7800547
Design of an Object-Oriented Database for Reverse Genetics
We present the design of an object-oriented database system for reverse genetics applications. Such a database will encapsulate not only the data in the genetic and physical maps, but also the methods used to create the maps as well as methods to link them to other databases, such as GenBank, PIR, and MedLine. The purpose of this database is to provide the fungal genetics community with an electronic tool for identifying the biochemical function of any DNA fragment in the database--electronic reverse genetics. Such a tool for reverse genetics will enable researchers to identify the biochemical functions associated with genes encoding proteins in fungal development pathways, purine metabolism, the heat shock response, and molecular chromosome mechanics and evolution. Our initial goal is to apply the database for the genome mapping of the filamentous fungi, Aspergillus nidulans and Neurospora crassa, at the University of Georgia and the University of Leeds in England.
9294328
Performance Modeling of Database Recovery Protocols
The performance modeling described in this paper compares several protocols which ensure that a database can be recovered to a consistent state after a transaction failure or system crash. The contributions of the paper include a collection of simple analytic models, based on Markov processes, for these protocols and some surprising results on the relative performance of the protocols. We consider only two-stage transactions (all reads before writes) and ignore effects of serializing transactions. The most interesting performance result presented is that, for systems obeying the assumptions of this paper, the "pessimistic" policy of holding write locks to commit point is considerably less efficient than the "optimistic" policy which allows reading of uncommitted data, but risks cascading aborts. A multiversion policy introduced in [2] was also studied and found always to be nearly as good as the optimistic policy and sometimes much better.
3039342
Adding Semantics to Web Services Standards
With the increasing growth in popularity of Web services, discovery of relevant Web services becomes a significant challenge. One approach is to develop semantic Web services where by the Web services are annotated based on shared ontologies, and use these annotations for semantics-based discovery of relevant Web services. We discuss one such approach that involves adding semantics to WSDL using DAML+OIL ontologies. Our approach also uses UDDI to store these semantic annotations and search for Web services based on them. We compare our approach with another initiative to add semantics to support Web service discovery, and show how our approach may fit current standards-based industry approach better.
10095666
Simulation modeling within workflow technology
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 Systems (LSDIS) Lab at the University of Georgia. Simulation modeling can be used for studying the efficiency of workflow designs as well as studying the general performance and reliability of WFMSs. We also discuss the importance of using sophisticated monitoring and animation capabilities, and the use of workflow management technology to advance simulation technology itself. Finally, we demonstrate a sample simulation where tasks and task managers are simulated.
30146652
Workflow Quality of Service
Workflow management systems (WfMSs) have been used to support various types of business processes for more than a decade now. In ecommerce processes, suppliers and customers define a binding agreement or contract between the two parties, specifying quality of service (QoS) items such as products or services to be delivered, deadlines, quality of products, and cost of service. Management of such QoS directly impacts success of organizations participating in e-commerce. Organizations operating in modern markets require an excellent degree of quality of service management. Products and services must be available to customers with well-defined specifications. A good management of quality leads to the creation of quality products and services, which in turn fulfills customer expectations and achieves customer satisfaction. Therefore, when services or products are created or managed using workflow processes, the underlying WfMS must accept the specification, be able to predict, monitor, and control the QoS rendered to customers. To achieve these objectives the first step is to develop an adequate QoS model for workflow processes and develop methods to compute QoS.
8657310
Constraint driven Web service composition in METEOR-S
Creating Web processes using Web service technology gives us the opportunity for selecting new services, which best suit our need at the moment. Doing this automatically requires us to quantify our criteria for selection. In addition, there are challenging issues of correctness and optimality. We present a constraint driven Web service composition tool in METEOR-S, which allows the process designers to bind Web services to an abstract process, based on business and process constraints and generate an executable process. Our approach is to reduce much of the service composition problem to a constraint satisfaction problem. It uses a multiphase approach for constraint analysis. This work was done as part of the METEORS framework, which aims to support the complete lifecycle of semantic Web processes.
206463342
The User Experience
In this article the author provides perspective on user experience, usability and user-centered design. User experience is a broad collection of user-centric issues that cut through the full extent of a project. The author points out new developments in the user experience world that are opening up new opportunities for research and projects. The author also discusses how good user experience processes can be built into the kinds of system development projects that many of us are involved in.
14392520
An ethnographic study of distributed problem solving in spreadsheet development
In contrast to the common view of spreadsheets as “single-user” programs, we have found that spreadsheets offer surprisingly strong support for cooperative development of a wide variety of applications. Ethnographic interviews with spreadsheet users showed that nearly all of the spreadsheets used in the work environments studied were the result of collaborative work by people with different levels of programming and domain expertise. Cooperation among spreadsheet users was spontaneous and casual; users activated existing informal social networks to initiate collaboration.
11647322
Hembase: browser and genome portal for hematology and erythroid biology
Hembase (http://hembase.niddk.nih.gov) is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome. To date, Hembase contains 15,752 entries from erythroblast Expressed Sequenced Tags (ESTs) and 380 referenced genes relevant for erythropoiesis. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology.
8691336
Effectiveness for Embedded Spheres and Balls
Abstract We consider arbitrary dimensional spheres and closed balls embedded in Rn as ⫫01 classes. Such a strong restriction on the topology of a ⫫01 class has computability theoretic repercussions. Algebraic topology plays a crucial role in our exploration of these consequences; the use of homology chains as computational objects allows us to take algorithmic advantage of the topological structure of our ⫫01 classes. We show that a sphere embedded as a ⫫01 class is necessarily located, i.e., the distance to the class is a computable function, or equivalently, the class contains a computably enumerable dense set of computable points. Similarly, a ball embedded as a ⫫01 class has a dense set of computable points, though not necessarily c.e. To prove location for balls, it is sufficient to assume that both it and its boundary sphere are ⫫01. However, the converse fails, even for arcs; using a priority argument, we prove that there is a located arc in R2 without computable endpoints. Finally, the requirement that the embedding map itself be computable is shown to be stronger than the other effectiveness criteria considered. A characterization in terms of computable local contractibility is stated the proof will be the subject of a sequel.
7336432
Decidability and Complexity Results for Timed Automata and Semi-linear Hybrid Automata
We define a new class of hybrid automata for which reachability is decidable--a proper superclass of the initialized rectangular hybrid automata--by taking parallel compositions of simple components. Attempting to generalize, we encounter timed automata with algebraic constants. We show that reachability is undecidable for these algebraic timed automata by simulating two-counter Minsky machines. Modifying the construction to apply to parametric timed automata, we reprove the undecidability of the emptiness problem, and then distinguish the dense and discrete-time cases with a new result. The algorithmic complexity-- both classical and parametric--of one-clock parametric timed automata is also examined. We finish with a table of computability-theoretic complexity results, including that the existence of a Zeno run is Σ11 -complete for semi-linear hybrid automata; it is too complex to be expressed in first-order arithmetic.