Physics-based visual characterization of molecular interaction forces

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft

i-JEN: Visual interactive Malaysia crime news retrieval system

Supporting crime news investigation involves a mechanism to help monitor the current and past status of criminal events. We believe this could be well facilitated by focusing on the user interfaces and the event crime model aspects. In this paper we discuss on a development of Visual Interactive Malaysia Crime News Retrieval System (i-JEN) and describe the approach, user studies and planned, the system architecture and future plan. Our main objectives are to construct crime-based event; investigate the use of crime-based event in improving the classification and clustering; develop an interactive crime news retrieval system; visualize crime news in an effective and interactive way; integrate them into a usable and robust system and evaluate the usability and system performance. The system will serve as a news monitoring system which aims to automatically organize, retrieve and present the crime news in such a way as to support an effective monitoring, searching, and browsing for the target users groups of general public, news analysts and policemen or crime investigators. The study will contribute to the better understanding of the crime data consumption in the Malaysian context as well as the developed system with the visualisation features to address crime data and the eventual goal of combating the crimes

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

Supporting Project Comprehension with Revision Control System Repository Analysis

Context: Project comprehension is an activity relevant to all aspects of software engineering, from requirements specification to maintenance. The historical, transactional data stored in revision control systems can be mined and analysed to produce a great deal of information about a project. Aims: This research aims to explore how the data-mining, analysis and presentation of revision control systems can be used to augment aspects of project comprehension, including change prediction, maintenance, visualization, management, profiling, sampling and assessment. Method: A series of case studies investigate how transactional data can be used to support project comprehension. A thematic analysis of revision logs is used to explore the development process and developer behaviour. A benchmarking study of a history-based model of change prediction is conducted to assess how successfully such a technique can be used to augment syntax-based models. A visualization tool is developed for managers of student projects with the aim of evaluating what visualizations best support their roles. Finally, a quasi-experiment is conducted to determine how well an algorithmic model can automatically select a representative sample of code entities from a project, in comparison with expert strategies. Results: The thematic analysis case study classified maintenance activities in 22 undergraduate projects and four real-world projects. The change prediction study calculated information retrieval metrics for 34 undergraduate projects and three real-world projects, as well as an in-depth exploration of the model's performance and applications in two selected projects. File samples for seven projects were generated by six experts and three heuristic models and compared to assess agreement rates, both within the experts and between the experts and the models. Conclusions: When the results from each study are evaluated together, the evidence strongly shows that the information stored in revision control systems can indeed be used to support a range of project comprehension activities in a manner which complements existing, syntax-based techniques. The case studies also help to develop the empirical foundation of repository analysis in the areas of visualization, maintenance, sampling, profiling and management; the research also shows that students can be viable substitutes for industrial practitioners in certain areas of software engineering research, which weakens one of the primary obstacles to empirical studies in these areas

The Structured Process Modeling Theory (SPMT): a cognitive view on why and how modelers benefit from structuring the process of process modeling

After observing various inexperienced modelers constructing a business process model based on the same textual case description, it was noted that great differences existed in the quality of the produced models. The impression arose that certain quality issues originated from cognitive failures during the modeling process. Therefore, we developed an explanatory theory that describes the cognitive mechanisms that affect effectiveness and efficiency of process model construction: the Structured Process Modeling Theory (SPMT). This theory states that modeling accuracy and speed are higher when the modeler adopts an (i) individually fitting (ii) structured (iii) serialized process modeling approach. The SPMT is evaluated against six theory quality criteria