Modelling Cell Cycle using Different Levels of Representation

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study

Flow velocity mapping using contrast enhanced high-frame-rate plane wave ultrasound and image tracking: methods and initial in vitro and in vivo evaluation

Ultrasound imaging is the most widely used method for visualising and quantifying blood flow in medical practice, but existing techniques have various limitations in terms of imaging sensitivity, field of view, flow angle dependence, and imaging depth. In this study, we developed an ultrasound imaging velocimetry approach capable of visualising and quantifying dynamic flow, by combining high-frame-rate plane wave ultrasound imaging, microbubble contrast agents, pulse inversion contrast imaging and speckle image tracking algorithms. The system was initially evaluated in vitro on both straight and carotid-mimicking vessels with steady and pulsatile flows and in vivo in the rabbit aorta. Colour and spectral Doppler measurements were also made. Initial flow mapping results were compared with theoretical prediction and reference Doppler measurements and indicate the potential of the new system as a highly sensitive, accurate, angle-independent and full field-of-view velocity mapping tool capable of tracking and quantifying fast and dynamic flows

Wave Structure and Velocity Profiles in Downwards Gas-Liquid Annular Flow

The downwards co-current gas-liquid annular flows inside a vertically oriented pipe have been experimentally investigated. The measurements and characterisation were performed using advanced optical non-intrusive laser-based techniques, namely Laser Induced Fluorescence, and Particle Image/Tracking Velocimetry. The investigated conditions were in the range of ReL = 306 – 1,532 and ReG = 0 – 84,600. Temporal film thickness time traces were constructed using the Laser Induced Fluorescence images. Based on these, the wave frequency was evaluated using direct wave counting approach and power spectral density analysis. Additionally, qualitative PIV observations revealed the presence of recirculation zones within a wave front of disturbance waves

Current methods for characterising mixing and flow in microchannels

This article reviews existing methods for the characterisation of mixing and flow in microchannels, micromixers and microreactors. In particular, it analyses the current experimental techniques and methods available for characterising mixing and the associated phenomena in single and multiphase flow. The review shows that the majority of the experimental techniques used for characterising mixing and two-phase flow in microchannels employ optical methods, which require optical access to the flow, or off-line measurements. Indeed visual measurements are very important for the fundamental understanding of the physics of these flows and the rapid advances in optical measurement techniques, like confocal scanning laser microscopy and high resolution stereo micro particle image velocimetry, are now making full field data retrieval possible. However, integration of microchannel devices in industrial processes will require on-line measurements for process control that do not necessarily rely on optical techniques. Developments are being made in the areas of non-intrusive sensors, magnetic resonance techniques, ultrasonic spectroscopy and on-line flow through measurement cells. The advances made in these areas will certainly be of increasing interest in the future as microchannels are more frequently employed in continuous flow equipment for industrial applications

The Polarization of Drifting Subpulses

Using new techniques based on the polarimetric fluctuation spectrum, the fluctuation behaviour of the polarization of individual pulses is examined in three pulsars that show drifting subpulses, allowing various aspects of the fluctuations to be quantified for the first time. Of the three pulsars studied, only PSR B0809+74 shows behaviour completely consistent with the superposition of orthogonal polarization modes (OPMs), and this only at 328 MHz and in superposition with an apparently randomly polarized component. The observed periodic pattern is decomposed into the sum of two orthogonally polarized, out-of-phase drift patterns, one of which shows a dramatic jump in subpulse phase near the leading edge of the pulse window. For PSR B0320+39 and PSR B0818$-$13, considerable periodic fluctuations away from OPM orientations are seen, a condition that also occurs in the trailing half of the pulse in PSR B0809+74 at 1380 MHz. In some cases the deviation is so strong that the periodic locus of the polarization vector in the Poincar\'{e} sphere is almost circular, in contrast to the strictly colinear states of superposed OPMs. Several possibilities are discussed for the physical origin of these patterns. The similarity between the subpulse patterns in one of the OPMs of PSR B0809+74 at 328 MHz to that of the total intensity signal at 1380 MHz supports a picture of superposed, out of phase drift patterns. To explain the full range of behaviour seen in the three pulsars, it must be possible to produce at least three arbitrarily polarized superposed patterns. While the data do not suggest a particular approach for the empirical decomposition of patterns into non-orthogonally polarized components, the specific, quantitative nature of the results should provide strong constraints for theoretically driven modelling.Comment: 11 pages, 6 figures (1 colour), accepted for publication in A&A. Abstract abridge

Development of a Powerwall-based solution for the manual flagging of radio astronomy data from eMerlin

This project was created with the intention of establishing an optimisation method for the manual flagging of interferometric data of the eMerlin radio astronomy array, using a Powerwall as a visualisation tool. The complexity of this process which is due to the amount of variables and parameters demands a deep understanding of the data treatment. Once the data is achieved by the antennas the signals are correlated. This process generates undesired signals which mostly coming from radio frequency interference. Also when the calibration is performed some values can mislead the expected outcome. Although the flagging is supported with algorithms this method is not one hundred percent accurate. That is why visual inspection is still required. The possibility to use a Powerwall as a visualisation system allows different and new dynamics in terms of the interaction of the analyst with the information required to make the flagging

Animating the evolution of software

The use and development of open source software has increased significantly in the last decade. The high frequency of changes and releases across a distributed environment requires good project management tools in order to control the process adequately. However, even with these tools in place, the nature of the development and the fact that developers will often work on many other projects simultaneously, means that the developers are unlikely to have a clear picture of the current state of the project at any time. Furthermore, the poor documentation associated with many projects has a detrimental effect when encouraging new developers to contribute to the software. A typical version control repository contains a mine of information that is not always obvious and not easy to comprehend in its raw form. However, presenting this historical data in a suitable format by using software visualisation techniques allows the evolution of the software over a number of releases to be shown. This allows the changes that have been made to the software to be identified clearly, thus ensuring that the effect of those changes will also be emphasised. This then enables both managers and developers to gain a more detailed view of the current state of the project. The visualisation of evolving software introduces a number of new issues. This thesis investigates some of these issues in detail, and recommends a number of solutions in order to alleviate the problems that may otherwise arise. The solutions are then demonstrated in the definition of two new visualisations. These use historical data contained within version control repositories to show the evolution of the software at a number of levels of granularity. Additionally, animation is used as an integral part of both visualisations - not only to show the evolution by representing the progression of time, but also to highlight the changes that have occurred. Previously, the use of animation within software visualisation has been primarily restricted to small-scale, hand generated visualisations. However, this thesis shows the viability of using animation within software visualisation with automated visualisations on a large scale. In addition, evaluation of the visualisations has shown that they are suitable for showing the changes that have occurred in the software over a period of time, and subsequently how the software has evolved. These visualisations are therefore suitable for use by developers and managers involved with open source software. In addition, they also provide a basis for future research in evolutionary visualisations, software evolution and open source development

ASPECT: A spectra clustering tool for exploration of large spectral surveys

We present the novel, semi-automated clustering tool ASPECT for analysing voluminous archives of spectra. The heart of the program is a neural network in form of Kohonen's self-organizing map. The resulting map is designed as an icon map suitable for the inspection by eye. The visual analysis is supported by the option to blend in individual object properties such as redshift, apparent magnitude, or signal-to-noise ratio. In addition, the package provides several tools for the selection of special spectral types, e.g. local difference maps which reflect the deviations of all spectra from one given input spectrum (real or artificial). ASPECT is able to produce a two-dimensional topological map of a huge number of spectra. The software package enables the user to browse and navigate through a huge data pool and helps him to gain an insight into underlying relationships between the spectra and other physical properties and to get the big picture of the entire data set. We demonstrate the capability of ASPECT by clustering the entire data pool of 0.6 million spectra from the Data Release 4 of the Sloan Digital Sky Survey (SDSS). To illustrate the results regarding quality and completeness we track objects from existing catalogues of quasars and carbon stars, respectively, and connect the SDSS spectra with morphological information from the GalaxyZoo project.Comment: 15 pages, 14 figures; accepted for publication in Astronomy and Astrophysic