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检索条件"任意字段=IEEE Computational Systems Bioinformatics Conference"

共 878 条记录，以下是191-200 订阅

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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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Proceedings of the Third ieee International conference on Cognitive Informatics = ICCI 2004

Proceedings of the Third IEEE International Conference on Co...

引用

Proceedings of the Third ieee International conference on Cognitive Informatics, ICCI 2004

ISBN: (纸本)0769521908

The proceedings contain 31 papers from the Proceedings of the Third ieee International conference on Cognitive Informatics ICCI 2004. The topics discussed include: language, logic, and the brain;on autonomous computing and cognitive processes;is entropy suitable to characterize data and signals for cognitive informatics?;on the cognitive informatics foundations of software engineering;a parallel language for cognitive informatics;concept formation and learning: a cognitive informatics perspective;specification of the RTPA grammar and its recognition;formal description of the cognitive process of problem solving;and cognitive bioinformatics: computational cognitive model for dynamic problem solving.

关键词： Cognitive systems

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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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Improve spark-based application performance using bayesian hyperparameter optimization 8

Improve spark-based application performance using bayesian h...

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8th ieee Data Driven Control and Learning systems conference, DDCLS 2019

作者： Li, Kexue Deng, Li Lu, Yakang Wu, Jinda Shanghai Key Laboratory of Power Station Automation Technology Shanghai200072 China

ISBN: (纸本)9781728114545

Metagenomics sequences assembly has an insurmountable obstacle in computational and memory resources limitations. SpaRC, a scalable sequence clustering application using Apache Spark, provides a scalable solution for clustering billions of reads from the next-generation sequencing(NGS) technologies. However, optimizing parameters to achieve better accuracy at this scale becomes very challenging and expensive. Here we explored Bayesian hyperparameter optimization to alleviate this problems by tuning the parameters to achieve near optimal cluster accuracy, without expensive parameter exploration. We report cluster performance on both short reads (Illumina) and long reads (PacBio) sequencing platforms. Results indicates that the methods offers great improvement in clustering performance. We hope insights we gained in this experiment can be generally applied to similar genomics applications based on Spark. © 2019 ieee.

关键词： bioinformatics

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RiboSW - A web server for identifying RNA riboswitches

RiboSW - A web server for identifying RNA riboswitches

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2009 9th ieee International conference on bioinformatics and BioEngineering, BIBE 2009

作者： Chang, Tzu-Hao Liu, Baw-Jhiune Wu, Li-Ching Huang, Hsien-Da Yeh, Chi-Ta Horng, Jorng-Tzong Chang, Cheng-Wei Department of Computer Science and Information Engineering National Central University Jhongli 320 Taiwan Department of Computer Science and Engineering Yuan Ze University Jhongli 320 Taiwan Institute of Systems Biology and Bioinformatics National Central University Jhongli 320 Taiwan Department of Biological Science and Technology Institute of Bioinformatics National Chiao-Tung University Hsinchu 300 Taiwan Department of Computer Science and Information Engineering National Central University Jhongli Taiwan Department of Bioinformatics Asia University Wufeng Taiwan Department of Information Management Hsing Wu College LinKou 224 Taiwan

ISBN: (纸本)9780769536569

Riboswitches are cis-acting genetic regulatory elements within a specific mRNA, and can regulate both transcription and translation by interacting with their corresponding metabolites. Recently, more and more riboswitches were identified and investigated about their roles in regulatory functions in different species. Both of the sequence contexts and structural conformations are important characteristics of riboswitches. None of previous developed tools, such Covariance Models (CMs), Riboswitch finder, and RibEx, provides a web server for efficiently searching homologous instances to known riboswitches and considers two crucial characteristics of each riboswitch, such as structural conformations and sequence contexts of functional regions. Therefore, we developed a systematic method to identify twelve kinds of riboswitches. The method is implemented and provided as a web server, RiboSW, to efficiently and conveniently identify riboswitches within messenger RNA sequences. RiboSW is now available on the web at http://***/RiboSW/. The predictive accuracy of the proposed method is comparable with other previous tools. The efficiency of the proposed method for identifying riboswitches was improved in order to achieve a reasonable computational time required for the prediction. That makes it possible to have an accurate and convenient web server for biologists to obtain their analyzing results in a given mRNA sequence. The supplementary data is available on the web at http://***/ RiboSW/***. © 2009 ieee.

关键词： RNA

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Abstracts of the Controlling Complexity Workshop

Abstracts of the Controlling Complexity Workshop

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Proceedings of the ieee computational systems bioinformatics conference, CSB

Summary form only given. Presents a series of abstracts from the conference proceedings.

关键词： bioinformatics Biology computing computational modeling Biological system modeling Distributed computing Computer vision

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Profilins, formins and katanins as flagellar proteins of Leishmania spp.: A genome-based, multi-step bioinformatics-driven description

Profilins, formins and katanins as flagellar proteins of Lei...

引用

7th ieee International conference on bioinformatics and Bioengineering, BIBE

作者： Vasconcelos, Elton J. R. Pacheco, Ana C. L. Gouveia, João J. S. Araújo, Fabiana F. Diniz, Michely C. Kamimura, Michel T. Costa, Marcília P. Maggioni, Rodrigo Araújo-Filho, Raimundo Costa, Raimundo B. De Oliveira, Diana Magalhães Núcleo Tarcísio Pimenta de Pesquisa Genômica e Bioinformáitica - NUGEN Universidade Estadual do Ceará - UECE Fortaleza Ceará Brazil

ISBN: (纸本)1424415098

Flagellum plays a key role in Leishmania motility and sensory reception, and it is essential for parasite migration, invasion and persistence on host tissues. In search for genomic and/or proteomic evidences of flagellar genes/proteins in Leishmania spp., we have used available databases and computational biology tools to predict and distinguish putative flagellar proteins that are either actin-, tubulin-, axoneme- or microtubule-related sequences and, also, probable virulence factors. Here we present results of sequence and structural analyses of profilins, formins and katanins as possible flagellar proteins of Leishmania spp., whose sequences were in silico selected for predicting viable roles on flagellum assembly, disassembly and dynamics in terms of intraflagellar mechanisms. Taken together, our results provide the filrst integrated bioinformatics analyses of Leishmania profilin, katanin and formin genes and their gene products to contribute to a more detailed annotation of these important actin-related proteins not yet properly characterized in flagellate trypanosomatids or in their flagellar activities towards virulence. ©2007 ieee.

关键词： bioinformatics

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Using Supervised Machine Learning Algorithms For Drug Target Interaction Prediction

Using Supervised Machine Learning Algorithms For Drug Target...

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2022 Innovations in Intelligent systems and Applications conference, ASYU 2022

作者： Yildiz, Nilay Fatma Ozcan, Alper Akdeniz University Department of Computer Engineering Antalya Turkey

ISBN: (数字)9781665488945

ISBN: (纸本)9781665488945

In conjunction with the advent of bioinformatics, the evolution occurred in the field of drug discovery worldwide. In the literature numerous machine learning (ML), deep learning, and graph theory approaches have been implemented for drug discovery tasks. However, the drug-target interaction (DTI) problem for the existing and new drugs has been anticipated for a long time in drug repurposing and drug discovery areas. The proposed study predicts the drug-target interactions and to achieve this, a computational pipeline has been developed for the heterogeneous network. Firstly, this study obtains the low dimensional vector for the graphical nodes using the node2vec method. Secondly, multiple machine learning methods have been applied to predict drug-target interactions. Lastly, for the evaluation of the proposed models, we calculated the AUROC and AUPRC values and the obtained results indicate that non-linear SVM and Logistic regression performed better than other models with the AUROC, and AUPRC values of 0.8317 and 0.8260 respectively. © 2022 ieee.

关键词： bioinformatics

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Abstracts of the BioSPICE Workshop

Abstracts of the BioSPICE Workshop

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Proceedings of the ieee computational systems bioinformatics conference, CSB

Summary form only given. Presents a series of abstracts from the conference proceedings.

关键词： Computer aided software engineering Clustering methods Intelligent structures Clustering algorithms Prediction algorithms computational intelligence bioinformatics

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Predicting conserved domain and structural variations of prenyl transferase sequence variants in Triticum urartu

Predicting conserved domain and structural variations of pre...

引用

2016 International conference on bioinformatics and systems Biology, BSB 2016

作者： Sagar, Mamta Ramteke, Pramod Wasudev Kumar Yadav, Arvind Department of Computational Biology and Bioinformatics Jacob Institute of Biotechnology and Bioengineering Sam Higginbottom Institute of Agriculture Technology and Sciences Allahabad India Department of Bioinformatics University Institute of Engineering and Technology Chhatrapati Shahu Ji Maharaj University Kanpur India Department of Biological Science School of Basic Science Sam Higginbottom Institute of Agriculture Technology and Sciences Allahabad India

ISBN: (纸本)9781509022618

Prenyl transferase enzyme is widely distributed among plants. This enzyme catalyses prenylation reaction, that leads to increased flavonoid's activity. In this research, highly conserved polyprenyl patterns have been analysed in plants. Prenyl transferase in Triticum urartu, Oryza sativa japonica and Zea mays share presence of conserved motif LIhDDviDdsgmRRG. This protein share the presence of motif LVlDDimDnsqtRRG in Lupinus albus and Phaseolus vulgaris, both motifs belong to polyprenyl signature 1. Prenyl transferase of Triticum urartu do not contain polyprenyl signature 2. Here, polyprenyl signature 2 motif has been inserted into the protein of Triticum urartu at 273 position, which was extracted from above plants. Structural variations have been analysed using homology modelling after insertion of LGlsFQVvDDIlD and MGtyFQVqDDYlD motifs into protein of Triticum urartu. Modifications in protein do not show any unfavourable changes or disruption in structure. Analysis of Conserved domain Trans-Isoprenyl Diphosphate Synthases shows presence of enhanced substrate binding pocket, catalytic residues in modified Prenyl Transferase. © 2016 ieee.

关键词： Enzymes

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