Search results for "Software visualization"
showing 3 items of 3 documents
EFMviz
2020
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1…
A metrics suite for evaluating agent-oriented architectures
2010
The Multi-agent Systems (MASs) paradigm continues to consolidate itself as a new branch of software engineering. Traditional software engineering strongly recommends to apply metrics in software developments. However, several research groups of experts in agent-oriented software engineering agree that classical software metrics and object-oriented metrics cannot directly measure the quality of MAS architectures. For this reason, this work proposes a suite of metrics to measure certain quality attributes of MAS architectures, considering agents and their organization. Most of these metrics are inspired by object-oriented metrics but they are adapted to agent-oriented concepts. Proposed metri…
Graph grammar engineering: A software specification method
1987
Graphs as conceptual data models are accepted and used in a wide range of different problem areas. Giving some examples we outline common aspects for modeling complex structures by graphs. We present a formal frame-work based on graph grammars to specify graph classes and the corresponding graph manipulations. We show that such a specification can be written in a systematic, engineering-like manner. This is achieved by an extension of the known programmed, attributed graph grammars. Node-set operators are introduced to facilitate graph queries. Concepts like abstraction, decomposition, refinement, parameterization, and integration have been adopted from software engineering to yield a compr…