Automating embedded analysis capabilities and managing software complexity in multiphysics simulation part I: template-based generic programming

An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering

Formally Specifying and Proving Operational Aspects of Forensic Lucid in Isabelle

A Forensic Lucid intensional programming language has been proposed for intensional cyberforensic analysis. In large part, the language is based on various predecessor and codecessor Lucid dialects bound by the higher-order intensional logic (HOIL) that is behind them. This work formally specifies the operational aspects of the Forensic Lucid language and compiles a theory of its constructs using Isabelle, a proof assistant system.Comment: 23 pages, 3 listings, 3 figures, 1 table, 1 Appendix with theorems, pp. 76--98. TPHOLs 2008 Emerging Trends Proceedings, August 18-21, Montreal, Canada. Editors: Otmane Ait Mohamed and Cesar Munoz and Sofiene Tahar. The individual paper's PDF is at http://users.encs.concordia.ca/~tphols08/TPHOLs2008/ET/76-98.pd

Transitioning Applications to Semantic Web Services: An Automated Formal Approach

Semantic Web Services have been recognized as a promising technology that exhibits huge commercial potential, and attract significant attention from both industry and the research community. Despite expectations being high, the industrial take-up of Semantic Web Service technologies has been slower than expected. One of the main reasons is that many systems have been developed without considering the potential of the web in integrating services and sharing resources. Without a systematic methodology and proper tool support, the migration from legacy systems to Semantic Web Service-based systems can be a very tedious and expensive process, which carries a definite risk of failure. There is an urgent need to provide strategies which allow the migration of legacy systems to Semantic Web Services platforms, and also tools to support such a strategy. In this paper we propose a methodology for transitioning these applications to Semantic Web Services by taking the advantage of rigorous mathematical methods. Our methodology allows users to migrate their applications to Semantic Web Services platform automatically or semi-automatically

Deriving Models for Software Project Effort Estimation By Means of Genetic Programming

Software engineering, effort estimation, genetic programming, symbolic regression. This paper presents the application of a computational intelligence methodology in effort estimation for software projects. Namely, we apply a genetic programming model for symbolic regression; aiming to produce mathematical expressions that (1) are highly accurate and (2) can be used for estimating the development effort by revealing relationships between the project’s features and the required work. We selected to investigate the effectiveness of this methodology into two software engineering domains. The system was proved able to generate models in the form of handy mathematical expressions that are more accurate than those found in literature.

The development of a program analysis environment for Ada

A unit level, Ada software module testing system, called Query Utility Environment for Software Testing of Ada (QUEST/Ada), is described. The project calls for the design and development of a prototype system. QUEST/Ada design began with a definition of the overall system structure and a description of component dependencies. The project team was divided into three groups to resolve the preliminary designs of the parser/scanner: the test data generator, and the test coverage analyzer. The Phase 1 report is a working document from which the system documentation will evolve. It provides history, a guide to report sections, a literature review, the definition of the system structure and high level interfaces, descriptions of the prototype scope, the three major components, and the plan for the remainder of the project. The appendices include specifications, statistics, two papers derived from the current research, a preliminary users' manual, and the proposal and work plan for Phase 2

Automated design of bacterial genome sequences

Background: Organisms have evolved ways of regulating transcription to better adapt to varying environments. Could the current functional genomics data and models support the possibility of engineering a genome with completely rearranged gene organization while the cell maintains its behavior under environmental challenges? How would we proceed to design a full nucleotide sequence for such genomes? Results: As a first step towards answering such questions, recent work showed that it is possible to design alternative transcriptomic models showing the same behavior under environmental variations than the wild-type model. A second step would require providing evidence that it is possible to provide a nucleotide sequence for a genome encoding such transcriptional model. We used computational design techniques to design a rewired global transcriptional regulation of Escherichia coli, yet showing a similar transcriptomic response than the wild-type. Afterwards, we “compiled” the transcriptional networks into nucleotide sequences to obtain the final genome sequence. Our computational evolution procedure ensures that we can maintain the genotype-phenotype mapping during the rewiring of the regulatory network. We found that it is theoretically possible to reorganize E. coli genome into 86% fewer regulated operons. Such refactored genomes are constituted by operons that contain sets of genes sharing around the 60% of their biological functions and, if evolved under highly variable environmental conditions, have regulatory networks, which turn out to respond more than 20% faster to multiple external perturbations. Conclusions: This work provides the first algorithm for producing a genome sequence encoding a rewired transcriptional regulation with wild-type behavior under alternative environments