CHAIMS MegaGene – Stanford University References [AbernethyA:98] N. F. Abernethy & R. B. Altman. SOPHIA: Providing Basic Knowledge Services With A Common DBMS. 1998, SMI Report Number: SMI-98-0710 . [AdveEa:96] V.S. Adve, J. Mellor-Crummey, M. Anderson, K. Kennedy, J-C. Wang, and D. A. Reed: “Integrating compilation and performance analysis for data-parallel programs”; Debugging and Perform. Tuning for Parallel Comput. Syst., Simmons, Hayes, Broron, Reed, eds.; IEEE Computer Soc. Press, 1996, pp. 25-51. [AgarwalKSW:95] Shailesh Agarwal, A.M. Keller, K. Saraswat, and G. Wiederhold: ”Flexible Relation: An Approach for Integrating Data from Multiple, Possibly Inconsistent Databases”; Proc. IEEE Data Engineering Conference, Taipei, Taiwan, March 1995. [AhoU:79] A.V. Aho and J.D. Ullman: “Universality of Data Retrieval Languages”; ACM Symp. on Principles of Progr. Languages, 1979, pp. 110-120. [AltmanAC:97] B. Altman, N. F. Abernethy and R. O. Chen: “Standardized Representations of the Literature: Combining Diverse Sources of Ribosomal Data.” Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology, Halikidiki, Greece, 1997, AAAI Press, Menlo Park, p. 15-24. [AshishK:97] N. Ashish and C.A. Knoblock: “Semi-automated Wrapper Generation for Internet Information Sources”; Proc. 2nd IFCIS Int. Conf. on Cooperative Information Systems (Coopis '97), Kiawah Island, June 1997 [AtkinsonBM:95] M.P. Atkinson, V. Benzaken, and D. Maier (eds.) “Persistent Object Systems”; Springer-Verlag and British Computer Society, 1995. [Barsalou:88] Thierry Barsalou: “An Object-based Architecture for Biomedical Expert Database Systems”; SCAMC 12, IEEE CS Press, Washington DC, November 1988. [BarsalouSKW:91] T. Barsalou, N. Siambela, A. Keller, and G. Wiederhold: “Updating Relational Databases through Object-Based Views”; ACM SIGMOD Conf. on the Management of Data 91, Boulder CO, May 1991. [BeringerTJW:98C] D. Beringer, C. Tornabene, P. Jain, G. Wiederhold: “Composition of Autonomous, Heterogeneous and Distributed Megamodules”; submitted for publication 1998. [BeringerTJW:98L] D. Beringer, C. Tornabene, P. Jain, G. Wiederhold: “A Language and System for Composing Autonomous, Heterogeneous and Distributed Megamodules”; submitted for publication 1998. [Betz:94] M. Betz: “Interoperable Objects”; Dr. Dobbs Journal, Vol.19 no.11, pp.18 af. [BlumeEa:96] B. Blume, R. Eigenmann, K. Faigin, J. Grout, J. Lee, T. Lawrence, J. Hoeflinger, D. Padua, Y. Paek, P. Petersen, L. Rauchwerger, P. Tu, And S. Weatherford: “Restructuring programs for high-speed computers with Polaris”; Proc. 1996 ICPP Wkshp. on Challenges for Parallel Processing, Bloomingdale, Ill., Aug. 1996, pp. 149-161. [BoehmS:92] B. Boehm and B. Scherlis: “Megaprogramming”; Proc. DARPA Software Technology Conference 1992, Los Angeles CA, April 28-30, Meridien Corp., Arlington VA 1992. [ChenFA:97] R. O. Chen, R. Felciano, and R. B. Altman. RiboWeb: “Linking Structural Computations to a Knowledge Base of Published Experimental Data.”; Proceedings of the Fifth International Conference on Intelligent Systems in Molecular Biology, Halikidiki, Greece, 1997, AAAI Press, Menlo Park, p. 84-87. [DavidsonOB:95] S.B. Davidson, C. Overton and P. Buneman: “Challenges in Integrating Biological Data Sources”; Computational Biology 2, 1995, pp 557-572. [DavidsonOTW:96] Susan B. Davidson, Christian Overton, Val Tannen and Limsoon Wong, “A Digital Library for Biomedical Researchers”; Journal of Digital Libraries, November 1996. [DeZegherEa:88] I. DeZegher-Geets., A.G. Freeman, M.G. Walker, R.L. Blum and G. Wiederhold: “Summarization and Display of On-line Medical Records”; M.D. Computing, Vol.5 no.3, March 1988, pp.38-46. [DoE:93] Dep. of Energy: “Report of the Invitational DoE Workshop on Genome Informatics”, 26-27 April 1993, Baltimore, R. J. Robbins editor, 1993. [ElMasriW:79] Ramez El-Masri and Gio Wiederhold: “Data Model Integration Using the Structural Model” ; Proceedings 1979 ACM SIGMOD Conference, 1979, pages 191-202. 1 CHAIMS MegaGene – Stanford University [FelicianoA:98] R. M. Felciano & R. B. Altman: “Graphical Style Sheets: Towards Reusable Representations of Biomedical Graphics”; Computer-Human Interactions (CHI) conference, in press, 1998. [FelicianoCA:97] R. M. Felciano, R. O. Chen and R. B. Altman: “RNA Secondary Structure as a Reusable Interface to Biological Information Resources”; Gene 190, GC 59-70, 1997. [GeneserethSS:94] Michael R. Genesereth, Narinder P. Singh and Mustafa A.Syed: “A Distributed and Anonymous Knowledge Sharing Approach to Software Interoperation” ; Proc. Int.Symp. on Fifth Generation Comp Systems, ICOT, Tokyo, Japan, Vol.W3, Dec.1994, pp.125-139. [GeneserethKD:97] M.R. Genesereth, A.M. Keller, and O. Duschka: “Infomaster: An Information Integration System”; Proceedings of 1997 ACM SIGMOD Conference, May 1997. [GennariCAM:98] J. H. Gennari, H. Cheng, R. B. Altman, & M. A. Musen: “Reuse, CORBA, and Knowledge-Based Systems”; Int. J. Human-Computer Sys., in press, 1998. [GrafeK:89] G. Grafe and K. Karen: “Dynamic Query Evaluation Plans”; In James Clifford, Bruce Lindsay, and David Maier, eds., Proceedings of the 1989 ACM SIGMOD International Conference on Management of Data, Portland, Oregon, June 1989. [HartW:94] Kyle Hart and Limsoon Wong: “A Query Interface for Heterogenous Biological Data Sources”; Manuscript, February 1994. [HonEa:98] L. Hon, N.F. Abernethy, V. Brusic, J. Chai, and R.B. Altman: “MHCWeb: Converting a WWW database into a knowledge-based collaborative environment”; American Medical Informatics Fall Symposium, 1998, submitted. [ISO:87] “Information Processing -- Open Systems Interconnection -- Specification of Abstract Syntax Notation One” and “Specification of Basic Encoding Rules for Abstract Syntax Notation One”; International Organization for Standardization and International Electrotechnical Committee, International Standards 8824 and 8825, 1987. [JanninkPVW:98] J. Jannink, S. Pichai, D. Verheijen and G. Wiederhold: “Encapsulation and Composition of Ontologies”; Stanford University, CSD, submitted for publication 1998. [KellerJA:93] A.M. Keller, R. Jensen, and S. Agarwal: “Persistence Software: Bridging Object-Oriented Programming and Relational Databases”; ACM SIGMOD, International Conference on Management of Data, May 1993. [MusenGETP:94] M.A. Musen, J. H. Gennari, H. Eriksson, S.W. Tu., and A.R. Puerta: “PROTEGE II: Computer Support For Development Of Intelligent Systems From Libraries Of Components”; MEDINFO 95, The Eighth World Congress on Medical Informatics, Vancouver, B.C., Canada, 1995, pp.766-770. [MusenS:95] M. A. Musen & A. T. Schreiber: “Architectures for Intelligent Systems Based on Reusable Components”; Artificial Intelligence in Medicine, Vol.7 pp.189-199, 1995. [ONeil:76] J.T. O’Neil: MUMPS language Standard, NBS handbook 118. U.S. Gov.Printing Office, 1976. [PerrochonWB:97] L. Perrochon, G. Wiederhold, and R. Burback: “A Compiler for Composition: CHAIMS”; Fifth International Symposium on Assessment of Software Tools and Technologies (SAST `97), Pittsburgh, June 35, 1997. [Platt:97] D. Platt: “The Essence of COM and ActiveX”; Prentice-Hall, 1997. [ReedEa:96] D.A. Reed, C. L. Elford, T. M. Madhyastha, E. Smirni, and S. E. Lamm: “The next frontier: interactive and closed loop performance steering”; Proc. 1996 ICPP Wkshp. on Challenges for Parallel Process, Bloomingdale, Ill., Aug. 1996, pp. 20-31. [RosenberryKF:94] W. Rosenberry, D. Kenney and G. Fisher: “Understanding DCE”; O'Reilly, 1994. [Roy:92] Shaibal Roy: Parallel Execution of Database Queries; PhD Thesis, Stanford CSD report 92-1397, 1992. [Searls:98] David Searls; “Biowidgets”; Computational Methods in Molecular Biology, Elsevier Science, 1998. [SchmidtGA:97] R. Schmidt, M. Gerstein and R. B. Altman, “LPFC: an internet library of protein family core structures” Protein Science, 6, p246-248, 1997. [Siegel:96] J. Siegel: “CORBA fundamentals and programming”; Wiley New York, 1996. [StickelEa:94] Mark Stickel, Richard Waldinger, Michael Lowry, Thomas Pressburger, and Ian Underwood: “Deductive Composition of Astronomical Software from Subroutine Libraries”; Twelfth International Conference on Automated Deduction, Nancy, France, June 1994, pages 341-355. 2 CHAIMS MegaGene – Stanford University [StuderEa:96] R. Studer, H. Eriksson, J. Gennari, S. Tu, D. Fensel, & M. Musen: “Ontologies and the Configuration of Problem-solving Methods”; in B.R. Gains and M.A. Musen, Ed., 10th Banff Knowledge Acquisition for Knowledge-Based Systems Workshop, Banff, Canada, pp. 11-1 - 11-20. 1996. [Szyperski:98] Clemens Szyperski, “Component Software: Beyond Object-Oriented Programming”; Addison-Wesley and ACM-Press New York, 1998. [TornabeneJW:98] C. Tornabene, P. Jain, G. Wiederhold: “Software for Composition: CHAIMS”; position paper for the Workshop on Compositional Software Architectures of OMG, DARPA and MCC in Monterey, CA, January 68, 1998. [TornabeneDJW:98] C. Tornabene, D. Beringer, P. Jain, G. Wiederhold: “Composition on a Higher Level: CHAIMS”; submitted for publication 1998. [WeiA:98] L. Wei and R.B.Altman. Recognizing protein binding sites using statistical descriptions of their 3D environments, 1998 Pacific Symposium on Biocomputing, World Scientific Publishers, Singapore, p. 497-508. [Widom:98] J. Widom, H. Garcia-Molina, M. Levitt, J. Sussman, O. Ritter: “Advanced Data Warehousing for Structural Biology Applications”, Proposal for KDI, 1998 [Wiederhold:86v] Gio Wiederhold: “Views, Objects, and Databases”; <i>IEEE Computer</i>, Vol.19 No.12, December 1986, Pages 37-44. [WiederholdEa:88] Wiederhold, Gio et al.: “KBMS: A Precis of Research on Knowledge-based Management Systems, 1977-1988; Stanford University, KBMS project, 1988; updated for WWW Aug.1995 [http://wwwdb.stanford.edu/pub/gio/1988/kbms.html]. [WiederholdWC:92] Gio Wiederhold, P. Wegner and S. Ceri: “Towards Megaprogramming: A Paradigm for Component-Based Programming”; Communications of the ACM, 1992(11): p.89-99. [Wiederhold:92m] Gio Wiederhold: “Model-free Optimization” ; <i>DARPA Software Technology Conference 1992</i>, April 1992, Meridien Corp., Arlington VA, pages 83-96. [Wiederhold:92a] Gio Wiederhold: “Mediation in the Architecture of Future Information Systems” ; IEEE Computer Magazine, March 1992, pages 38-49. [WiederholdBSQ:96] Gio Wiederhold, Michel Bilello, Vatsala Sarathy, and XiaoLei Qian, “A Security Mediator for Health Care Information”; Journal of the AMIA issue containing the Proceedings of the 1996 AMIA Conference, Washington DC, Oct. 1996, pp.120-124. [WiederholdBSQ:96C] Gio Wiederhold, Michel Bilello, Vatsala Sarathy, and XiaoLei Qian: “Protecting Collaboration”; Proceedings of the National Information Systems Security Conference (NISSC'96), Baltimore MD, Oct. 1996, pp.561-569. [WiederholdBD:98] Gio Wiederhold, Michel Bilello, and Chris Donahue: “Web Implementation of a Security Mediator for Medical Databases”; in T.Y. Lin and Shelly Qian: Database Security XI, Status and Prospects, IFIP / Chapman & Hall, 1998, pp.60-72. 3