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HPC selection of models of DNA substitution 11

HPC selection of models of DNA substitution

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9th International conference on computational Methods in systems Biology, CMSB'11

作者： Darriba, Diego Taboada, Guillermo L. Doallo, Ramón Posada, David Computer Architecture Group University of A Coruña 15071 A Coruña Spain Bioinformatics and Molecular Evolution Group University of Vigo 36310 Vigo Spain

ISBN: (纸本)9781450308175

Statistical model selection has become an essential step for the estimation of phylogenies from DNA sequence alignments. The program jModelTest offers different strategies to identify best-fit models for the data at hand, but for large DNA alignments, this task can demand vast computational resources. This paper presents a High Performance Computing (HPC) adaptation of jModelTest for shared memory multi-core systems and distributed memory cluster platforms. The performance evaluation of this HPC version on a shared memory system and on a cluster shows significant performance advantages, with speedups up to 39. This could represent a reduction in the execution time of some analyses from almost one day to half an hour. © 2011 ACM.

关键词： Message passing

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OntoHealth: A system to process ontologies applied to health pervasive environment

OntoHealth: A system to process ontologies applied to health...

引用

ieee International conference on Ubi-media Computing

作者： Librelotto, Giovani R. Freitas, Leandro O. Fiorin, André Mozzaquatro, Bruno A. Pasetto, Leandro Martini, Ricardo G. De Azevedo, Renato P. Pereira, Rafael T. PPGI/DELC - Technology Center Federal University of Santa Maria Santa Maria - RS Brazil Department of Bioinformatics University of Minho Braga Portugal

ISBN: (纸本)9780769544939

In the last years ontologies are being used in the development of pervasive computing applications. It is habitual their use for facilitating the interoperability among context-aware applications and the entities that may enter in the context at any time. This paper presents OntoHealth: a system to process ontologies applied to health pervasive environment. The main idea is that a hospital could be seen as this pervasive environment, where someone, through ubiquitous computing, engages a range of computational devices and systems simultaneously, in the course of ordinary activities, and may not necessarily even be aware that they are doing so. With the proposed ontology and the tool for its processing, the medical tasks can be shared by all components of this pervasive environment. © 2011 ieee.

关键词： Ontology

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Scaling HMMER performance on multicore architectures

Scaling HMMER performance on multicore architectures

引用

5th International conference on Complex, Intelligent and Software Intensive systems, CISIS 2011

作者： Isaza, Sebastian Houtgast, Ernst Sanchez, Friman Ramirez, Alex Gaydadjiev, Gergi Computer Engineering Laboratory Delft University of Technology Netherlands Computer Architecture Department Technical University of Catalonia Spain Barcelona Supercomputing Center Spain

ISBN: (纸本)9780769543734

In bioinformatics, protein sequence alignment is one of the fundamental tasks that scientists perform. Since the growth of biological data is exponential, there is an ever-increasing demand for computational power. While current processor technology is shifting towards the use of multicores, the mapping and parallelization of applications has become a critical issue. In order to keep up with the processing demands, applications' bottlenecks to performance need to be found and properly addressed. In this paper we study the parallelism and performance scalability of HMMER, a bioinformatics application to perform sequence alignment. After our study of the bottlenecks in a HMMER version ported to the Cell processor, we present two optimized versions to improve scalability in a larger multicore architecture. We use a simulator that allows us to model a system with up to 512 processors and study the performance of the three parallel versions of HMMER. Results show that removing the I/O bottleneck improves performance by 3X and 2.4X for a short and a long HMM query respectively. Additionally, by offloading the sequence pre-formatting to the worker cores, larger speedups of up to 27X and 7X are achieved. Compared to using a single worker processor, up to 156X speedup is obtained when using 256 cores. © 2011 ieee.

关键词： bioinformatics

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Sequencing and disease variation detection tools and techniques

Sequencing and disease variation detection tools and techniq...

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9th ACS/ieee International conference on Computer systems and Applications, AICCSA 2011

作者： DeLuca, Adam P. Wagner, Alex H. Taylor, Kyle R. Faga, Ben Thole, David Sheffield, Val C. Stone, Edwin M. Casavant, Thomas L. Scheetz, Todd E. Braun, Terry A. Center for Bioinformatics and Computational Biology University of Iowa Iowa City IA United States Howard Hughes Medical Institute Iowa City IA United States

ISBN: (纸本)9781457704741

Next-generation sequencing technology provides greater sequencing capacity to identify disease-causing variations. Currently there are many alignment tools and variation detection techniques, multiple SNP data sets used to filter out benign polymorphisms with the intent of enriching for disease-causing variations, and many tools and websites for annotating variations and performing pathogenicity prediction of variations. There is no consensus or standard with regards to which tools and corresponding parameter settings for each tool is appropriate for the different application of next-generation sequencing technologies for disease-causing variation identification. We have implemented an annotation pipeline that can easily use the output from different alignment tools (BLAT, BWA, BFAST, Bowtie) typically used to align sequence from next-generation sequencing and Sanger sequencing experiments. The Automated Sequence Analysis Pipeline (ASAP) reports variations using the HGVS standardized nomenclature[1] to facilitate comparison across tools and publications. To date, we have annotated the sequence from 13 exomes in an effort to identify disease-causing mutations. © 2011 ieee.

关键词： Pipelines

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Non linear modeling of cell survival/death using artificial neural network

Non linear modeling of cell survival/death using artificial ...

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2011 International conference on computational Intelligence and Communication systems, CICN 2011

作者： Jain, Shruti Naik, Pradeep K. Bhooshan, Sunil V. Department of Electronics and Communication Engineering Jaypee University of Information Technology Solan-173215 India Department of Biotechnology and Bioinformatics Jaypee University of Information Technology Solan-173215 India

ISBN: (纸本)9780769545875

Signal transduction pathways control cellular responses to stimuli, but it is unclear how molecular information is processed as a network. Large-scale collection and systematization of such data is likely to have a great impact on cell biology as complete genome sequencing has had on genetics. Cell signaling pathways interact with one another to form networks. Such networks are complex in their organization and exhibit emergent properties such as bistability and ultra sensitivity. Analysis of signaling networks requires a combination of experimental and theoretical approaches including the development and analysis of models. This work examines signaling networks that control the survival decision treated with combinations of the pro-death cytokine, tumor necrosis factor-α (TNF), and the pro-survival growth factors, epidermal growth factor (EGF) and insulin. A non linear model using Artificial Neural Network was proposed for cell survival/ death. With this we have made software which is used by doctors in doing chemotherapy without doing any experiments. © 2011 ieee.

关键词： Neural networks

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Towards a pervasive computing enabled modeling environment for integrated coevolving energy systems

Towards a pervasive computing enabled modeling environment f...

引用

2011 EPU-CRIS International conference on Science and Technology, EPU-CRIS 2011

作者： Marathe, Achla Marathe, Madhav V. Kumar, V. S. Anil Network Dynamics and Simulation Science Laboratory Virginia Bioinformatics Institute Virginia Tech. Blacksburg VA 24061 United States

ISBN: (纸本)9783940961693

We present elements of a pervasive computing enabled modeling environment for integrated national energy systems (CI-MINES) to support policy and decision making as it pertains to co-evolving socio-energy systems. Decision support systems built using CI-MINES will provide public policy makers as well as private stakeholders entirely new ways to design and architect next-generation energy systems. When complete, CI-MINES can be used to evaluate the relative merits of competing conceptual architectures for interactive energy grids and markets before substantial investment is made in realizing them. It will also help evaluate new ways to invest in renewable energy sources and assess the reliability and security of the emerging grid architectures. CI-MINES is based on recent computational advances for modeling extremely large, complex, multi-scale socio-technical systems. © 2011 CRIS.

关键词： Decision support systems

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AudioGene: Computer-based prediction of genetic factors involved in non-syndromic hearing impairment

AudioGene: Computer-based prediction of genetic factors invo...

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9th ACS/ieee International conference on Computer systems and Applications, AICCSA 2011

作者： Taylor, Kyle R. DeLuca, Adam P. Goodman, Corey W. Tompkins, Bruce W. Scheetz, Todd E. Hildebrand, Michael S. Huygen, Patrick L. M. Smith, Richard J. H. Braun, Terry A. Casavant, Thomas L. Center for Bioinformatics and Computational Biology University of Iowa Iowa City IA 52242 United States Department of Otolaryngology Head and Neck Surgery University of Iowa Iowa City IA 52242 United States Department of Otorhinolaryngology University Hospital P.O. Box 9101 6500 HB Nijmegen Netherlands

ISBN: (纸本)9781457704741

AudioGene is a software system developed at the University of Iowa to classify and predict gene mutations that indicate causal or increased risk factors of disease. We focus on a concise example - the most likely genetic causes of a particular form of inherited hearing loss - ADNSHL. Whereas the cost and throughput involved in the collection of genomic data have advanced dramatically during the past decade, gathering and interpreting clinical information regarding disease diagnosis remains slow, costly and error-prone. AudioGene employs machine-learning techniques in an iterative procedure to prioritize probable genetic risk factors of disease, which are then verified with a molecular (wet lab) assay. In our current implementation AudioGene achieves 67% first-choice accuracy (versus 23% using a majority classifier). When the top three choices are considered, accuracy increases to 83%. This has numerous implications for reducing the cost of genetic screening as well as increasing the power of novel gene discovery efforts. While AudioGene is focused on hearing loss, the design and underlying mechanisms are generalizable to many other diseases including heart disease, cancer and mental illness. © 2011 ieee.

关键词： Diseases

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Simultaneous identification for synergistic transcription factors and their transcription factor binding sites

Simultaneous identification for synergistic transcription fa...

引用

5th International conference on Complex, Intelligent and Software Intensive systems, CISIS 2011

作者： Tsai, Zing Tsung-Yeh Huang, Grace Tzu-Wei Tsai, Huai-Kuang Institute of Information Science Academia Sinica Taipei 115 Taiwan Bioinformatics Program Taiwan International Graduate Program Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh PA United States Research Center for Information Technology Innovation Taipei 115 Taiwan Computer Science and Engineering National Taiwan Ocean University Keelung 202 Taiwan

ISBN: (纸本)9780769543734

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. © 2011 ieee.

关键词： Yeast

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Predicting non-classical secretory proteins by using Gene Ontology terms and physicochemical properties

Predicting non-classical secretory proteins by using Gene On...

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2011 ieee International conference on Computer Science and Automation Engineering, CSAE 2011

作者： Huang, Wen-Lin Liaw, Chyn Ho, Shinn-Ying Department of Management Information System Asia Pacific Institute of Creativity Miaoli Taiwan Institute of Bioinformatics and Systems Biology National Chiao Tung University Hsinchu 30068 Taiwan

ISBN: (纸本)9781424487257

Eukaryotic secretory proteins that traverse classical ER-Golgi pathway are usually characterized by short N-terminal signal peptides. However, several secretory proteins lacking the signal peptides are found to be exported by a non-classical secretion pathway. Therefore, predicting non-classical secretory proteins regardless of the N-terminal signal peptides is necessary for developing a critical computational approach. Several prediction methods have been proposed by using various types of features to predict secretory proteins. However, prediction performance seems not acceptable. This study proposes an SVM-based prediction method, namely ProSec-iGOX, which uses a major set of informative Gene Ontology (GO) terms and a minor set of assistance features. Physicochemical properties as the assistance features are useful when a query protein sequence without homologous protein with annotated GO terms. Two data sets, S25 and S40, having the identity 25% and 40%, respectively, are adopted for performance comparisons. The ProSec-iGOX yields test accuracies of 95.1% and 96.8% when adopting on the data sets S25 and S40 respectively. The latter accuracy (96.8%) is significantly higher than that of SPRED (82.2%), which uses frequency of tri-peptides and short peptides, secondary structure, physicochemical properties as input features to a random forest classifier. The experimental results show that GO terms are effective features for predicting non-classical secretory proteins. © 2011 ieee.

关键词： Gene Ontology

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Insect navigation and communication in flight and migration: A potential model for joining and collision avoidance in MAVs and mobile robots fleet control

Insect navigation and communication in flight and migration:...

引用

2011 ieee Aerospace conference, AERO 2011

作者： Ma, Zhanshan Krings, Axel W. Millar, Richard Wang, Feng Chao, Jun Computational Biology and Bioinformatics Lab. KIZ Chinese Academy of Sciences China Computer Science Department University of Idaho Moscow ID 83843 United States Department of Systems Engineering Naval Postgraduate School Patuxent River NAS MD United States Computer Science Department Kunming Univ. of Science and Technology Kunming 650223 China Chinese Academy of Sciences Kunming 650223 China Computer Science Dept. iBEST University of Idaho United States

ISBN: (纸本)9781424473502

The human being should be awarded the championship of navigation on the planet, on the virtues that they not only have invented and manufactured the compass, GPS, aircraft, vessel, spacecraft, but also have demonstrated exceptional non-instrumental navigation skills. The Austronesian expansion from the Asian mainland into the Pacific performed by the Pacific navigators, who eventually populated the most remote islands of the Pacific about 4000 years ago, is a vivid example (Wehner 1998). However, animals, especially flying birds and insects are strong contenders. Monarch butterflies can migrate up to 2000 miles from their reproductive sites in the eastern US and Canada to their over-wintering sites in the forests of Mexico, and it is postulated that they may possess a biological equivalent of a low-resolution GPS system that is based on the magnetic field of the earth. In fact, even the long-legged ants (Cataglyphis fortis) in the Saharan desert use the dead-reckoning navigation strategy, which is attributed to the Polynesians, but the ants apparently have acquired the capability much earlier, given the relative short evolutionary history of humans. In this article, we briefly review the state-of-the-art research on insect navigation and communication used in flight and communication, with the objective to inspire cross-disciplinary studies in aerospace engineering, biology and computer science. After a brief review, we overview and identify seven cross-disciplinary research topics that may draw on inspirations from insect navigation and communication in flight and migration. These topics include: ants colony inspired swarm intelligence, honeybee inspired group decision-making, insect sociobiology, MAV/mobile robot flight control and remote control of insect flights, optimal migration strategy, Quorum sensing, and joining and collision avoidance for MAV fleet control. An interesting question one may pose is: given the rich and advanced navigation and communication t

关键词： Global positioning system

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