Design and Development of Software Tools for Bio-PEPA

This paper surveys the design of software tools for the Bio-PEPA process algebra. Bio-PEPA is a high-level language for modelling biological systems such as metabolic pathways and other biochemical reaction networks. Through providing tools for this modelling language we hope to allow easier use of a range of simulators and model-checkers thereby freeing the modeller from the responsibility of developing a custom simulator for the problem of interest. Further, by providing mappings to a range of different analysis tools the Bio-PEPA language allows modellers to compare analysis results which have been computed using independent numerical analysers, which enhances the reliability and robustness of the results computed.

A domain-specific analysis system for examining nuclear reactor simulation data for light-water and sodium-cooled fast reactors

Building a new generation of fission reactors in the United States presents many technical and regulatory challenges. One important challenge is the need to share and present results from new high-fidelity, high-performance simulations in an easily usable way. Since modern multiscale, multi-physics simulations can generate petabytes of data, they will require the development of new techniques and methods to reduce the data to familiar quantities of interest (e.g., pin powers, temperatures) with a more reasonable resolution and size. Furthermore, some of the results from these simulations may be new quantities for which visualization and analysis techniques are not immediately available in the community and need to be developed. This paper describes a new system for managing high-performance simulation results in a domain-specific way that naturally exposes quantities of interest for light water and sodium-cooled fast reactors. It describes requirements to build such a system and the technical challenges faced in its development at all levels (simulation, user interface, etc.). An example comparing results from two different simulation suites for a single assembly in a light-water reactor is presented, along with a detailed discussion of the system's requirements and design.Comment: Article on NiCE's Reactor Analyzer. 23 pages. Keywords: modeling, simulation, analysis, visualization, input-outpu

Vary: An IDE for Designing Algorithms and Measuring Quality

Pseudocode is one of the recommended methods for teaching students to design algorithms. Having a tool that performs the automatic translation of an algorithm into pseudocode to a programming language would allow the student to understand the complete process of program development. In addition, the introduction of quality measurement of algorithms designed from the first steps of learning programming would enable the student to understand the importance of code quality for maintenance of software processes. This work describes Vary, an integrated development environment based on Eclipse for writing and running pseudocode algorithms. The environment automatically transforms abstract pseudocode into runnable C/C++ source code that can be later executed. Computer programming learners and even computational scientists can use Vary to write and run algorithms, while taking advantage of modern development environment features. Vary is provided with an additional extension to automatically carry out algorithm analysis with SonarQube

Formal Reasoning Using an Iterative Approach with an Integrated Web IDE

This paper summarizes our experience in communicating the elements of reasoning about correctness, and the central role of formal specifications in reasoning about modular, component-based software using a language and an integrated Web IDE designed for the purpose. Our experience in using such an IDE, supported by a 'push-button' verifying compiler in a classroom setting, reveals the highly iterative process learners use to arrive at suitably specified, automatically provable code. We explain how the IDE facilitates reasoning at each step of this process by providing human readable verification conditions (VCs) and feedback from an integrated prover that clearly indicates unprovable VCs to help identify obstacles to completing proofs. The paper discusses the IDE's usage in verified software development using several examples drawn from actual classroom lectures and student assignments to illustrate principles of design-by-contract and the iterative process of creating and subsequently refining assertions, such as loop invariants in object-based code.Comment: In Proceedings F-IDE 2015, arXiv:1508.0338