Advanced Computer Graphics Aided Molecular Visualization and Manipulation Softwares: The Hierarchy of Research Methodologies

In the present day, the huge obstacles, and the major technical problems encountered by the teaching and research faculties, academicians, industrial specialists, laboratory demonstrators and instructors, fellow students and researchers, etc. are to adopt integrative approaches of demonstrating (learning) chemistry and chemical education, and the realistic ways of delivering (grasping) scientific materials articulately with graceful and effortless manner. Towards minimizing these challenges, various audio-visual tools and technologies, advanced computer aided molecular graphics, freely available electronic gadgets assisted chemistry and chemical education apps, human unreadable data reading and accessing softwares, etc. are being incorporated worldwide as the most indispensable physical and electronic means for successful professionalisms. This short article is essentially a collective report underscoring extraordinary approaches, incredible efforts, and innovative skills of the computer based chemical and molecular graphics towards illuminating intrinsic parts of the chemistry and chemical education, and revealing various aspects of the cutting -edge research. As their representatives, herein, the different type computer coding languages based graphical tools such as Molden, GaussView, Jmol, and Visual Molecular Dynamics (VMD) are referred, and elucidated their potential applications and remarkable attempts in the advancement of diverse areas of chemistry and chemical education. Beside this, the most essential graphical features, unique rendering abilities with magnificent views, splendid visualizing skills, awesome data accessing functionalities, etc. of each of them, and their invaluable roles for studying complex molecules, biomolecules, crystals, and the entire material assemblies as well as for investigating global and local molecular physicochemical properties are presented concisely with the special stresses on their relatively better and comparatively more applicable distinctive attributes explicitl

Tracking marine mammals in 3D using electronic tag data

1. Information about at-depth behaviour of marine mammals is fundamental yet very hard to obtain from direct visual observation. Animal-borne multisensor electronic tags provide a unique window of observation into such behaviours. 2. Electronic tag sensors allow the estimation of the animal's 3-dimensional (3D) orientation, depth and speed. Using tag flow noise level to provide an estimate of animal speed, we extend existing approaches of 3D track reconstruction by allowing the direction of movement to differ from that of the animal's longitudinal axis. 3. Data are processed by a hierarchical Bayesian model that allows processing of multisource data, accounting for measurement errors and testing hypotheses about animal movement by comparing models. 4. We illustrate the approach by reconstructing the 3D track of a 52-min deep dive of a Blainville's beaked whale Mesoplodon densirostris adult male fit with a digital tag (DTAG) in the Bahamas. At depth, the whale alternated regular movements at large speed (>1·5 m s-1) and more complex movements at lower speed (<1·5 m s-1) with differences between movement and longitudinal axis directions of up to 28°. The reconstructed 3D track agrees closely with independent acoustic-based localizations. 5. The approach is potentially applicable to study the underwater behaviour (e.g. response to anthropogenic disturbances) of a wide variety of species of marine mammals fitted with triaxial magnetometer and accelerometer tags.PostprintPeer reviewe

SUPPORTING DEVELOPER-ONBOARDING WITH ENHANCED RESOURCE FINDING AND VISUAL EXPLORATION

Understanding the basic structure of a code base and a development team are essential to get new developers up to speed in a software development project. Developers do so through the process of early experimentation with code and the creation of mental models of technical and social structures in a project. However, getting up-to-speed in a new project can be challenging due to difficulties in: finding the right place to begin explorations, expanding the focus to determine relevant resources for tasks, and identifying dependencies across project elements to gain a high-level overview of project structures. In this thesis, I first identified six challenges that developers face during the process of developer onboarding from recent research studies and informal interviews with developers. To address these challenges, I implemented automated tool support with enhanced resource finding and visual exploration. Specifically, I proposed six functional requirements for supporting developers onboarding. I then extended the project tool Tesseract to support these functionalities to help novice developers and relevant resources (files, developers, bugs, etc.) and understand project structures when joining a new project. To understand how the onboarding functionalities work in supporting developers\u27 onboarding process, I conducted a user study with typical onboarding tasks requiring early experimentation and internalizing project structures. The results indicated that enhanced search features, the ability to explore semantic relationships across repositories, and network-centric visualizations of project structures were very effective in supporting onboarding

DrAST - An attribute debugger for JastAdd

Here we present a solution for debugging compilers that use abstract-syntax trees as their internal structure. The solution focuses on capturing one specific state of the compilation process, and should not be confused with the more known step-by-step debugging. The goal is to visualize the current state of the abstract-syntax tree and present its data to the user in an intuitive and interactive way. We believe that deeper understanding of an abstract-syntax tree, and bugs in its structure, can be achieved by visualization of the tree. Few such debuggers exist today however, but with this master thesis we aim to fill this gap. The main feature of the developed tool DrAST is the ability to visualize the abstract-syntax tree. It is also possible to filter the tree, so that only nodes of interest are visualized, while the rest are gathered in what we call clusters. Further, DrAST can display attributes, draw references between nodes, calculate parameterized attributes and is built for further extension. DrAST mainly debugs compilers created in the attribute-grammar-based system JastAdd. By the use of Java reflection and annotations from the JastAdd system, the debugger is able to extract the abstract-syntax tree from a compiler without knowing the specific grammar. In short, DrAST provides a new solution in compiler debugging which can be of use for both students and professionals