Publications

• see also: [@DBLP], [@Google-Scholar], [@CiteSeer], and [ACM]

2006

• Collection-Oriented Scientific Workflows for Integrating and Analyzing Biological Data, Timothy McPhillips, Shawn Bowers, Bertram Ludaescher. 3rd International Workshop on Data Integration in the Life Sciences (DILS'06), European Bioinformatics Institute (EBI), Hinxton, UK, July 20-22, 2006.
• A Model for User-Oriented Data Provenance in Pipelined Scientific Workflows, Shawn Bowers, Timothy McPhillips, Bertram Ludaescher, Shirley Cohen, Susan B. Davidson. International Provenance and Annotation Workshop (IPAW'06), Chicago, Illinois, USA, May 3-5, 2006.
• Enabling Scientific Workflow Reuse through Structured Composition of Dataflow and Control-Flow, Shawn Bowers, Bertram Ludaescher, Anne H.H. Ngu, Terence Critchlow. Post-ICDE IEEE Workshop on Workflow and Data Flow for Scientific Applications (SciFlow'06), Atlanta, GA, April 8th 2006.
• The Center for Plasma Edge Simulation Workflow Requirements, Scott A. Klasky, Bertram Ludaescher, and Manish Parashar. Post-ICDE IEEE Workshop on Workflow and Data Flow for Scientific Applications (SciFlow'06), Atlanta, GA, April 8th 2006.
• A Calculus for Propagating Semantic Annotations through Scientific Workflow Queries, Shawn Bowers, Bertram Ludaescher. Query Languages and Query Processing (QLQP'06), EDBT'06 Post-Conference Workshop, Munich, Germany. March 30-31, 2006.

2005

• Rewriting Queries Using Views with Access Patterns Under Integrity Constraints, A. Deutsch, B. Ludäscher, and A. Nash, Intl. Conference on Database Theory (ICDT'05), Edinburgh, Scotland, January 2005.
• Managing Scientific Data: From Data Integration to Scientific Workflows, B. Ludäscher, K. Lin, S. Bowers, E. Jaeger-Frank, B. Brodaric, C. Baru, GSA Today, Special Issue on Geoinformatics, to appear, 2005.
• Scientific Workflow Management and the Kepler System, B. Ludäscher, I. Altintas, C. Berkley, D. Higgins, E. Jaeger-Frank, M. Jones, E. Lee, J. Tao, Y. Zhao, Concurrency and Computation: Practice & Experience, Special Issue on Scientific Workflows, to appear, 2005.
• Actor-Oriented Design of Scientific Workflows, Shawn Bowers and Bertram Ludäscher, 24th Intl. Conference on Conceptual Modeling (ER'05), Klagenfurt, Austria, LNCS, Springer, 2005.
• A Framework for the Design and Reuse of Grid Workflows, Ilkay Altintas, Adam Birnbaum, Kim Baldridge, Wibke Sudholt, Mark Miller, Celine Amoreira, Yohann Potier, and Bertram Ludaescher, Intl. Workshop on Scientific Applications on Grid Computing (SAG'04), LNCS 3458, Springer, 2005
• Towards Automatic Generation of Semantic Types in Scientific Workflows, Shawn Bowers and Bertram Ludaescher, Intl. Workshop on Scalable Semantic Web Knowledge Base Systems (SSWS'05), LNCS, Springer, 2005.
• Incorporating Semantics in Scientific Workflow Authoring, C. Berkley, S. Bowers, M. Jones, B. Ludäscher, M. Schildhauer, J. Tao, 17th International Conference on Scientific and Statistical Database Management (SSDBM'05), 27-29 June 2005, Santa Barbara, California.
• Creating and Providing Data Management Services for the Biological and Ecological Sciences (SEEK), S. Romanello, J. Beach, S. Bowers, M. Jones, B. Ludäscher, W. Michener, D. Pennington, A. Rajasekar, M. Schildhauer, 17th International Conference on Scientific and Statistical Database Management (SSDBM'05), 27-29 June 2005, Santa Barbara, California.
• A Scientific Workflow Approach to Distributed Geospatial Data Processing using Web Services, E. Jaeger, I. Altintas, J. Zhang, B. Ludäscher, D. Pennington, W. Michener, 17th International Conference on Scientific and Statistical Database Management (SSDBM'05), 27-29 June 2005, Santa Barbara, California.

2004

• An Ontology-Driven Framework for Data Transformation in Scientific Workflows, S. Bowers and B. Ludäscher, Intl. Workshop on Data Integration in the Life Sciences (DILS'04), March 25-26, 2004 Leipzig, Germany, LNCS 2994.
• On Integrating Scientific Resources through Semantic Registration, S. Bowers, K. Lin, and B. Ludäscher, 16th International Conference on Scientific and Statistical Database Management (SSDBM'04), 21-23 June 2004, Santorini Island, Greece.
• Processing First-Order Queries under Limited Access Patterns, Alan Nash and B. Ludäscher, Proc. 23rd ACM Symposium on Principles of Database Systems (PODS'04) Paris, France, June 2004.
• Processing Unions of Conjunctive Queries with Negation under Limited Access Patterns, Alan Nash and B. Ludäscher., 9th Intl. Conference on Extending Database Technology (EDBT'04) Heraklion, Crete, Greece, March 2004, LNCS 2992.
• Web Service Composition Through Declarative Queries: The Case of Conjunctive Queries with Union and Negation, B. Ludäscher and Alan Nash. Research abstract (poster), 20th Intl. Conference on Data Engineering (ICDE'04) Boston, IEEE Computer Society, April 2004.
• A Web Service Composition and Deployment Framework for Scientific Workflows, I. Altintas, E. Jaeger, K. Lin, B. Ludaescher, A. Memon, In the 2nd Intl. Conference on Web Services (ICWS), San Diego, California, July 2004.
• Kepler: An Extensible System for Design and Execution of Scientific Workflows, I. Altintas, C. Berkley, E. Jaeger, M. Jones, B. Ludäscher, S. Mock, 16th International Conference on Scientific and Statistical Database Management (SSDBM'04), 21-23 June 2004, Santorini Island, Greece.
• Kepler: Towards a Grid-Enabled System for Scientific Workflows, Ilkay Altintas, Chad Berkley, Efrat Jaeger, Matthew Jones, Bertram Ludäscher, Steve Mock, Workflow in Grid Systems (GGF10), Berlin, March 9th, 2004.

2003

• A Model-Based Mediator System for Scientific Data Management, B. Ludäscher, A. Gupta, and M. E. Martone. In Z. Lacroix and T. Critchlow editors, Bioinformatics: Managing Scientific Data. Morgan Kaufmann, 2003.
• Towards a Formalization of Disease-Specific Ontologies for Neuroinformatics, A. Gupta, B. Ludäscher, J. S. Grethe, and M. E. Martone. Neural Networks, 16 (2003) 1277-1292, Special Issue on Neuroinformatics, 2003.
• A System for Semantic Integration of Geologic Maps via Ontologies, K. Lin and B. Ludäscher. In Semantic Web Technologies for Searching and Retrieving Scientific Data (SCISW), Sanibel Island, Florida, 2003.
• Towards a Generic Framework for Semantic Registration of Scientific Data, S. Bowers and B. Ludäscher. In Semantic Web Technologies for Searching and Retrieving Scientific Data (SCISW), Sanibel Island, Florida, 2003.
• Compiling Abstract Scientific Workflows into Web Service Workflows, B. Ludäscher, I. Altintas, and A. Gupta, 15th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Boston, Massachusetts, 2003.
• On Providing Declarative Design and Programming Constructs for Scientific Workflows based on Process Networks, B. Ludäscher I. Altintas, Technical Report, SciDAC-SPA-TN-2003-01, 2003.
• A Modeling and Execution Environment for Distributed Scientific Workflows, I. Altintas, S. Bhagwanani, D. Buttler, S. Chandra, Z. Cheng, M. Coleman, T. Critchlow, A. Gupta, W. Han, L. Liu, B. Ludäscher, C. Pu, R. Moore, A. Shoshani, and M. Vouk, demonstration track, 15th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Boston, Massachusetts, 2003.
• BIRN-M: A Semantic Mediator for Solving Real-World Neuroscience Problems, A. Gupta, B. Ludäscher, and M. Martone. demonstration track, ACM Intl. Conference on Management of Data (SIGMOD), 2003.
• The Many Faces of Process Interaction Graphs: A Data Management Perspective, A. Gupta and B. Ludäscher. Workshop on Data Management for Molecular and Cell Biology, to appear in OMICS - A Journal of Integrative Biology, NIH Campus, Bethesda, MD, 2003.
• The Role of XML in Mediated Data Integration Systems with Examples from Geological (Map) Data Interoperability, B. Brodaric, B. Ludäscher, and K. Lin. In Geological Society of America (GSA) Annual Meeting, volume 35(6), November 2003.
• Semantic Mediation Services in Geologic Data Integration: A Case Study from the GEON Grid, K. Lin, B. Ludäscher, B. Brodaric, D. Seber, C. Baru, and K. A. Sinha. In Geological Society of America (GSA) Annual Meeting, volume 35(6), November 2003.
• Igneous Rocks, Terranes and GEON, K. A. Sinha, C. Smyth, A. Zendel, B. Brodaric, C. Barnes, A. Snoke, B. Ludäscher, D. Seber, and C. Baru. In Geological Society of America (GSA) Annual Meeting, volume 35(6), November 2003.
• Mining the Frequency Distribution of Transcription Factor Binding Sites of Ionizing Radiation Responsive Genes, L. Peterson, E. Yin, D. Nelson, I. Altintas, B. Ludäscher, T. Critchlow, A. J. Wyrobek, and M. A. Coleman. In New Horizons in Genomics, DOE/SC-0071, Santa Fe, New Mexico., March 30-April 1 2003.

2002

• A Transducer-Based XML Query Processor, B. Ludäscher, P. Mukhopadhyay, Y. Papakonstantinou, 28th Intl. Conference on Very Large Databases (VLDB), Hong Kong, August 2002.
• Understanding the Global Semantics of Referential Actions using Logic Rules, W. May, B. Ludäscher, ACM Transactions on Database Systems (TODS), 27(4), 343-397, 2002.
• Federation of Brain Data through Knowledge-Guided Mediation M. E. Martone, A. Gupta, B. Ludäscher, I. Zaslavsky, and M. H. Ellisman. In R. Kötter, editor, Neuroscience Databases. A Practical Guide, pp. 275-292. Kluwer Academic Publishers, 2002.
• Scientific Data Integration. Report on the EDBT'02 Panel O. Boucelma, S. Castano, C. A. Goble, V. Josifovski, Z. Lacroix, and B. Ludäscher. In ACM SIGMOD Record, 31(4):107-112, 2002.
• Time to Leave the Trees: From Syntactic to Conceptual Querying of XML, B. Ludäscher, I. Altintas, A. Gupta, Intl. Workshop on XML Data Management (XMLDM), Prague, Czech Republic, March 2002, LNCS 2490, Springer, pp. 148-168.
• Registering Scientific Information Sources for Semantic Mediation, A. Gupta, B. Ludäscher, M. E. Martone, 21st International Conference on Conceptual Modeling, (ER), LNCS 2503, Tampere, Finland, October 2002.
• Ontology Services for Curriculum Development in NSDL, A. Gupta, B. Ludäscher, R. Moore, Joint Conference on Digital Libraries (JCDL), Portland, Oregon, July 2002.
• Navigating Virtual Information Sources with Know-ME, X. Qian, B. Ludäscher, M. E. Martone, A. Gupta, demonstration track, Intl. Conference on Extending Database Technology (EDBT), Prague, Czech Republic, March 2002.
• A System for Managing Alternate Models in Model-based Mediation, A. Gupta, B. Ludäscher, M. E. Martone, X. Qian, E. Ross, J. Tran, I. Zaslavsky, demonstration track, British Natl. Conf. on Databases (BNCOD), Sheffield, UK, July 2002.
• Multi-Level Information Modeling and Preservation of eGOV Data, R. Marciano, B. Ludäscher, R. Moore, I. Zaslavsky, K. Pezzoli, Intl. Conference on E-Government (EGOV), LNCS 2456, pp. 93-100, Aix-en-Provence, France, September 2002.
• A Cell-Centered Database for Electron Tomographic Data, M. E. Martone, A. Gupta, M. Wong, X. Qian, G. Sosinsky, S. Lamont, B. Ludäscher, M. H. Ellisman, Journal of Structural Biology, 138(1-2), 145-155, 2002.
• Distributed Data Management Architecture for Embedded Computing, Hans-Werner Braun, Todd Hansen, Kent Lindquist, Bertram Ludäscher, John Orcutt, Arcot Rajasekar, Frank Vernon, 6th Workshop on High Performance Embedded Computing, MIT Lincoln Laboratory, Sept. 2002.
• Generalizing Seismic Processing Systems to Diverse Signal Domains, K.G. Lindquist, F.L. Vernon, T.S. Hansen, A. Rajasekar, B. Ludaescher, J. Orcutt, J. Berger, H.W. Braun, Y. Bock (2002). in Abstracts from the Fourteenth Annual IRIS Workshop, Waikoloa, Hawaii, June 12-16, The IRIS Consortium.

2001

• Model-Based Mediation with Domain Maps, B. Ludäscher, A. Gupta, M. E. Martone, 17th Intl. Conference on Data Engineering (ICDE), Heidelberg, Germany, IEEE Computer Society, April 2001.
• An Extensible Model-Based Mediator System with Domain Maps, A. Gupta, B. Ludäscher, M. E. Martone, demonstration track, 17th Intl. Conference on Data Engineering (ICDE), Heidelberg, Germany, IEEE Computer Society, April 2001.
• Towards a Federated Neuroscientific Knowledge Management System using Brain Atlases, Gully A.P.C.Burns, Klaas Stephan, Bertram Ludäscher, Amarnath Gupta, Rolf Kötter, Neurocomputing 38-40, pp. 1633-1641, Elsevier, 2001.
• Preservation of Digital Data with Self-Validating, Self-Instantiating Knowledge-Based Archives, B. Ludäscher, R. Marciano, R. Moore, ACM SIGMOD Record, 30(3), 54-63, 2001.
• Towards Self-Validating Knowledge-Based Archives, B. Ludäscher, R. Marciano, R. Moore, 11th Workshop on Research Issues in Data Engineering (RIDE), Heidelberg, Germany, IEEE Computer Society, April 2001.

2000

• Model-Based Information Integration in a Neuroscience Mediator System, B. Ludäscher, A. Gupta, M. E. Martone, demonstration track, 26th Intl. Conference on Very Large Databases (VLDB), Cairo, Egypt, September 2000.
• Knowledge-Based Integration of Neuroscience Data Sources, A. Gupta, B. Ludäscher, M. E. Martone, 12th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Berlin, Germany, IEEE Computer Society, July 2000.
• Navigation-Driven Evaluation of Virtual Mediated Views, B. Ludäscher, Y. Papakonstantinou, P. Velikhov, Intl. Conference on Extending Database Technology (EDBT), Konstanz, Germany, LNCS 1777, Springer, March 2000.
• Games and Total DatalogNeg Queries, J. Flum, M. Kubierschky, B. Ludäscher, Theoretical Computer Science, 239(2), pp.257-276, Elsevier, 2000.
• BBQ: Blended Browsing and Querying of XML in a Lazy Mediator System, K. Munroe, B. Ludäscher, Y. Papakonstantinou, demonstration track, Intl. Conference on Extending Database Technology (EDBT), Konstanz, Germany, March 2000.
• Collection-Based Persistent Digital Archives, Reagan Moore, Chaitan Baru, Arcot Rajasekar, Bertram Ludäscher, Richard Marciano, Michael Wan, Wayne Schroeder, Amarnath Gupta, D-Lib Magazine, 6(3 & 4), March [Part 1] and April [Part 2], 2000.
• Search Middleware and the Simple Digital Library Interoperability Protocol, Andreas Paepcke, Robert Brandriff, Greg Janee, Ray Larson, Bertram Ludäscher, Sergey Melnik, Sriram Raghavan, D-Lib Magazine, 6(3), March 2000.

1999

• Modeling Interactive Web Sources for Information Mediation, B. Ludäscher, A. Gupta, Intl. Workshop on the World-Wide Web and Conceptual Modeling (WWWCM'99), Paris, France, LNCS 1727, Springer, November 1999.
• A Framework for Navigation-Driven Lazy Mediators, B. Ludäscher, Y. Papakonstantinou, P. Velikhov, ACM Workshop on the Web and Databases (WebDB'99), Philadelphia, June 1999.
• XML-Based Information Mediation with MIX, C. Baru, A. Gupta, B. Ludäscher, R. Marciano, Y. Papakonstantinou, P. Velikhov, V. Chu, exhibition program, ACM Conf. on Management of Data (SIGMOD'99), Philadelphia, June 1999.
• View Definition and DTD Inference for XML, B. Ludäscher, Y. Papakonstantinou, P. Velikhov, V. Vianu, Post-ICDT Workshop on Query Processing for Semistructured Data and Non-Standard Data Formats (SSD99), Jerusalem, January 1999.
• XML-Based Information Mediation for Digital Libraries, C. Baru, A. Gupta, V. Chu, B. Ludäscher, R. Marciano, Y. Papakonstantinou, P. Velikhov, exhibition program, ACM Conf. on Digital Libraries (DL'99), Berkeley, August 1999.
• A Unified Framework for Wrapping, Mediating and Restructuring Information from the Web, W. May, R. Himmeröder, G. Lausen, B. Ludäscher, Intl. Workshop on the World-Wide Web and Conceptual Modeling (WWWCM'99), Paris, France, LNCS 1727, Springer, November 1999.
• FLORA: The Secret of Object-Oriented Logic Programming, B. Ludäscher, Guizhen Yang, Michael Kifer, Technical Manual, SUNY at Stony Brook, 1999 (see also the new Flora-2 system by G. Yang and M. Kifer)

1998

• Managing Semistructured Data with FLORID: A Deductive Object-Oriented Perspective, B. Ludäscher, R. Himmeröder, G. Lausen, W. May, C. Schlepphorst, Information Systems, 23(8), Special Issue on Semistructured Data, 1998.
• Referential Actions: From Logical Semantics to Implementation, B. Ludäscher, W. May. Proc. 6th Intl. Conference on Extending Database Technology (EDBT'98), Valencia, Spain, LNCS 1377, Springer, March 1998.
• Features and Requirements for an XML View Definition Language: Lessons from XML Information Mediation, C. Baru, B. Ludäscher, Y. Papakonstantinou, P. Velikhov, V. Vianu, position paper, W3C Query Languages Workshop (QL'98), Boston, Massachusetts, December 1998.
• Techniques and Rule Patterns for Declaratively Querying Web Data with FLORID, B. Ludäscher, R. Himmeröder, W. May, Deklarative KI-Methoden zur Implementierung und Nutzung von Systemen in Netzen (Workshop KI-98), Bremen, Germany, September 1998.
• Search, Analysis, and Integration of Web Documents: A Case Study with FLORID, R. Himmeröder, P.-Th. Kandzia, B. Ludäscher, W. May, G. Lausen, Proc. Intl. Workshop on Deductive Databases and Logic Programming (DDLP'98), Manchester, UK, June 1998.
• Querying the Web with FLORID, R. Himmeröder, B. Ludäscher, 10. GI-Workshop: Grundlagen von Datenbanken (GvD'98), Konstanz, Germany, June 1998.
• FLORID: A DOOD-System for Querying the Web, R. Himmeröder, G. Lausen, B. Ludäscher, Christian Schlepphorst, Demonstration Session at EDBT'98, Valencia, Spain, March 1998.
• Integration of Active and Deductive Database Rules, B. Ludäscher, PhD thesis, DISDBIS 45, infix-Verlag, Sankt Augustin, ISBN 3-89601-445-5, 1998.
• On Active Deductive Databases: The Statelog Approach, G. Lausen, B. Ludäscher, and W. May. In Transactions and Change in Logic Databases, Hendrik Decker, Burkhard Freitag, Michael Kifer, and Andrei Voronkov, editors. LNCS 1472, Springer, 1998.
• On Logical Foundations of Active Databases, G. Lausen, B. Ludäscher, and W. May. In Logics for Databases and Information Systems, Jan Chomicki and Gunter Saake, editors. Kluwer Academic Publishers, 1998.
• Maintaining Well-Founded Views in Constraint Databases, James Lu, B. Ludäscher, J. Schü, V.S. Subrahmanian. In T. Martin and F. A. Fontana, editors, Logic Programming and Soft Computing, pp.129-144, Wiley, 1998.

1997

• Referential Actions as Logical Rules, B. Ludäscher, W. May, G. Lausen, Proc. 16th ACM Symposium on Principles of Database Systems (PODS'97), Tucson, Arizona, ACM Press, May 1997.
• Total and Partial Well-Founded Datalog Coincide, J. Flum, M. Kubierschky, B. Ludäscher, Proc. 6th Intl. Conference on Database Theory (ICDT'97), LNCS 1186, Springer, Delphi, Greece, January 1997.
• Handling Termination in a Logical Language for Active Rules, B. Ludäscher, G. Lausen. Informatica, Vol. 9, No. 1, 65-87, Lithuanian Academy of Sciences, Special Issue on the 7th Advanced Course on Artificial Intelligence (ACAI'97), Vilnius, June 1997.
• On a Declarative Semantics for Web Queries, R. Himmeröder, G. Lausen, B. Ludäscher, Christian Schlepphorst, Proc. 5th Intl. Conf. on Deductive and Object-Oriented Databases (DOOD'97), Montreux, Switzerland, LNCS 1341, Springer, December 1997.
• Well-Founded Semantics for Deductive Object-Oriented Database Languages, W. May, B. Ludäscher, G. Lausen, Proc. 5th Intl. Conf. on Deductive and Object-Oriented Databases (DOOD'97), Montreux, Switzerland, LNCS 1341, Springer, December 1997.

1992 - 1996

• Nested Transactions in a Logical Language for Active Rules, B. Ludäscher, W. May, G. Lausen, Proc. Intl. Workshop on Logic in Databases (LID'96), San Miniato, Italy, LNCS 1154, Springer, 1996.
• Towards a Logical Semantics for Referential Actions in SQL, B. Ludäscher, W. May, J. Reinert, Proc. 6th Intl. Workshop on Foundations of Models and Languages for Data and Objects: Integrity in Databases, Dagstuhl, Germany, September 1996.
• A Logical Framework for Active Rules, B. Ludäscher, U. Hamann, G. Lausen, Proc. 7th Intl. Conf. on Management of Data (COMAD'95), Tata-McGraw Hill, Pune, India, December 1995.
• Reconciling Active and Deductive Databases by States, B. Ludäscher, U. Hamann, G. Lausen, Technical Report 70, Institut für Informatik, Universität Freiburg, 1995.
• Zustandsorientierte Beschreibung von Updates in deduktiven Datenbanken (in German), U. Hamann, B. Ludäscher, 7. GI-Workshop: Grundlagen von Datenbanken (GvD'95), Hildesheim, Germany, 1995.
• Updates by Reasoning about States, G. Lausen, B. Ludäscher, Proc. 2nd Intl. East/West Database Workshop (EWDW'94), Klagenfurt, Austria, Workshops in Computing, Springer, 1994.
• Towards First-Order Deduction Based on Shannon-Graphs, J. Posegga, B. Ludäscher, Proc. 16th German Conf. on AI (GWAI), LNAI 671, Springer, 1992.
• A First-Order Deduction System Based on Shannon Graphs, B. Ludäscher, Masters thesis, (in German), Universität Karlsruhe, 1992.

Reports

• Report to DOE on Scientific Process Automation (SPA), DOE SciDAC Scientific Data Management Integrated Software Infrastructure Center (SDM/ISIC), March 2005.