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6th International conference on Practical Applications of computational Biology and bioinformatics

6th International Conference on Practical Applications of Co...

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6th International conference on Practical Applications of computational Biology and bioinformatics, PACBB'12

ISBN: (纸本)9783642288388

The proceedings contain 32 papers. The topics discussed include: prognostic prediction using clinical expression time series: towards a supervised learning approach based on meta-biclusters;parallel e-CCC-biclustering: mining approximate temporal patterns in gene expression time series using parallel biclustering;parameter influence in genetic algorithm optimization of support vectormachines;biological knowledge integration in DNA microarray gene expression classification based on rough set theory;quantitative assessment of estimation approaches for mining over incomplete data in complex biomedical spaces: a case study on cerebral aneurysms;case-based reasoning to classify endodontic retreatments;a comparative analysis of balancing techniques and attribute reduction algorithms;sliced model checking for phylogenetic analysis;and a systematic approach to the interrogation and sharing of standardized biofilm signatures.

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Efficient basin hopping in the protein energy surface 2012

Efficient basin hopping in the protein energy surface

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2012 ieee International conference on bioinformatics and Biomedicine, BIBM2012

作者： Olson, Brian Shehu, Amarda Department of Computer Science George Mason University Fairfax VA 22030 United States Department of Bioinformatics and Computational Biology George Mason University Fairfax VA 22030 United States Department of Bioengineering George Mason University Fairfax VA 22030 United States

ISBN: (纸本)9781467325585

The vast and rugged protein energy surface can be effectively represented in terms of local minima. The basin-hopping framework, where a structural perturbation is followed by an energy minimization, is particularly suited to obtaining this coarse-grained representation. Basin hopping is effective for small systems both in locating lower-energy minima and obtaining conformations near the native structure. The efficiency decreases for large systems. Our recent work improves efficiency on large systems through molecular fragment replacement. In this paper, we conduct a detailed investigation of two components in basin hopping, perturbation and minimization, and how they work in concert to affect the sampling of near-native local minima. We show that controlling the magnitude of perturbation jumps is related to the ability to effectively steer the exploration towards conformations near the protein native state. In minimization, we show that a simple greedy search is just as effective as Metropolis Monte Carlo-based minimization. Finally, we show that an evolutionary-inspired approach based on the Pareto front is particularly effective in reducing the ensemble of sampled local minima and obtains a simpler representation of the probed energy surface. © 2012 ieee.

关键词： Proteins

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Efficient Processing of Models for Large-scale Shotgun Proteomics Data

Efficient Processing of Models for Large-scale Shotgun Prote...

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8th ieee International conference on Collaborative Computing: Networking, Applications and Worksharing (CollaborateCom)

作者： Grover, Himanshu Gopalakrishnan, Vanathi Univ Pittsburgh Dept Biomed Informat Pittsburgh PA 15206 USA Univ Pittsburgh Intelligent Syst Program Pittsburgh PA 15206 USA Univ Pittsburgh Computat & Syst Biol Dept Pittsburgh PA 15206 USA

ISBN: (纸本)9781467327404;9781467327404

Mass-spectrometry (MS) based proteomics has become a key enabling technology for the systems approach to biology, providing insights into the protein complement of an organism. bioinformatics analyses play a critical role in interpretation of large, and often replicated, MS datasets generated across laboratories and institutions. A significant amount of computational effort in the workflow is spent on the identification of protein and peptide components of complex biological samples, and consists of a series of steps relying on large database searches and intricate scoring algorithms. In this work, we share our efforts and experience in efficient handling of these large MS datasets through database indexing and parallelization based on multiprocessor architectures. We also identify important challenges and opportunities that are relevant specifically to the task of peptide and protein identification, and more generally to similar multi-step problems that are inherently parallelizable.

关键词： bioinformatics High-throughput Proteomics Indexing Multiprocessing Parallelization

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A GRASP-based heuristic for the project portfolio selection problem

A GRASP-based heuristic for the project portfolio selection ...

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15th ieee International conference on computational Science and Engineering, CSE 2012 and 10th ieee/IFIP International conference on Embedded and Ubiquitous Computing, EUC 2012

作者： Mira, Cleber Feijão, Pedro Souza, Maria Angélica Moura, Arnaldo Meidanis, João Lima, Gabriel Schmitz, Rafael Bossolan, Renato P. Freitas, Ítalo T. Scylla Bioinformatics Campinas Brazil Institute of Computing Unicamp Campinas Brazil AES-Tietê Brazil Mechanical Engineering Department Unicamp Campinas Brazil

ISBN: (纸本)9780769549149

The project portfolio selection (PPS) problem consists of constructing a project portfolio, that is, a selection of projects scheduled over a period of time using various, potentially conflicting, criteria and resource constraints. The PPS is a well-known problem, recurrently occurring in several applications, with a rich history of approaches for modeling it and a large number of techniques for solving it. In this work we present a model for the PPS problem based on a real-world situation of selection and scheduling of projects in the power generation industry. We also propose a heuristic, based on the metaheuristic GRASP, to solve the problem, and assess its quality and performance through computational experiments. We describe the implementation of a decision support system prototype for the PPS problem that uses the proposed heuristic and includes several usability features that may help decision makers through the selection process. © 2012 ieee.

关键词： Decision support systems

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Development of Multi-compartment Model of the Liver Using Image-based Meshing Software

Development of Multi-compartment Model of the Liver Using Im...

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34th Annual International conference of the ieee Engineering-in-Medicine-and-Biology-Society (EMBS)

作者： Barthod-Malat, Annick Kopylova, Veronika Podoprigora, Gennady I. Nartsissov, Yaroslav R. Angoue, Orland Young, Philippe G. Crolet, Jean-Marie Blagosklonov, Oleg Univ Hosp Inst Engn Franche Comte F-25030 Besancon France

ISBN: (纸本)9781457717871

Computer simulation of biological systems for in silico validation has the potential of increasing the efficiency of pharmaceutical research and development by expanding the number of parameters tested virtually. Then only the most interesting subset of these has to be probed in vivo. By focusing on variables with the greatest influence on clinical end points, valuable drug targets can be advanced more quickly. A large number of methods have been developed to rebuild a three-dimensional (3D) model of a liver, mostly to prepare a liver surgery. These models are often not accurate and most of the them don't take into account the fluidics inside the vessels. The aim of this work is to provide an accurate computational multi-compartement model of the healthy and the pathological liver with their network of blood vessels (vasculature) using a finite-element-modeling software. Computed tomography (CT) slices, in DICOM format, from two different patients were used to provide the datasets of transverse images for the modeling. Each dataset of images was segmented in order to extract the liver's shape and define the vein and artery networks. On CT images, the contrast between the liver and the nearby organs (background) is very low because all these structures are a similar density. Thus, we used semi-automatic tools to determine liver contours. Manual segmentation was used as a last resort. Then, strong filtering (bilateral filter) and confidence-connected-region-growing algorithm were applied to rebuild from each - healthy and pathological - liver a multi-compartment model including parenchyma, arteries and veins. The precision of the obtained vasculature model allowed anatomical classification of hepatic segments and the quantification of their volumes. Although our study demonstrated the difficulties in use of CT images for computational modeling of the liver, it also confirmed that semi-automatic tools can be used to develop anatomically accurate models of hepatic vascu

关键词： bioinformatics

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The emerging field of synthetic biology: A review

The emerging field of synthetic biology: A review

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2012 4th International conference on Intelligent and Advanced systems, ICIAS 2012

作者： Habibi, Narjeskhatoon Hashim, Siti Zaiton Mohd Rodriguez, Cesar A. Mohamad, Mohd Saberi Bin Deris, Safaai Bin Soft Computing Research Group Faculty of Computer Science and Information Systems Universiti Teknologi Malaysia Malaysia Genome Compiler Corporation United States Artificial Intelligence And. Bioinformatics Laboratory Faculty of Computer Science and Information Systems Universiti Teknologi Malaysia Malaysia

ISBN: (纸本)9781457719677

Synthetic biology which is concerned with engineering organisms to perform novel functions and developing the ways by which organisms can be engineered easily and robustly, is a relatively young field with a large potential for growth. Much of the work in the field involves design and construction of genetic circuitry, the piecing together of biological parts, such as promoters and ribosome binding sites, to form the basis for biological devices which are organisms that have an engineered, well-specified input-output behavior. The idea in synthetic biology is applying engineering principles, such as hierarchical design, modular reusable parts and standard interfaces to construct bio-systems. The results of these engineering efforts can be of great value to human interests such as medicine and industry. In this paper first some related terms and resources for synthetic biology are described. Then existing computational tools and methods for synthetic biology are explored. It is followed by a discussion on current challenges in the field and future directions and finally by conclusion. © 2012 ieee.

关键词： Binding sites

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A Scalable Architecture for Intrusion-Detection systems Based on a Broadband Network of Embedded Set-Top Boxes

A Scalable Architecture for Intrusion-Detection Systems Base...

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54th ieee International Midwest Symposium on Circuits and systems (MWSCAS)

作者： Neill, Richard Carloni, Luca P. Columbia Univ Dept Comp Sci New York NY 10027 USA

ISBN: (纸本)9781612848570

As the processing power of set-top box (STB) devices continnes to grow with each new product generation and multiple service operators directly manage millions of these devices through a dedicated broadband network, we propose to harness this massive aggregate computational power to execute large-scale parallel applications. We present a prototype implementation of a heterogeneous distributed embedded system that combines a complete head-end cable system with a DOCSIS broadband network of STBs and an interoperable embedded implementation of Open MPI running on the STB operating system. We demonstrate the operations and performance of this system by reporting the experimental results that we obtained for the execution of various instances of Multiple Sequence Alignment, a parallel bioinformatics application. Based on these results we propose a new distributed embedded system architecture for highly-scalable intrusion-detection systems.

关键词： Broadband communication DOCSIS broadband network Frequency modulation Linux Radio frequency Servers Transform coding bioinformatics bioinformatics application computer networks dedicated broadband network embedded set-top boxes embedded systems head end cable system heterogeneous distributed embedded system intrusion detection systems large scale parallel applications massive aggregate computational power multiple sequence alignment scalable architecture security of data set-top boxes

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Unifying the Integration, Analysis and Interpretation of multi-omic datasets: Exploration of the disease networks of Obstructive Nephropathy in children

Unifying the Integration, Analysis and Interpretation of mul...

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33rd Annual International conference of the ieee Engineering-in-Medicine-and-Biology-Society (EMBS)

作者： Moulos, Panagiotis Valavanis, Ioannis Klein, Julie Maglogiannis, Ilias Schanstra, Joost Chatziioannou, Aristotelis Natl Hellen Res Fdn Inst Biol Res & Biotechnol Athens Greece

ISBN: (纸本)9781424441228

The wealth of data amassed by the utilization of various high-throughput techniques, in various layers of molecular dissection, stresses the critical role of the unification of the computational methodologies applied in biological data handling, storage, analysis and visualization. In this article, a generic workflow is showcased in a multi-omic dataset that is used to study Obstructive Nephropathy (ON) in children, integrating microarray data from several biological layers (transcriptomic, post-transcriptomic, proteomic). The workflow exploits raw measurements and through several analytical stages (preprocessing, statistical and functional), which entail various parsing steps, reaches the visualization stage of the heterogeneous, broader, molecular interacting network derived. This network, where the interconnected entities are exploiting the knowledge stored in public repositories, represents a systems level interpretation of the pathological state probed.

关键词： bioinformatics Data visualization Genomics Mice Proteins Proteomics bioinformatics biological data analysis biological data handling biological data storage biological data visualization biological techniques biomedical engineering complex networks comput

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FPGA implementation of K-means algorithm for bioinformatics application: An accelerated approach to clustering Microarray data

FPGA implementation of K-means algorithm for bioinformatics ...

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NASA/ESA conference on Adaptive Hardware and systems

作者： Hussain, Hanaa M. Benkrid, Khaled Seker, Huseyin Erdogan, Ahmet T. System Level Integration Group University of Edinburgh King's Buildings Mayfield Road Edinburgh EH9 3JL United Kingdom Bio-Health Informatics Research Group Center for Computational Intelligence De Montfort University Leicester LE1 9BH United Kingdom

ISBN: (纸本)9781457705984

The Microarray is a technique used by biologists to perform many genome experiments simultaneously, which produces very large datasets. Analysis of these datasets is a challenge for scientists especially as the number of genome databases is increasing rapidly every year. K-means clustering is an unsupervised data mining technique used widely by bioinformaticians to analyze Microarray data. However, K-means can take between a few seconds to several days to process Microarray data depending on the size of these datasets. This puts a limit on the complexity of biological problems which can be asked by bioinfomaticians, and hence may result in an incomplete solution to the problem. In order to overcome such problems, we propose a highly parallel hardware design to accelerate the K-means clustering of Microarray data by implementing the K-means algorithm in Field Programmable Gate Arrays (FPGA). Our implementation is particularly suitable for server solution as it allows for processing many different datasets simultaneously. We have designed, and implemented five k-mean cores on Xilinx Virtex4 XC4VLX25 FPGA, and tested them on a sample of real Yeast Microarray data. Our design achieved about 51.7 speed-up when compared to a software model while being 206.8 more energy efficient. © 2011 ieee.

关键词： Field programmable gate arrays (FPGA)

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A profile of today's SBML-compatible software

A profile of today's SBML-compatible software

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7th ieee International conference on e-Science Workshops, eScienceW 201

作者： Hucka, Michael Bergmann, Frank T. Keating, Sarah M. Smith, Lucian P. California Institute of Technology Pasadena CA United States EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge United Kingdom University of Washington Seattle WA United States

ISBN: (纸本)9780769545981

computational systems biologists today have a healthy selection of software resources to help them do research. Many software packages, especially those concerned with computational modeling, have adopted SBML (the systems Biology Markup Language) as a machine-readable format to permit users to exchange models. Our group has a keen interest in understanding the landscape of SBML support. To help us ascertain the state of modern SBML-compatible software, in mid-2011 we initiated a survey of software packages that support SBML. Here we report the preliminary survey results. Based on 81 packages for which we have data so far, we summarize the trends in six areas: (1) What are the major types of functionality offered by the software systems? (2) What mathematical frameworks do they support? (3) What are their SBML-specific capabilities? (4) What other standards do they support besides SBML? (5) What are their characteristics with respect to run-time environments? And finally, (6) what are the availability and licensing terms? © 2011 ieee.

关键词： Data handling

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