, Keator DB, Potkin SG, Brown GG, Grethe JS, Morphometry BIRN; Function BIRN; BIRN Coordinating Center (2004) "A user-friendly, web-accessible system for the management, discovery, retrieval, and analysis of clinical and brain imaging data." In: Human Brain Project Neuro-Informatics meeting. Bethesda, MD. (presentation)

Nash A, Ludäscher B (2004) "Processing Unions of Conjunctive Queries with Negation under Limited Access Patterns." In: 9th Int'l Conference on Extending Database Technology (EDBT). Heraklion, Crete, Greece. (Paper PDF) (Slides PDF)

Peterson B (2004) "Biomedical Informatics Research Network Integrating Distributed Data and Expertise." In: MedInfo Imaging Informatics Workshop. San Francisco, CA.

2003

(2003) BIRN All Hands Meeting. In. UCSD.

Grethe JS, Jovicich J, Martone ME, Pieper S, Brown GG, Ellisman MH, Gollub RL, Brain Morphometry BIRN, Mouse BIRN, FIRST BIRN, BIRN Coordinating Center (2003) "The Biomedical Informatics Research Network: Educational and Teaching Resources". In: Society for Neurosciences. New Orleans, USA. (Poster PDF)

Ludäscher B (2003) "Query Containment, Minimization, and Semantic Optimization of Conjunctive Queries." (or: More on Uncles and Aunts), SDSC/BIRN Technical Report.

2002

2001

(2001) "Scalable Visualization Toolkits for Bays to Brains". In: 17th Int'l Conference on Data Engineering (ICDE) demonstration track. (PDF) (PowerPoint)

2000