High Performance Computational Solutions In Protein Bioinformatics
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| Author | : Dariusz Mrozek |
| Publisher | : Springer |
| Total Pages | : 120 |
| Release | : 2014-06-04 |
| Genre | : Computers |
| ISBN | : 3319069713 |
Recent developments in computer science enable algorithms previously perceived as too time-consuming to now be efficiently used for applications in bioinformatics and life sciences. This work focuses on proteins and their structures, protein structure similarity searching at main representation levels and various techniques that can be used to accelerate similarity searches. Divided into four parts, the first part provides a formal model of 3D protein structures for functional genomics, comparative bioinformatics and molecular modeling. The second part focuses on the use of multithreading for efficient approximate searching on protein secondary structures. The third and fourth parts concentrate on finding 3D protein structure similarities with the support of GPUs and cloud computing. Parts three and four both describe the acceleration of different methods. The text will be of interest to researchers and software developers working in the field of structural bioinformatics and biomedical databases.
| Author | : Bertil Schmidt |
| Publisher | : CRC Press |
| Total Pages | : 425 |
| Release | : 2010-07-15 |
| Genre | : Computers |
| ISBN | : 1439858365 |
New sequencing technologies have broken many experimental barriers to genome scale sequencing, leading to the extraction of huge quantities of sequence data. This expansion of biological databases established the need for new ways to harness and apply the astounding amount of available genomic information and convert it into substantive biological
| Author | : Albert Y. Zomaya |
| Publisher | : John Wiley & Sons |
| Total Pages | : 817 |
| Release | : 2006-04-21 |
| Genre | : Computers |
| ISBN | : 0471718483 |
Discover how to streamline complex bioinformatics applications with parallel computing This publication enables readers to handle more complex bioinformatics applications and larger and richer data sets. As the editor clearly shows, using powerful parallel computing tools can lead to significant breakthroughs in deciphering genomes, understanding genetic disease, designing customized drug therapies, and understanding evolution. A broad range of bioinformatics applications is covered with demonstrations on how each one can be parallelized to improve performance and gain faster rates of computation. Current parallel computing techniques and technologies are examined, including distributed computing and grid computing. Readers are provided with a mixture of algorithms, experiments, and simulations that provide not only qualitative but also quantitative insights into the dynamic field of bioinformatics. Parallel Computing for Bioinformatics and Computational Biology is a contributed work that serves as a repository of case studies, collectively demonstrating how parallel computing streamlines difficult problems in bioinformatics and produces better results. Each of the chapters is authored by an established expert in the field and carefully edited to ensure a consistent approach and high standard throughout the publication. The work is organized into five parts: * Algorithms and models * Sequence analysis and microarrays * Phylogenetics * Protein folding * Platforms and enabling technologies Researchers, educators, and students in the field of bioinformatics will discover how high-performance computing can enable them to handle more complex data sets, gain deeper insights, and make new discoveries.
| Author | : Naiara Rodríguez-Ezpeleta |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 258 |
| Release | : 2011-10-26 |
| Genre | : Science |
| ISBN | : 1461407826 |
Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.
| Author | : Dariusz Mrozek |
| Publisher | : Springer |
| Total Pages | : 331 |
| Release | : 2018-09-25 |
| Genre | : Computers |
| ISBN | : 3319988395 |
This book presents a focus on proteins and their structures. The text describes various scalable solutions for protein structure similarity searching, carried out at main representation levels and for prediction of 3D structures of proteins. Emphasis is placed on techniques that can be used to accelerate similarity searches and protein structure modeling processes. The content of the book is divided into four parts. The first part provides background information on proteins and their representation levels, including a formal model of a 3D protein structure used in computational processes, and a brief overview of the technologies used in the solutions presented in the book. The second part of the book discusses Cloud services that are utilized in the development of scalable and reliable cloud applications for 3D protein structure similarity searching and protein structure prediction. The third part of the book shows the utilization of scalable Big Data computational frameworks, like Hadoop and Spark, in massive 3D protein structure alignments and identification of intrinsically disordered regions in protein structures. The fourth part of the book focuses on finding 3D protein structure similarities, accelerated with the use of GPUs and the use of multithreading and relational databases for efficient approximate searching on protein secondary structures. The book introduces advanced techniques and computational architectures that benefit from recent achievements in the field of computing and parallelism. Recent developments in computer science have allowed algorithms previously considered too time-consuming to now be efficiently used for applications in bioinformatics and the life sciences. Given its depth of coverage, the book will be of interest to researchers and software developers working in the fields of structural bioinformatics and biomedical databases.
| Author | : Nenad Filipovic |
| Publisher | : Springer |
| Total Pages | : 169 |
| Release | : 2021-03-12 |
| Genre | : Technology & Engineering |
| ISBN | : 9783030436605 |
This book explores the latest and most relevant topics in the field of computational bioengineering and bioinformatics, with a particular focus on patient-specific, disease-progression modeling. It covers computational methods for cardiovascular disease prediction, with an emphasis on biomechanics, biomedical decision support systems, data mining, personalized diagnostics, bio-signal processing, protein structure prediction, biomedical image processing, analysis and visualization, and high-performance computing. It also discusses state-of-the-art tools for disease characterization, and recent advances in areas such as biomechanics, cardiovascular engineering, patient-specific modeling, population-based modeling, multiscale modeling, image processing, data mining, biomedical decision-support systems, signal processing, biomaterials and dental biomechanics, tissue and cell engineering, computational chemistry and high-performance computing. As such, it is a valuable resource for researchers, medical and bioengineering students, and medical device and software experts
| Author | : Bryan P. Bergeron |
| Publisher | : Prentice Hall Professional |
| Total Pages | : 472 |
| Release | : 2003 |
| Genre | : Computers |
| ISBN | : 9780131008250 |
Comprehensive and concise, this handbook has chapters on computing visualization, large database designs, advanced pattern matching and other key bioinformatics techniques. It is a practical guide to computing in the growing field of Bioinformatics--the study of how information is represented and transmitted in biological systems, starting at the molecular level.
| Author | : Rabinarayan Satpathy |
| Publisher | : John Wiley & Sons |
| Total Pages | : 433 |
| Release | : 2021-01-20 |
| Genre | : Computers |
| ISBN | : 111978560X |
Machine learning techniques are increasingly being used to address problems in computational biology and bioinformatics. Novel machine learning computational techniques to analyze high throughput data in the form of sequences, gene and protein expressions, pathways, and images are becoming vital for understanding diseases and future drug discovery. Machine learning techniques such as Markov models, support vector machines, neural networks, and graphical models have been successful in analyzing life science data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. Machine Learning in Bioinformatics compiles recent approaches in machine learning methods and their applications in addressing contemporary problems in bioinformatics approximating classification and prediction of disease, feature selection, dimensionality reduction, gene selection and classification of microarray data and many more.
| Author | : Carlos Jaime Barrios Hernández |
| Publisher | : Springer |
| Total Pages | : 418 |
| Release | : 2017-04-28 |
| Genre | : Computers |
| ISBN | : 331957972X |
This book constitutes the proceedings of the Third Latin American Conference on High Performance Computing, CARLA 2016, held in Mexico City, Mexico, in August/September 2016. The 30 papers presented in this volume were carefully reviewed and selected from 70 submissions. They are organized in topical sections named: HPC Infrastructure and Applications; Parallel Algorithms and Applications; HPC Applications and Simulations.
| Author | : R. Meersman |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 905 |
| Release | : 2004-10-14 |
| Genre | : Computers |
| ISBN | : 3540236643 |
This book constitutes the joint refereed proceedings of seven international workshops held as part of OTM 2004 in Agia Napa, Cyprus in October 2004. The 73 revised papers presented together with 31 abstracts of posters from the OTM main conferences were carefully reviewed and selected from more than 150 submissions. In accordance with the 7 workshops, the papers are organized in topical sections on grid computing and its applications to data analysis; Java technologies for real-time and embedded systems; modeling inter-organizational systems; regulatory ontologies; ontologies, semantics and e-learning; PhD symposium; and interoperability.
