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ieee International conference on bioinformatics and Biomedicine - Medical Informatics and Decision Making

作者： Guimaraes, Valeria Hondo, Fernanda Almeida, Rodrigo Vera, Harley Holanda, Maristela Araujo, Aleteia Walter, Maria Emilia Lifschitz, Sergio Univ Brasilia Dept Comp Sci Brasilia DF Brazil Pontifical Catholic Univ Rio de Janeiro Dept Informat Rio De Janeiro Brazil

ISBN: (纸本)9781467367981

this work considers a scientific experiment as a computational workflow. Provenance models store details of each workflow execution, including produced data, computational tools parameters and their versions, among others. This way, scientists can review details of a particular workflow execution, compare information generated among different executions and plan new ones efficiently. In the bioinformatics domain, particularly in the presence of large volumes of data, persistency of those data generated during the workflow execution is still a research challenge. In this article, we consider a study on provenance data storage for bioinformatics in a document-oriented NoSQL database system. We present data modeling issues and discuss an actual implementation into MongoDB.

关键词： provenance workflow genomics bioinformatics data modeling NoSQL MongoDB

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Development and assessment of bioinformatics tools for species conservation and habitat management 2

Development and assessment of bioinformatics tools for speci...

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2nd International computational systems bioinformatics conference

作者： Sutton, MA Deneke, L Eme, J Bennett, W Wray, F Univ W Florida Dept Biol Pensacola FL 32514 USA

ISBN: (纸本)0769520006

This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of sensitive habitats. We specifically developed bioinformatics tools for the study of (1) beach mouse communities and (2) marginal fish habitats. Data mining was used in these projects to intelligently query databases and to elucidate broad patterns that facilitate overall data interpretation. Visualization techniques that were developed present mined data in ways where context, perceptual cues, and spatial reasoning skills can be applied to uncover significant trends in behavioral patterns, habitat use, species diversity, and community composition.

关键词： Data visualization

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Neural Network based Cloud computing Platform for bioinformatics

Neural Network based Cloud computing Platform for Bioinforma...

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9th Annual conference on ieee Long Island systems, Applications and Technology (LISAT)

作者： Ikram, Ataul Aziz Ibrahim, Salma Sardaraz, Muhammad Tahir, Muhammad Bajwa, Hassan Bach, Christian Iqra Univ Dept Comp & Technol Islamabad 44000 Pakistan Univ Bridgeport Dept Biomed Engn Bridgeport CT 06604 USA Univ Bridgeport Dept Elect Engn Bridgeport CT 06604 USA

ISBN: (纸本)9781467362443

Advances in genomics, proteomics, and bioinformatics have revolutionized the drug discovery and drug development. computational systems biology, computational bioinformatics, and many biomedical applications are also growing at a rapid pace with an increasing demand for processing power. Hardware clusters and grid computing solutions are approached to fulfill the high demand for the processing power. The grid clusters approach proved success but introduced the need of frameworks to hide the complexity of parallel programming and enable the programmer to focus on the application logic. In this paper we present a novel cloud computing based neural network framework. We will further present results of implementation of Multiple Sequence Alignment (MSA) algorithms in cloud architecture. The experiments show optimal results in terms of computational complexity and preserve accuracy as well.

关键词： component Artificial Neural Networks Cloud Computing bioinformatics

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Advances in neural networks research: An introduction

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NEURAL NETWORKS 2009年第5-6期22卷 489-490页

作者： Kozma, Robert Bressler, Steven Perlovsky, Leonid Venayagamoorthy, Ganesh Kumar Univ Memphis FedEx Inst Technol Memphis TN 38152 USA Florida Atlantic Univ Boca Raton FL 33431 USA Harvard Univ Cambridge MA 02138 USA Missouri Sci & Technol Univ Rolla MO USA

The present Special Issue "Advances in Neural Networks Research: IJCNN2009" provides a state-of-art overview of the field of neural networks. It includes 39 papers from selected areas of the 2009 International joint conference on Neural Networks (IJCNN2009). IJCNN2009 took place on June 14-19, 2009 in Atlanta, Georgia, USA, and it represents an exemplary collaboration between the International Neural Networks Society and the ieee computational Intelligence Society. Topics in this issue include neuroscience and cognitive science, computational intelligence and machine learning, hybrid techniques, nonlinear dynamics and chaos, various soft computing technologies, intelligent signal processing and pattern recognition, bioinformatics and biomedicine, and engineering applications. (C) 2009 Elsevier Ltd. All rights reserved.

关键词： Neuroscience Cognition Machine Learning Hybrid systems Soft Computing Dynamic systems Image Processing bioinformatics Robotics Power systems

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On discriminating a TATA-box from putative TATA boxes: A case study using plant genome

On discriminating a TATA-box from putative TATA boxes: A cas...

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2005 ieee computational systems bioinformatics conference, Workshops and Poster Abstracts

作者： Loganantharaj, Raja Bioinformatics Research Lab. Center for Advanced Computer Studies University of Louisiana Lafayette

ISBN: (纸本)0769524427

Prediction of a promoter is one of the many active areas of bioinformatics. The outcome of a promoter detection algorithm is directly or indirectly influenced by the success of identifying the location of a TATA box in a promoter sequence. A profiling technique is very often used to find putative TATA boxes, but discriminating a TATA box from putative TATA boxes is still a challenging problem. In this work, we formulate the problem and provide solutions using both a linear and a non linear classifiers. © 2005 ieee.

关键词： Genes

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A Formative Usability Study to Improve Prescriptive systems for bioinformatics Big Data

A Formative Usability Study to Improve Prescriptive Systems ...

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ieee International conference on bioinformatics and Biomedicine (ieee BIBM)

作者： Singh, Kanupriya Li, Shangman Jahnke, Isa Pandey, Ashish Lyu, Zhen Joshi, Trupti Calyam, Prasad Univ Missouri Sch Informat Sci & Learning Technol Columbia MO 65211 USA Univ Missouri Dept Elect Engn & Comp Sci Columbia MO 65211 USA Univ Missouri Dept Hlth Management & Informat Columbia MO 65211 USA

ISBN: (纸本)9781728162157

Big data computation tools are vital for researchers and educators from various domains such as plant science, animal science, biomedical science and others. With the growing computational complexity of biology big data, advanced analytic systems, known as prescriptive systems, are being built using machine learning models to intelligently predict optimum computation solutions for users for better data analysis. However, lack of user-friendly prescriptive systems poses a critical roadblock to facilitating informed decision-making by users. In this paper, we detail a formative usability study to address the complexities faced by users while using prescriptive systems. Our usability research approach considers bioinformatics workflows and community cloud resources in the KBCommons framework's science gateway. The results show that recommendations from usability studies performed in iterations during the development of prescriptive systems can improve user experience, user satisfaction and help novice as well as expert users to make decisions in a well-informed manner.

关键词： Usability User experience bioinformatics Big data Prescriptive analytics Cloud solution

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Sesame: A New bioinformatics Semantic Workflow Design System

Sesame: A New Bioinformatics Semantic Workflow Design System

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ieee International conference on bioinformatics and Biomedicine (ieee BIBM)

作者： Zhang, Lu Wang, Yunsheng Xuan, Pengfei Duvall, Alexander Lowe, Jonathan Wang, Yanyan Subramanian, Arvind Srimani, Pradip K. Luo, Feng Duan, Yongping Clemson Univ Sch Comp Clemson SC 29634 USA Hunan Agr Univ Coll Plant Protection Changsha 410128 Hunan Peoples R China US Horticultural Res Lab Agr Res Serv Ft Pierce FL 34945 USA

ISBN: (纸本)9781479913091;9781479913107

Biologists have become increasingly dependent on bioinformatics tools to analyze and interpret their datasets. The number, variety and complexity of these bioinformatics tools have increased dramatically and they have become more and more computationally complex, expensive and resource intensive. Powerful workflow design systems have been developed to automate the execution of set of tools for a specific task. However, designing a complex executable workflow using such tools still requires considerable computational expertise or the help from a bioinformatics expert. In this paper, we developed Sesame, a bioinformatics semantic workflow design system. We have designed a new ontology for bioinformatics tools and services (OBTS) and proposed an ontology driven semantic workflow design mechanism, using this new OBTS. Compared to an executable workflow, the semantic workflow is at the level of biological concepts that are closer to the scientific research. Biologists will greatly benefit from the decoupling of semantic workflow design from executable workflow design with computational implementation details. Currently, a prototype version of Sesame system has been implemented and deployed. Sesame will allow biologists to efficiently perform complex data analysis to address scientific questions.

关键词： semantic workflow design bioinformatics

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Data Provenance Management for bioinformatics Workflows using NoSQL Database systems in a Cloud Computing Environment

Data Provenance Management for Bioinformatics Workflows usin...

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Biological Ontologies and Knowledge Bases Workshop at ieee International conference on bioinformatics and Biomedicine (ieee BIBM)

作者： Hondo, Fernanda Wercelens, Polyane da Silva, Waldeyr Castro, Klayton Santana, Ingrid Walter, Maria Emilia Araujo, Aleteia Holanda, Maristela Lifschitz, Sergio Univ Brasilia Dept Comp Sci Brasilia DF Brazil Pontificia Catolica Univ Rio de Janeiro Informat Dept Rio De Janeiro Brazil

ISBN: (纸本)9781509030507

Computer science solutions for molecular biology problems are often presented in the form of workflows. There is a set of activities performed by different processing entities through managed tasks. Knowledge about the data trajectory throughout a given workflow enables reproducibility by data provenance. In order to reproduce an in silico bioinformatics experiment one must consider other aspects besides those steps followed by a workflow. Indeed, the computational settings in which the involved programs run is a requirement for reproducibility. Cloud computing technology may hide the technical details and make it easier for the user to set up such an ondemand environment. NoSQL database systems have also gained popularity, particularly in the cloud. Considering this particular scenario, we have planned and executed a research study about a bioinformatics workflow running in an IaaS cloud computing environment. We have persisted provenance data according to the PROV-DM model, using different types of NoSQL database systems. We present in this paper some preliminary results from our reseach work, where we have explored the characteristics of several NoSQL database systems to persist provenance data.

关键词： bioinformatics workflows cloud computing NoSQL data provenance

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Towards Reproducible bioinformatics: The OpenBio-C Scientific Workflow Environment 19

Towards Reproducible Bioinformatics: The OpenBio-C Scientifi...

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19th Annual ieee International conference on bioinformatics and Bioengineering (BIBE)

作者： Kanterakis, Alexandros Iatraki, Galateia Pityanou, Konstantina Koumakis, Lefteris Kanakaris, Nikos Karacapilidis, Nikos Potamias, George FORTH Inst Comp Sci Iraklion Greece Hellen Mediterranean Univ Heraklion Dept Elect & Comp Engn Iraklion Greece Univ Patras MEAD Ind Management & Informat Syst Lab Patras Greece

ISBN: (纸本)9781728146171

The highly competitive environment of post-genomics biomedical research is pushing towards the production of highly qualified results and their utilization in clinical practice. Due to this pressure, an important factor of scientific progress has been underestimated namely, the reproducibility of the results. To this end, it is critical to design and implement computational platforms that enable seamless and unhindered access to distributed bio-data, software and computational infrastructures. Furthermore, the need to support collaboration and form synergistic activities between the engaged researchers is also raised, as the mean to achieve consensus on respective scientific discoveries. The aforementioned needs and requirements underlie the motivations for the development of OpenBio-C workflow environment, and determine its fundamental objectives. The insufficiencies of current workflow editing and execution environments are explored, and the key-directions to advance over an environment that supports reproducibility are stated. The basic components and functionality of the OpenBio-C initial implementation (beta version) are detailed.

关键词： bioinformatics scientific workflows collaborative systems open science

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Guest Editors' Introduction to the Special Section on the 14th International conference on computational Methods in systems Biology (CMSB 2016)

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ieee-ACM TRANSACTIONS ON computational BIOLOGY AND bioinformatics 2018年第4期15卷 1122-1123页

作者： Bartocci, Ezio Lio, Pietro Paoletti, Nicola Vienna Univ Technol Fac Informat Treitlstr 3 A-1040 Vienna Austria Univ Cambridge Dept Comp Sci & Technol William Gates Bldg15 JJ Thomson Ave Cambridge CB3 0FD England SUNY Stony Brook Dept Comp Sci Stony Brook NY 11794 USA

No abstract available.

关键词： Special issues and sections Meetings computational biology

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