22 papers · ranked by Valyu relevance
Eric Schulte, Zachary P. Fry, Ethan Fast, Westley Weimer + 1 more
'Stephanie Forrest'] Neutral landscapes and mutational robustness are believed to be important enablers of evolvability in biology. We apply these concepts to software, defining mutational robustness to be the fraction of random mutations to program code that leave a program's behavior unchanged. Test cases are used to…
Ali Parsai, Alessandro Murgia, Serge Demeyer
Mutation testing is a well-studied method for increasing the quality of a test suite. We designed LittleDarwin as a mutation testing framework able to cope with large and complex Java software systems, while still being easily extensible with new experimental components. LittleDarwin addresses two existing problems in…
Ali Parsai, Serge Demeyer
The state-of-the-practice in software development is driven by constant change fueled by continuous integration servers. Such constant change demands for frequent and fully automated tests capable to detect faults immediately upon project build. As the fault detection capability of the test suite becomes so important…
Ali Parsai, Alessandro Murgia, Quinten David Soetens, Serge Demeyer
Refactoring is an activity that improves the internal structure of the code without altering its external behavior. When performed on the production code, the tests can be used to verify that the external behavior of the production code is preserved. However, when the refactoring is performed on test code, there is no…
Mike Papadakis, Nicos Malevris
Mutation testing is usually regarded as an important method towards fault revealing. Despite this advantage, it has proved to be impractical for industrial use because of its expenses. To this extend, automated techniques are needed in order to apply and reduce the method’s demands. Whilst there is much evidence that…
Eike Stein, Steffen Herbold, Fabian Trautsch, Jens Grabowski
The competent programmer hypothesis states that most programmers are competent enough to create correct or almost correct source code. Because this implies that bugs should usually manifest through small variations of the correct code, the competent programmer hypothesis is one of the fundamental assumptions of…
Savaş Takan, Xiangjie Kong
Mutation testing is a method widely used to evaluate the effectiveness of the test suite in hardware and software tests or to design new software tests. In mutation testing, the original model is systematically mutated using certain error assumptions. Mutation testing is based on well-defined mutation operators that…
Ali Parsai, Serge Demeyer
Many academic studies in the field of software testing rely on mutation testing to use as their comparison criteria. However, recent studies have shown that redundant mutants have a significant effect on the accuracy of their results. One solution to this problem is to use mutant subsumption to detect redundant…
Thierry Titcheu Chekam, Mike Papadakis, Yves Le Traon
Recent research demonstrated that mutation-based fault localization techniques are relatively accurate and practical. However, these methods have never been compared and have only been assessed with simple hand-seeded faults. Therefore, their actual practicality is questionable when it comes to real-wold faults. To…
Mikaela Teodoro, Rosana V. das Chagas, José A. Yunes, Natacha A. Migita + 1 more
Next-generation sequencing (NGS) has accelerated precision medicine by enabling simultaneous analysis of multiple genes and detection of low-frequency mutations. However, few open-source tools allow non-specialized users to transparently adjust quality parameters during mutation analysis. Mutation Reporter was…
Shanxiang Shen, Dahui Qin
Background Pyrosequencing is a new technology and can be used for mutation tests. However, its data analysis is a manual process and involves sophisticated algorithms. During this process, human errors may occur. A better way of analyzing pyrosequencing data is needed in clinical diagnostic laboratory. Computer…
Mikaela Teodoro, Rosana V. das Chagas, José A. Yunes, Natacha A. Migita + 1 more
Next-generation sequencing (NGS) has accelerated precision medicine by enabling analysis of multiple genes at once and detection of low-frequency mutations. Nevertheless, there is a paucity of software applications enabling users not trained in bioinformatics to discern and adjust the quality parameters employed for…
David L. Patton, Thomas Cardenas, Perrin Mele, Jon Navarro + 1 more
The Context-dependent Mutation Analysis Package and Visualization Software (CDMAP/CDVIS) is an automated, modular toolkit used for analysis and visualization of context-dependent mutation patterns (site-specific variation in mutation rate from neighboring-nucleotide effects). The CDMAP algorithm calculates…
William S. DeWitt
Characterization of germline mutation spectrum variation from population genomics data has shed light on the biological complexity of the mutation process, and its evolution within and between species. This analysis augments available population SNP data with estimates of local ancestral genomic context to assign…
Michelle Philipp, Christopher W. Moth, Nikola Ristic, Johanna K.S. Tiemann + 7 more
The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D…
David J. Winter, Steven H. Wu, Abigail A. Howell, Ricardo B. R. Azevedo + 2 more
Mutation accumulation (MA) experiments are the most widely used method for directly studying the effects of mutation. Modern sequencing technologies have led to an increased interest in MA experiments. By sequencing whole genomes from MA lines, researchers can directly study the rate and molecular spectra of…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
Jesus M Gonzalez-Barahona, Gregorio Robles, Israel Herraiz, Felipe Ortega
'Felipe Ortega'] Some free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15…
Jonathan Kidner, Panagiotis Theodorou, Jan O. Engler, Martin Taubert + 1 more
Population genetics is a field of research that predates the current generations of sequencing technology. Those approaches, that were established before massively parallel sequencing methods, have been adapted to these new marker systems (in some cases involving the development of new methods) that allow genome-wide…
Gordon Chalmers, Rustem Ustun, Daniel Tehrani, Bulent Uzun
Crop management through the use of herbicides is an integral part of modern high-yield farming. The identification of resistant mutated strains of normal plants amongst a background of weeds is important to the usage of herbicides, their development, and resistance. In this work a computational study of a point…
Authors not listed
Free energy calculations have become invaluable in protein design, offering a powerful means to rapidly and accurately screen potential variants. Here, we provide a step-by-step protocol that combines molecular dynamics simulations with non-equilibrium alchemical free energy methods to tackle open questions in protein…
Brianna Greenstein, Danielle Elsey, Geoffrey Hutchison
Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this work, we examine the general effects of a number of hyperparameters, such as population…