125,984 research outputs found
MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME
Computational experiments using spatial stochastic simulations have led to
important new biological insights, but they require specialized tools, a
complex software stack, as well as large and scalable compute and data analysis
resources due to the large computational cost associated with Monte Carlo
computational workflows. The complexity of setting up and managing a
large-scale distributed computation environment to support productive and
reproducible modeling can be prohibitive for practitioners in systems biology.
This results in a barrier to the adoption of spatial stochastic simulation
tools, effectively limiting the type of biological questions addressed by
quantitative modeling. In this paper, we present PyURDME, a new, user-friendly
spatial modeling and simulation package, and MOLNs, a cloud computing appliance
for distributed simulation of stochastic reaction-diffusion models. MOLNs is
based on IPython and provides an interactive programming platform for
development of sharable and reproducible distributed parallel computational
experiments
Performance comparison of point and spatial access methods
In the past few years a large number of multidimensional point access methods, also called
multiattribute index structures, has been suggested, all of them claiming good performance. Since no
performance comparison of these structures under arbitrary (strongly correlated nonuniform, short
"ugly") data distributions and under various types of queries has been performed, database
researchers and designers were hesitant to use any of these new point access methods. As shown in
a recent paper, such point access methods are not only important in traditional database applications.
In new applications such as CAD/CIM and geographic or environmental information systems, access
methods for spatial objects are needed. As recently shown such access methods are based on point
access methods in terms of functionality and performance. Our performance comparison naturally
consists of two parts. In part I we w i l l compare multidimensional point access methods, whereas in
part I I spatial access methods for rectangles will be compared. In part I we present a survey and
classification of existing point access methods. Then we carefully select the following four methods
for implementation and performance comparison under seven different data files (distributions) and
various types of queries: the 2-level grid file, the BANG file, the hB-tree and a new scheme, called
the BUDDY hash tree. We were surprised to see one method to be the clear winner which was the
BUDDY hash tree. It exhibits an at least 20 % better average performance than its competitors and is
robust under ugly data and queries. In part I I we compare spatial access methods for rectangles.
After presenting a survey and classification of existing spatial access methods we carefully selected
the following four methods for implementation and performance comparison under six different data
files (distributions) and various types of queries: the R-tree, the BANG file, PLOP hashing and the
BUDDY hash tree. The result presented two winners: the BANG file and the BUDDY hash tree.
This comparison is a first step towards a standardized testbed or benchmark. We offer our data and
query files to each designer of a new point or spatial access method such that he can run his
implementation in our testbed
Query processing of spatial objects: Complexity versus Redundancy
The management of complex spatial objects in applications, such as geography and cartography,
imposes stringent new requirements on spatial database systems, in particular on efficient
query processing. As shown before, the performance of spatial query processing can be improved
by decomposing complex spatial objects into simple components. Up to now, only decomposition
techniques generating a linear number of very simple components, e.g. triangles or trapezoids, have
been considered. In this paper, we will investigate the natural trade-off between the complexity of
the components and the redundancy, i.e. the number of components, with respect to its effect on
efficient query processing. In particular, we present two new decomposition methods generating
a better balance between the complexity and the number of components than previously known
techniques. We compare these new decomposition methods to the traditional undecomposed representation
as well as to the well-known decomposition into convex polygons with respect to their
performance in spatial query processing. This comparison points out that for a wide range of query
selectivity the new decomposition techniques clearly outperform both the undecomposed representation
and the convex decomposition method. More important than the absolute gain in performance
by a factor of up to an order of magnitude is the robust performance of our new decomposition
techniques over the whole range of query selectivity
Parallel earcons: reducing the length of audio messages
This paper describes a method of presenting structured audio messages, earcons, in parallel so that they take less time to play and can better keep pace with interactions in a human-computer interface. The two component parts of a compound earcon are played in parallel so that the time taken is only that of a single part. An experiment was conducted to test the recall and recognition of parallel compound earcons as compared to serial compound earcons. Results showed that there are no differences in the rates of recognition between the two groups. Non-musicians are also shown to be equal in performance to musicians. Some extensions to the earcon creation guidelines of Brewster, Wright and Edwards are put forward based upon research into auditory stream segregation. Parallel earcons are shown to be an effective means of increasing the presentation rates of audio messages without compromising recognition rates
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