Computing Science, School of

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The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2008
Abstract: 

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding.  A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive,  high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.

Document type: 
Article

Conditional Random Fields and Supervised Learning in Automated Skin Lesion Diagnosis

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2011
Abstract: 

Many subproblems in automated skin lesion diagnosis (ASLD) canbe unified under a single generalization of assigning a label, from an predefinedset, to each pixel in an image. We first formalize this generalizationand then present two probabilistic models capable of solving it. The firstmodel is based on independent pixel labeling using maximum a-posteriori(MAP) estimation. The second model is based on conditional randomfields (CRFs), where dependencies between pixels are defined using agraph structure. Furthermore, we demonstrate how supervised learningand an appropriate training set can be used to automatically determineall model parameters. We evaluate both models' ability to segment achallenging dataset consisting of 116 images and compare our results to5 previously published methods.

Document type: 
Article

Improvement and Performance Evaluation for Multimedia Files Transmission in Vehicle-Based DTNs

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2013
Abstract: 

In recent years, P2P file sharing has been widely embraced and becomes the largest application of the Internet traffic. And thedevelopment of automobile industry has promoted a trend of deploying Peer-to-Peer (P2P) networks over vehicle ad hoc networks(VANETs) for mobile content distribution. Due to the high mobility of nodes, nodes’ limited radio transmission range and sparsedistribution, VANETs are divided and links are interrupted intermittently. At this moment, VANETs may become Vehicle-basedDelay Tolerant Network (VDTNs). Therefore, this work proposes an Optimal Fragmentation-based Multimedia Transmissionscheme (OFMT) based on P2P lookup protocol in VDTNs, which can enable multimedia files to be sent to the receiver fast andreliably in wireless mobile P2P networks over VDTNs. In addition, a method of calculating the most suitable size of the fragmentis provided, which is tested and verified in the simulation. And we also show that OFMT can defend a certain degree of DoS attackand senders can freely join and leave the wireless mobile P2P network. Simulation results demonstrate that the proposed schemecan significantly improve the performance of the file delivery rate and shorten the file delivery delay compared with the existingschemes.

Document type: 
Article

Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2007-09
Abstract: 

The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.

Document type: 
Article
File(s): 

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2007-07
Abstract: 

The (asymptotic) degree distributions of the best-known “scale-free” network models are all similar and are independent of the seed graph used; hence, it has been tempting to assume that networks generated by these models are generally similar. In this paper, we observe that several key topological features of such networks depend heavily on the specific model and the seed graph used. Furthermore, we show that starting with the “right” seed graph (typically a dense subgraph of the protein–protein interaction network analyzed), the duplication model captures many topological features of publicly available protein–protein interaction networks very well

Document type: 
Article
File(s): 

Ambient Data Collection with Wireless Sensor Networks

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

One of the most important applications for wireless sensor networks (WSNs) is Data Collection, where sensing data arecollected at sensor nodes and forwarded to a central base station for further processing. Since using battery powers and wirelesscommunications, sensor nodes can be very small and easily attached at specified locations without disturbing surroundingenvironments. This makes WSN a competitive approach for data collection comparing with its wired counterpart. In this paper,we review recent advances in this research area. We first highlight the special features of data collection WSNs, by comparingwith wired data collection network and other WSN applications. With these features in mind, we then discuss issues and priorsolutions on the data gathering protocol design. Our discussion also covers different approaches for message dissemination, whichis a critical component for network control and management and greatly affects the overall performance of a data collectionWSNsystem.

Document type: 
Article

Cooperative Coding and Caching for Streaming Data in Multihop Wireless Networks

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2010
Abstract: 

This paper studies the distributed caching managements for the current flourish of the streaming applications inmultihop wirelessnetworks. Many caching managements to date use randomized network coding approach, which provides an elegant solution forubiquitous data accesses in such systems. However, the encoding, essentially a combination operation, makes the coded datadifficult to be changed. In particular, to accommodate new data, the system may have to first decode all the combined datasegments, remove some unimportant ones, and then reencode the data segments again. This procedure is clearly expensivefor continuously evolving data storage. As such, we introduce a novel Cooperative Coding and Caching (C3) scheme, whichallows decoding-free data removal through a triangle-like codeword organization. Its decoding performance is very close to theconventional network coding with only a sublinear overhead. Our scheme offers a promising solution to the caching managementfor streaming data.

Document type: 
Article

A Replica Exchange Monte Carlo Algorithm for Protein Folding in the HP Model

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2007
Abstract: 

Background: The ab initio protein folding problem consists of predicting protein tertiary structurefrom a given amino acid sequence by minimizing an energy function; it is one of the most importantand challenging problems in biochemistry, molecular biology and biophysics. The ab initio proteinfolding problem is computationally challenging and has been shown to be -hard even whenconformations are restricted to a lattice. In this work, we implement and evaluate the replicaexchange Monte Carlo (REMC) method, which has already been applied very successfully to morecomplex protein models and other optimization problems with complex energy landscapes, incombination with the highly effective pull move neighbourhood in two widely studied HydrophobicPolar (HP) lattice models.Results: We demonstrate that REMC is highly effective for solving instances of the square (2D)and cubic (3D) HP protein folding problem. When using the pull move neighbourhood, REMCoutperforms current state-of-the-art algorithms for most benchmark instances. Additionally, weshow that this new algorithm provides a larger ensemble of ground-state structures than theexisting state-of-the-art methods. Furthermore, it scales well with sequence length, and it findssignificantly better conformations on long biological sequences and sequences with a provablyunique ground-state structure, which is believed to be a characteristic of real proteins. We alsopresent evidence that our REMC algorithm can fold sequences which exhibit significant interactionbetween termini in the hydrophobic core relatively easily.Conclusion: We demonstrate that REMC utilizing the pull move neighbourhood significantlyoutperforms current state-of-the-art methods for protein structure prediction in the HP model on2D and 3D lattices. This is particularly noteworthy, since so far, the state-of-the-art methods for2D and 3D HP protein folding – in particular, the pruned-enriched Rosenbluth method (PERM) and,to some extent, Ant Colony Optimisation (ACO) – were based on chain growth mechanisms. Tothe best of our knowledge, this is the first application of REMC to HP protein folding on the cubiclattice, and the first extension of the pull move neighbourhood to a 3D lattice.

Document type: 
Article

Trombone Synthesis by Model and Measurement

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2011
Abstract: 

A physics-based synthesis model of a trombone is developed using filter elements that are both theoretically-based and estimatedfrom measurement. The model consists of two trombone instrument transfer functions: one at the position of the mouthpieceenabling coupling to a lip-valve model and one at the outside of the bell for sound production. The focus of this work is onextending a previously presented measurement technique used to obtain acoustic characterizations of waveguide elements forcylindrical and conical elements, with further development allowing for the estimation of the flared trombone bell reflection andtransmission functions for which no one-parameter traveling wave solution exists. A one-dimensional bell model is developedproviding an approximate theoretical expectation to which estimation results may be compared. Dynamic trombone modelelements, such as those dependent on the bore length, are theoretically and parametrically modeled. As a result, the trombonemodel focuses on accuracy, interactivity, and efficiency, making it suitable for a number of real-time computer music applications.

Document type: 
Article