Matthew Eavenson, Maciej Janik, Shravya Nimmagadda, John A. Miller, Krys J. Kochut, William S. York
Abstract. This paper introduces GlycoBrowser, a dynamic biological pathway exploration and visualization tool. Its capabilities include incremental navigation of pathways, as well as overlaying...
Security in Web-Based Workflow Management Systems (2008)
John A. Miller, Mei Fan, Amit P. Sheth, Krys J. Kochut
Web-based workflows are increasingly becoming a viable choice for workflows that span multiple organizations. Until recently, Web technology has not been terribly secure. However, by utilizing...
_ Semantic Web Services/Automatic Composition (2008)
John A. Miller, Krys J. Kochut, Zhiming Wang, Amrita Basu
− XPDL based WfMS used in CCRC
Matthew Eavenson, Maciej Janik, Shravya Nimmagadda, John A. Miller, Krys J. Kochut, William S. York
Abstract. This paper introduces GlycoBrowser, a dynamic biological pathway exploration and visualization tool. Its capabilities include incremental navigation of pathways, as well as overlaying...
Security for the METEOR Work ow Management System Abstract (2008)
John A. Miller, Mei Fan, Shengli Wu, Ismailcem B. Arpinar, Amit P. Sheth, Krys J. Kochut
actment services, WebWork which is purely Web-based and ORBWork, which usesbothWeb and
JCPNet Tool and Automated Analysis of Distributed Systems ABSTRACT (2008)
Model based approach is crucial to the analysis of system design. Colored Petri Nets (CPNet) have been used as software model with good success. It can be used to complement UML diagrams by providing...
S. Nimmagadda, A. Basu, M. Evenson, J. Han, M. Janik, R. Narra, ...
Glycan biosynthesis is the process by which glycans are built in the cells. Information about the process is available from several Web accessible databases, published papers, experimental data...
Security in Web-Based Workflow Management Systems (2007)
John A. Miller, Mei Fan, Amit P. Sheth, Krys J. Kochut
Web-based workflows are increasingly becoming a viable choice for workflows that span multiple organizations. Until recently, Web technology has not been terribly secure. However, by utilizing...
SPARQLeR: Extended SPARQL for Semantic Association Discovery (2007)
Abstract. Complex relationships, frequently referred to as semantic associations, are the essence of the Semantic Web. Query and retrieval of semantic associations has been an important task in many...
SPARQLeR: Extended SPARQL for Semantic Association Discovery (2007)
Abstract. Complex relationships, frequently referred to as semantic associations, are the essence of the Semantic Web. Query and retrieval of semantic associations has been an important task in many...
A Framework for Schema-Driven Relationship Discovery from Unstructured text (2006)
Cartic Ramakrishnan, Krys J. Kochut, Amit P. Sheth
Abstract. We address the issue of extracting implicit and explicit relationships between entities in biomedical text. We argue that entities seldom occur in text in their simple form and that...
A Framework for Schema-Driven Relationship Discovery from Unstructured text (2006)
Cartic Ramakrishnan, Krys J. Kochut, Amit P. Sheth
Abstract. We address the issue of extracting implicit and explicit relationships between entities in biomedical text. We argue that entities seldom occur in text in their simple form and that...
A CP-nets-based design and verification framework for web services composition (2004)
Web services aim to support efficient integration of applications over Web. Most Web services are stateful, such as services for business processes, and they converse with each other via properly...
Intelligen: A distributed workflow system for discovering protein-protein interactions (2003)
Krys J. Kochut, Jonathan Arnold, Amit Sheth, John Miller, Eileen Kraemer, Budak Arpinar, ...
In the new millennium biology has gone through a paradigm shift with the advent of Genomics, the study of the structure, function, and evolution of whole genomes. The term “genomics ” was coined...
John A. Miller, Amit P. Sheth, Krys J. Kochut
Abstract. Development of today’s advanced applications is increasingly being accomplished using multi-faceted modeling. For example, the areas of simulation and workflow modeling generally need...
Krys J. Kochut, Amit P. Sheth, John A. Miller
Second generation workflow management systems need to deal with heterogeneity of platforms within and across cooperating enterprises along with legacy applications and data. At the same time, there...
A Multilevel Secure Workflow Management System (1999)
Myong H. Kang, Judith N. Froscher, Amit P. Sheth, Krys J. Kochut, John A. Miller
Abstract. The Department of Defense (DoD) needs multilevel secure (MLS) workflow management systems to enable globally distributed users and applications to cooperate across classification levels to...
Security for the METEOR Workflow Management System (1999)
John A. Miller, Mei Fan, Shengli Wu, Ismailcem B. Arpinar, Amit P. Sheth, Krys J. Kochut
A Multilevel Secure Workflow Management System (1999)
Myong H. Kang, Judith N. Froscher, Amit P. Sheth, Krys J. Kochut, John A. Miller
. The Department of Defense (DoD) needs multilevel secure (MLS) workflow management systems to enable globally distributed users and applications to cooperate across classification levels to achieve...
A Multilevel Secure Workflow Management System (1999)
Myong H. Kang, Judith N. Froscher, Amit P. Sheth, Krys J. Kochut, John A. Miller
Abstract. The Department of Defense (DoD) needs multilevel secure (MLS) workflow management systems to enable globally distributed users and applications to cooperate across classification levels to...
A Multilevel Secure Workflow Management System (1999)
Myong H. Kang, Judith N. Froscher, Amit P. Sheth, Krys J. Kochut, John A. Miller
Abstract. The Department of Defense (DoD) needs multilevel secure (MLS) workflow management systems to enable globally distributed users and applications to cooperate across classification levels to...
A workflow is an activity involving the coordinated execution of multiple tasks performed by different processing entities [KS95]. These tasks could be manual, or automated, either created...
Object-Oriented Simulation Languages and Environments: A Four-Level Architecture (1997)
John A. Miller, Walter D. Potter, Krys J. Kochut, Deepa Ramesh
ly, this process adds another ordered pair to the instance -o f function. instance -of : Q ® K The instance -of function maps every q i Î Q to a unique k j Î K. This instantiation process then...
this paper, we focus on two issues. The first issue relates to the challenges that could be addressed by evolving the current workflow technology. Two of the challenges to which we focus our...
The Future of Web-Based Workflows (1997)
John Miller, Amit P. Sheth, Krys J. Kochut
In this position paper, we discuss the suitability of the Web as the primary infrastructure for supporting advanced workflows in heterogeneous, distributed environments in which security,...
Snake-in-the-box codes for dimension 7 (1996)
In the n-dimensional hypercube, an n-snake is a simple path with no chords, while an n-coil is a simple cycle without chords. There has been much interest in determining the length of a maximum...
Simulation Modeling Within Workflow Technology (1995)
John A. Miller, Amit P. Sheth, Krys J. Kochut, Xuzhong Wang, Arun Murugan
This paper presents an approach for integrating simulation modeling and analysis capabilities within the Workflow Management System (WFMS) being developed in the Large Scale Distributed Information...
Simulation Modeling Within Workflow Technology (1995)
John Miller, Amit P. Sheth, Krys J. Kochut, Xuzhong Wang, Arun Murugan
This paper presents an approach for integrating simulation modeling and analysis capabilities within the Workflow Management System (WFMS) being developed in the Large Scale Distributed Information...
Design of a WSRC Repository with an End-User Emphasis (1994)
John A. Miller, Walter D. Potter, Krys J. Kochut, Sunderraman Krishnan, Bonnie Edwards, Wensheng Zhang, ...
This report will go into depth about these and related issues. It will focus on the needs of WSRC and, in so doing, will enable the scope of the repository to be reduced somewhat. For example, one...
On the Integration of Knowledge, Data, and Models (1992)
John A. Miller, Walter D. Potter, Krys J. Kochut
this paper, we highlight some of our ongoing research on integrating knowledge, data, and models. Providing crisp definitions is a difficult proposition. After all, everything in a computer boils...
Query Driven Simulation As A Tool For Genetic Engineers (1992)
John A. Miller, Jonathan Arnold, Krys J. Kochut, A. Jamie Cuticchia, Walter D. Potter
Simulations/animations of genetic structures and functions, simulations of actual or conceived experiments, and animations of algorithms such as simulated annealing, which is used to reconstruct a...
The Active KDL Object-Oriented Database System and Its Application to Simulation Support (1991)
John A. Miller, Walter D. Potter, Krys J. Kochut, Ali A. Keskin, Ender Ucar
Active KDL (Knowledge/Data Language) is an object-oriented database system. It evolved from earlier work on KDL which has been ongoing since 1986 [Pott86]. The foundations of Active KDL are...
Query Driven Simulation Using Active KDL: A Functional Object-Oriented Database System (1991)
John A. Miller, Krys J. Kochut, Walter D. Potter, Ender Ucar, Ali A. Keskin
Because of the difficulty of simulating large complex systems with traditional tools, new approaches have and are being developed. One group of interrelated approaches attempts to simultaneously make...
Model Instantiation for Query Driven Simulation in Active KDL (1990)
John A. Miller, Walter D. Potter, Krys J. Kochut, Orville R. Weyrich
The focus of this paper is on how Active KDL can be used to provide a very powerful simulation support environment. Active KDL (Knowledge/Data Language) is an object-oriented database programming...
Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.
Xu, Zheng, Lance, Britton, Vargas, Claudia, Arpinar, Budak, Bhandarkar, Suchendra, Kraemer, Eileen, ...
A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits...
Mapping by sequencing the Pneumocystis genome using the ordering DNA sequences V3 tool.
Xu, Zheng, Lance, Britton, Vargas, Claudia, Arpinar, Budak, Bhandarkar, Suchendra, Kraemer, Eileen, ...
A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits...