Maintaining the Health of Software Monitors

Software health management (SWHM) techniques complement the rigorous verification and validation processes that are applied to safety-critical systems prior to their deployment. These techniques are used to monitor deployed software in its execution environment, serving as the last line of defense against the effects of a critical fault. SWHM monitors use information from the specification and implementation of the monitored software to detect violations, predict possible failures, and help the system recover from faults. Changes to the monitored software, such as adding new functionality or fixing defects, therefore, have the potential to impact the correctness of both the monitored software and the SWHM monitor. In this work, we describe how the results of a software change impact analysis technique, Directed Incremental Symbolic Execution (DiSE), can be applied to monitored software to identify the potential impact of the changes on the SWHM monitor software. The results of DiSE can then be used by other analysis techniques, e.g., testing, debugging, to help preserve and improve the integrity of the SWHM monitor as the monitored software evolves

The inference of gene trees with species trees

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can co-exist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. In this article we review the various models that have been used to describe the relationship between gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.Comment: Review article in relation to the "Mathematical and Computational Evolutionary Biology" conference, Montpellier, 201

Download the PDF of the Full Issue

No abstract available