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'BioNessie(G) - a grid enabled biochemical networks simulation environment
The simulation of biochemical networks provides insight and
understanding about the underlying biochemical processes and pathways
used by cells and organisms. BioNessie is a biochemical network simulator
which has been developed at the University of Glasgow. This paper
describes the simulator and focuses in particular on how it has been
extended to benefit from a wide variety of high performance compute resources
across the UK through Grid technologies to support larger scale
simulations
Specifying ODP computational objects in Z
The computational viewpoint contained within the Reference Model of Open Distributed Processing (RM-ODP) shows how collections of objects can be configured within a distributed system to enable interworking. It prescribes certain capabilities that such objects are expected to possess and structuring rules that apply to how these objects can be configured with one another. This paper highlights how the specification language Z can be used to formalise these capabilities and the associated structuring rules, thereby enabling specifications of ODP systems from the computational viewpoint to be achieved
UTOPIA—User-Friendly Tools for Operating Informatics Applications
Bioinformaticians routinely analyse vast amounts of information held both in large
remote databases and in flat data files hosted on local machines. The contemporary
toolkit available for this purpose consists of an ad hoc collection of data manipulation
tools, scripting languages and visualization systems; these must often be combined in
complex and bespoke ways, the result frequently being an unwieldy artefact capable of
one specific task, which cannot easily be exploited or extended by other practitioners.
Owing to the sizes of current databases and the scale of the analyses necessary,
routine bioinformatics tasks are often automated, but many still require the unique
experience and intuition of human researchers: this requires tools that support real-time
interaction with complex datasets. Many existing tools have poor user interfaces
and limited real-time performance when applied to realistically large datasets; much
of the user's cognitive capacity is therefore focused on controlling the tool rather
than on performing the research. The UTOPIA project is addressing some of these
issues by building reusable software components that can be combined to make
useful applications in the field of bioinformatics. Expertise in the fields of human
computer interaction, high-performance rendering, and distributed systems is being
guided by bioinformaticians and end-user biologists to create a toolkit that is both
architecturally sound from a computing point of view, and directly addresses end-user
and application-developer requirements
HypTrails: A Bayesian Approach for Comparing Hypotheses About Human Trails on the Web
When users interact with the Web today, they leave sequential digital trails
on a massive scale. Examples of such human trails include Web navigation,
sequences of online restaurant reviews, or online music play lists.
Understanding the factors that drive the production of these trails can be
useful for e.g., improving underlying network structures, predicting user
clicks or enhancing recommendations. In this work, we present a general
approach called HypTrails for comparing a set of hypotheses about human trails
on the Web, where hypotheses represent beliefs about transitions between
states. Our approach utilizes Markov chain models with Bayesian inference. The
main idea is to incorporate hypotheses as informative Dirichlet priors and to
leverage the sensitivity of Bayes factors on the prior for comparing hypotheses
with each other. For eliciting Dirichlet priors from hypotheses, we present an
adaption of the so-called (trial) roulette method. We demonstrate the general
mechanics and applicability of HypTrails by performing experiments with (i)
synthetic trails for which we control the mechanisms that have produced them
and (ii) empirical trails stemming from different domains including website
navigation, business reviews and online music played. Our work expands the
repertoire of methods available for studying human trails on the Web.Comment: Published in the proceedings of WWW'1
On the Interpretation of Supernova Light Echo Profiles and Spectra
The light echo systems of historical supernovae in the Milky Way and local
group galaxies provide an unprecedented opportunity to reveal the effects of
asymmetry on observables, particularly optical spectra. Scattering dust at
different locations on the light echo ellipsoid witnesses the supernova from
different perspectives and the light consequently scattered towards Earth
preserves the shape of line profile variations introduced by asymmetries in the
supernova photosphere. However, the interpretation of supernova light echo
spectra to date has not involved a detailed consideration of the effects of
outburst duration and geometrical scattering modifications due to finite
scattering dust filament dimension, inclination, and image point-spread
function and spectrograph slit width. In this paper, we explore the
implications of these factors and present a framework for future resolved
supernova light echo spectra interpretation, and test it against Cas A and SN
1987A light echo spectra. We conclude that the full modeling of the dimensions
and orientation of the scattering dust using the observed light echoes at two
or more epochs is critical for the correct interpretation of light echo
spectra. Indeed, without doing so one might falsely conclude that differences
exist when none are actually present.Comment: 18 pages, 22 figures, accepted for publication in Ap
The elements of a computational infrastructure for social simulation
Applications of simulation modelling in social science domains are varied and increasingly widespread. The effective deployment of simulation models depends on access to diverse datasets, the use of analysis capabilities, the ability to visualize model outcomes and to capture, share and re-use simulations as evidence in research and policy-making. We describe three applications of e-social science that promote social simulation modelling, data management and visualization. An example is outlined in which the three components are brought together in a transport planning context. We discuss opportunities and benefits for the combination of these and other components into an e-infrastructure for social simulation and review recent progress towards the establishment of such an infrastructure
Enabling quantitative data analysis through e-infrastructures
This paper discusses how quantitative data analysis in the social sciences can engage with and exploit an e-Infrastructure. We highlight how a number of activities which are central to quantitative data analysis, referred to as ‘data management’, can benefit from e-infrastructure support. We conclude by discussing how these issues are relevant to the DAMES (Data Management through e-Social Science) research Node, an ongoing project that aims to develop e-Infrastructural resources for quantitative data analysis in the social sciences
Specifying ODP Computational Objects in Z
The computational viewpoint contained within the Reference Model of Open Distributed Processing (RM-ODP) shows how collections of objects can be configured within a distributed system to enable interworking. It prescribes certain capabilities that such objects are expected to possess and structuring rules that apply to how these objects can be configured with one another. This paper highlights how the specification language Z can be used to formalise these capabilities and the associated structuring rules, thereby enabling specifications of ODP systems from the computational viewpoint to be achieved
Federating distributed clinical data for the prediction of adverse hypotensive events
The ability to predict adverse hypotensive events, where a patient's arterial blood pressure drops to abnormally low (and dangerous) levels, would be of major benefit to the fields of primary and secondary health care, and especially to the traumatic brain injury domain. A wealth of data exist in health care systems providing information on the major health indicators of patients in hospitals (blood pressure, temperature, heart rate, etc.). It is believed that if enough of these data could be drawn together and analysed in a systematic way, then a system could be built that will trigger an alarm predicting the onset of a hypotensive event over a useful time scale, e.g. half an hour in advance. In such circumstances, avoidance measures can be taken to prevent such events arising. This is the basis for the Avert-IT project (http://www.avert-it.org), a collaborative EU-funded project involving the construction of a hypotension alarm system exploiting Bayesian neural networks using techniques of data federation to bring together the relevant information for study and system development
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