Functionally Specified Distributed Transactions in Co-operative Scenarios

Addresses the problem of specifying co-operative, distributed transactions in a manner that can be subject to verification and testing. Our approach combines the process-algebraic language LOTOS and the object-oriented database modelling language TM to obtain a clear and formal protocol for distributed database transactions meant to describe co-operation scenarios. We argue that a separation of concerns, namely the interaction of database applications on the one hand and data modelling on the other, results in a practical, modular approach that is formally well-founded. An advantage of this is that we may vary over transaction models to support the language combinatio

Abstract State Machines 1988-1998: Commented ASM Bibliography

An annotated bibliography of papers which deal with or use Abstract State Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm

SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

A Survey of Languages for Specifying Dynamics: A Knowledge Engineering Perspective

A number of formal specification languages for knowledge-based systems has been developed. Characteristics for knowledge-based systems are a complex knowledge base and an inference engine which uses this knowledge to solve a given problem. Specification languages for knowledge-based systems have to cover both aspects. They have to provide the means to specify a complex and large amount of knowledge and they have to provide the means to specify the dynamic reasoning behavior of a knowledge-based system. We focus on the second aspect. For this purpose, we survey existing approaches for specifying dynamic behavior in related areas of research. In fact, we have taken approaches for the specification of information systems (Language for Conceptual Modeling and TROLL), approaches for the specification of database updates and logic programming (Transaction Logic and Dynamic Database Logic) and the generic specification framework of abstract state machine

Actors, actions, and initiative in normative system specification

The logic of norms, called deontic logic, has been used to specify normative constraints for information systems. For example, one can specify in deontic logic the constraints that a book borrowed from a library should be returned within three weeks, and that if it is not returned, the library should send a reminder. Thus, the notion of obligation to perform an action arises naturally in system specification. Intuitively, deontic logic presupposes the concept of anactor who undertakes actions and is responsible for fulfilling obligations. However, the concept of an actor has not been formalized until now in deontic logic. We present a formalization in dynamic logic, which allows us to express the actor who initiates actions or choices. This is then combined with a formalization, presented earlier, of deontic logic in dynamic logic, which allows us to specify obligations, permissions, and prohibitions to perform an action. The addition of actors allows us to expresswho has the responsibility to perform an action. In addition to the application of the concept of an actor in deontic logic, we discuss two other applications of actors. First, we show how to generalize an approach taken up by De Nicola and Hennessy, who eliminate from CCS in favor of internal and external choice. We show that our generalization allows a more accurate specification of system behavior than is possible without it. Second, we show that actors can be used to resolve a long-standing paradox of deontic logic, called the paradox of free-choice permission. Towards the end of the paper, we discuss whether the concept of an actor can be combined with that of an object to formalize the concept of active objects

A theorem prover-based analysis tool for object-oriented databases

We present a theorem-prover based analysis tool for object-oriented database systems with integrity constraints. Object-oriented database specifications are mapped to higher-order logic (HOL). This allows us to reason about the semantics of database operations using a mechanical theorem prover such as Isabelle or PVS. The tool can be used to verify various semantics requirements of the schema (such as transaction safety, compensation, and commutativity) to support the advanced transaction models used in workflow and cooperative work. We give an example of method safety analysis for the generic structure editing operations of a cooperative authoring system