8916884
cisRED: a database system for genome-scale computational discovery of regulatory elements
We describe cisRED, a database for conserved regulatory elements that are identified and ranked by a genome-scale computational system (). The database and high-throughput predictive pipeline are designed to address diverse target genomes in the context of rapidly evolving data resources and tools. Motifs are predicted in promoter regions using multiple discovery methods applied to sequence sets that include corresponding sequence regions from vertebrates. We estimate motif significance by applying discovery and post-processing methods to randomized sequence sets that are adaptively derived from target sequence sets, retain motifs with p-values below a threshold and identify groups of similar motifs and co-occurring motif patterns. The database offers information on atomic motifs, motif groups and patterns. It is web-accessible, and can be queried directly, downloaded or installed locally.
1306264
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
MOTIVATION
Our understanding of gene regulation is currently limited by our ability to collectively synthesize and catalogue transcriptional regulatory elements stored in scientific literature. Over the past decade, this task has become increasingly challenging as the accrual of biologically validated regulatory sequences has accelerated. To meet this challenge, novel community-based approaches to regulatory element annotation are required.


SUMMARY
Here, we present the Open Regulatory Annotation (ORegAnno) database as a dynamic collection of literature-curated regulatory regions, transcription factor binding sites and regulatory mutations (polymorphisms and haplotypes). ORegAnno has been designed to manage the submission, indexing and validation of new annotations from users worldwide. Submissions to ORegAnno are immediately cross-referenced to EnsEMBL, dbSNP, Entrez Gene, the NCBI Taxonomy database and PubMed, where appropriate.


AVAILABILITY
ORegAnno is available directly through MySQL, Web services, and online at http://www.oreganno.org. All software is licensed under the Lesser GNU Public License (LGPL).
1710827
A simulated annealing and hill-climbing algorithm for the traveling tournament problem
Abstract The Traveling Tournament Problem (TTP) [E. Easton, G. Nemhauser, M. Trick, The traveling tournament problem description and benchmarks, in: Proceedings of the 7th International Conference on Principles and Practice of Constraint Programming, CP 2001, 2001, pp. 580–584; M. Trick, Challenge Traveling Tournament Problems, 2004] schedules a double round-robin tournament to minimize the total distance traveled by competing teams. It involves issues of feasibility and optimality and is a challenge to constraint and integer programming. In this work, we divide the search space and use simulated annealing (SA) to search a timetable space and hill-climbing to explore a team assignment space. The SA component mutates timetables using conditional local jumps to find timetables which lead to better schedules while hill-climbing is enhanced by pre-computation and dynamic cost updating to provide fast and efficient search. Computational experiments using this hybrid approach on benchmark sets give results comparable to or better than current best known solutions.
39760063
Stripe-Based Wavelet Transform and its Coding
41465544
Towards automated progress assessment of workpackage components in construction projects using computer vision
Traditional methods of collecting data on the progress of construction projects often involve human judgement, high costs, and are too infrequent to provide managers with timely and accurate control data. This study proposes a system that aims to address some of these shortcomings through automation. Our first contribution is a framework for the automatic generation of work packages. We describe the conceptual model and develop a prototype implementation, based on the results of a survey designed to capture the current practice of formulating work packages as performed in the industry. Our second contribution is a system that employs computer vision (CV) techniques to report on the progress of these work packages automatically. This is achieved by analysing sequences of digital images acquired regularly by on-site cameras. The result of this analysis, when compared with the expected state of construction, provides progress feedback on the work packages, allowing a project to be monitored more effectively.
11105544
Solving Computational Fluid Dynamics Problems on Unstructured Grids with Distributed Parallel Processing
This paper describes a distributed parallel implementation of a finite element method for simulating incompressible viscous flows. When applied to unstructured finite element meshes, a conventional implementation of this algorithm becomes particularly space demanding for the storage of system matrices. This parallel implementation not only results in a faster computation but is also potentially capable of solving much larger problems as data and system matrix blocks are distributed. Experimental results demonstrating these key features are presented.
37723019
Mining Influential Association Rules