DOCKside II: Adding Functionality to Current Molecular Docking System

The DOCKside program makes use of Electron Microscopy (EM) maps and X-Ray Crystallography (XRC) maps to dock molecules. This can be achieved either manually or automatically. The automated functions include rigid- and flexible- docking functions. A solution space viewer was also designed to enable users to view the complete solution space that is generated by the automated docking feature of DOCKside. Testing revealed that the rigid docking procedures of DOCKside, especially Vector Quantization (VQ) performs just as well as the leading docking software packages like Situs. It was further revealed that the visualization tool was successful in conveying seven-dimensional data in an intuitive manner using three-dimensional graphics such as glyphs and starmaps. In pursuit of a novel flexible docking method, boundary constraints on a simple model, such as a sphere, were investigated. Successful simulations were obtained where external forces acted upon the molecular structure pushing it back into the boundary constraints

Explorative coastal oceanographic visual analytics : oceans of data

The widely acknowledged challenge to data analysis and understanding, resulting from the exponential increase in volumes of data generated by increasingly complex modelling and sampling systems, is a problem experienced by many researchers, including ocean scientists. The thesis explores a visualization and visual analytics solution for predictive studies of coastal shelf and estuarine modelled, hydrodynamics undertaken to understand sea level rise, as a contribution to wider climate change studies, and to underpin coastal zone planning, flood prevention and extreme event management. But these studies are complex and require numerous simulations of estuarine hydrodynamics, generating extremely large datasets of multi-field data. This type\ud of data is acknowledged as difficult to visualize and analyse, as its numerous attributes present significant computational challenges, and ideally require a wide range of approaches to provide the necessary insight. These challenges are not easily overcome with the current visualization and analysis methodologies employed by coastal shelf hydrodynamic researchers, who use several software systems to generate graphs, each taking considerable time to operate, thus it is difficult to explore different scenarios and explore the data interactively and visually. The thesis, therefore, develops novel visualization and visual analytics techniques to help researchers overcome the limitations of existing methods (for example in understanding key tidal components); analyse data in a timely manner and explore different scenarios. There were a number of challenges to this: the size of the data, resulting in lengthy computing time, also many data values becoming plotted on one pixel (overplotting). The thesis presents: (1) a new visualization framework (VINCA) using caching and hierarchical aggregation techniques to make the data more interactive, plus explorative, coordinated multiple views, to enable the scientists to explore the data. (2) A novel estuarine transect profiler and flux tool, which provides instantaneous flux calculations across an estuary. Measures of flux are of great significance in oceanographic studies, yet are notoriously difficult and time consuming to calculate with the commonly used tools. This derived data is added back into the database for further investigation and analysis. (3) New views, including a novel, dynamic, spatially aggregated Parallel Coordinate Plots (Sa-PCP), are developed to provide different perspectives of the spatial, time dependent data, also methodologies for developing high-quality (journal ready) output from the visualization tool. Finally, (4) the dissertation explored the use of hierarchical data-structures and caching techniques to enable fast analysis on a desktop computer and to overcome the overplotting challenge for this data