Filling the gaps of development logs and bug issue data

It has been suggested that the data from bug repositories is not always in sync or complete compared to the logs detailing the actions of developers on source code. In this paper, we trace two sources of information relative to software bugs: the change logs of the actions of developers and the issues reported as bugs. The aim is to identify and quantify the discrepancies between the two sources in recording and storing the developer logs relative to bugs. Focussing on the databases produced by two mining software repository tools, CVSAnalY and Bicho, we use part of the SZZ algorithm to identify bugs and to compare how the"defects-fixing changes" are recorded in the two databases. We use a working example to show how to do so. The results indicate that there is a significant amount of information, not in sync when tracing bugs in the two databases. We, therefore, propose an automatic approach to re-align the two databases, so that the collected information is mirrored and in sync.Dr. Felipe Orteg

SARS-CoV-2 Variants Are Selecting for Spike Protein Mutations That Increase Protein Stability

The emergence of variants of SARS-CoV-2 with mutations in their spike protein are a major cause for concern for the efficacy of vaccines and control of the pandemic. We show that mutations in the spike protein of SARS-CoV-2 are selecting for amino acid changes that result in a more thermodynamically stable protein than expected from background. We suggest that the computationally efficient analysis of mutational stability may aid in early screening of variants

Linear temporal logic for biologists in BMA

Medical Research Council, Royal SocietyThis is the author accepted manuscript. The final version is available from Springer via http://www.springer.com/in/book/978331945176

Reproducibility in Research: Systems, Infrastructure, Culture

The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around the ability to implement (and exploit) novel algorithms and models. Taking a new approach from the literature and applying it to a new codebase frequently requires local knowledge missing from the published manuscripts and transient project websites. Alongside this issue, benchmarking, and the lack of open, transparent and fair benchmark sets present another barrier to the verification and validation of claimed results. In this paper, we outline several recommendations to address these issues, driven by specific examples from a range of scientific domains. Based on these recommendations, we propose a high-level prototype open automated platform for scientific software development which effectively abstracts specific dependencies from the individual researcher and their workstation, allowing easy sharing and reproduction of results. This new e-infrastructure for reproducible computational science offers the potential to incentivise a culture change and drive the adoption of new techniques to improve the quality and efficiency – and thus reproducibility – of scientific exploration.Royal Society UR

Developing a Grounded Theory Model on Collaboration in Learning

The purpose of this research is to develop a grounded theory model to explain the factors influencing collaborative learning in higher education, the role of technology in facilitating collaboration, and the outcome of collaboration. We assigned 28 participants to small groups to work on course-related questions; half of the groups were face-to-face groups and the other half groups were collaborating in a simulated virtual environment with the aid of information technology. Interview data was collected and analyzed following the grounded theory approach. Congruent with distributed cognition theories, the results of our study suggest that both social and technological factors were important and interlocking. We also discussed the importance of designing learning technologies that have strong social and communications features

A Basic Strategy to Manage Global Health with Reference to Livestock Production in Asia

Newly emerging infectious diseases (nEIDs) have increased rapidly presenting alarming challenges to global health. We argue that for effective management of global health a basic strategy should include at least three essential tactical forms: actions of a directly focused nature, institutional coordination, and disciplinary integration in approaches to health management. Each level of action is illustrated with examples from the livestock sector in Asia. No clear example of all three tactical forms in place can be found from developing countries where food security is a significant threat although Vietnam is developing a comprehensive strategy. Finally, an ecosystem health approach to global health management is advocated; such an approach moves away from the traditional single disciplinary approach. Stronger guidance is needed to direct ecohealth research and application in the management of global health

A Toolbox for Discrete Modelling of Cell Signalling Dynamics

In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards systems biology and computational modelling to help unravel the complexities of gene and protein regulatory networks. In order to make such techniques more accessible to mainstream researchers, tools such as the BioModelAnalyzer (BMA) have been developed to provide a user-friendly graphical interface for discrete modelling of biological systems. Here we use the BMA to build a library of target functions of known molecular interactions, translated from ordinary differential equations (ODEs). We then show that these BMA target functions can be used to reconstruct complex networks, which can correctly predict many known genetic perturbations. This new library supports the accessibility ethos behind the creation of BMA, providing a toolbox for the construction of complex cell signalling models without the need for extensive experience in computer programming or mathematical modelling, and allows for construction and simulation of complex biological systems with only small amounts of quantitative data.Royal Societ

Flavor Structure in F-theory Compactifications

F-theory is one of frameworks in string theory where supersymmetric grand unification is accommodated, and all the Yukawa couplings and Majorana masses of right-handed neutrinos are generated. Yukawa couplings of charged fermions are generated at codimension-3 singularities, and a contribution from a given singularity point is known to be approximately rank 1. Thus, the approximate rank of Yukawa matrices in low-energy effective theory of generic F-theory compactifications are minimum of either the number of generations N_gen = 3 or the number of singularity points of certain types. If there is a geometry with only one E_6 type point and one D_6 type point over the entire 7-brane for SU(5) gauge fields, F-theory compactified on such a geometry would reproduce approximately rank-1 Yukawa matrices in the real world. We found, however, that there is no such geometry. Thus, it is a problem how to generate hierarchical Yukawa eigenvalues in F-theory compactifications. A solution in the literature so far is to take an appropriate factorization limit. In this article, we propose an alternative solution to the hierarchical structure problem (which requires to tune some parameters) by studying how zero mode wavefunctions depend on complex structure moduli. In this solution, the N_gen x N_gen CKM matrix is predicted to have only N_gen entries of order unity without an extra tuning of parameters, and the lepton flavor anarchy is predicted for the lepton mixing matrix. We also obtained a precise description of zero mode wavefunctions near the E_6 type singularity points, where the up-type Yukawa couplings are generated.Comment: 148 page