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

Applying the FAHP to Improve the Performance Evaluation Reliability of Software Defect Classifiers

Today's software complexity makes developing defect-free software almost impossible. Consequently, developing classifiers to classify software modules into defective and non-defective before software releases have attracted great interest in academia and software industry alike. Although many classifiers have been proposed, no one has been proven superior over others. The major reason is that while a research shows that classifier A is better than classifier B, we can find other research that shows the opposite. These conflicts are usually triggered when researchers report results using their preferable performance evaluation measures such as, recall and precision. Although this approach is valid, it does not examine all possible facets of classifiers performance characteristics. Thus, the performance evaluation might improve or deteriorate if researchers choose other performance measures. As a result, software developers usually struggle to select the most suitable classifier to use in their projects. The goal of this paper is to apply the fuzzy analytical hierarchy process (FAHP) as a popular multicriteria decision-making technique to reliably evaluate classifiers' performance. This evaluation framework incorporates a wider spectrum of performance measures to evaluate classifiers performance rather than relying on selected preferable measures. The results show that this approach will increase software developers' confidence in research outcomes and help them in avoiding false conclusions and infer reasonable boundaries for them. We exploited 22 popular performance measures and 11 software defect classifiers. The analysis was carried out using KNIME data mining platform and 12 software defect data sets provided by the NASA metrics data program (MDP) repository.https://doi.org/10.1109/ACCESS.2019.291596

Multidimensional Pareto optimization of touchscreen keyboards for speed, familiarity and improved spell checking

The paper presents a new optimization technique for keyboard layouts based on Pareto front optimization. We used this multifactorial technique to create two new touchscreen phone keyboard layouts based on three design metrics: minimizing finger travel distance in order to maximize text entry speed, a new metric to maximize the quality of spell correction quality by minimizing neighbouring key ambiguity, and maximizing familiarity through a similarity function with the standard Qwerty layout. The paper describes the optimization process and resulting layouts for a standard trapezoid shaped keyboard and a more rectangular layout. Fitts' law modelling shows a predicted 11% improvement in entry speed without taking into account the significantly improved error correction potential and the subsequent effect on speed. In initial user tests typing speed dropped from approx. 21wpm with Qwerty to 13wpm (64%) on first use of our layout but recovered to 18wpm (85%) within four short trial sessions, and was still improving. NASA TLX forms showed no significant difference on load between Qwerty and our new layout use in the fourth session. Together we believe this shows the new layouts are faster and can be quickly adopted by users