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Accelerating Molecular Docking And Binding Site Mapping Using Fpgas And Gpus
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Book Synopsis Accelerating Molecular Docking and Binding Site Mapping Using FPGAs and GPUs by : Bharat Sukhwani
Download or read book Accelerating Molecular Docking and Binding Site Mapping Using FPGAs and GPUs written by Bharat Sukhwani and published by . This book was released on 2011 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Computational accelerators such as Field Programmable Gate Arrays (FPGAs) and Graphics Processing Units (GPUs) possess tremendous compute capabilities and are rapidly becoming viable options for effective high performance computing (HPC). In addition to their huge computational power, these architectures provide further benefits of reduced size and power dissipation. Despite their immense raw capabilities, achieving overall high performance for production HPC applications remains challenging due to programmability, lack of parallelism in existing codes, poor resource utilization, and communication overheads. In this dissertation, we present methods for the effective use of these platforms for the acceleration of two production molecular modeling applications: molecular docking and binding site mapping. Molecular docking refers to the computational prediction of the structure of the intermolecular complex formed when two independent proteins interact. Binding site mapping, on the other hand, aims at finding the region on the surface of a protein that is likely to bind a small molecule with high affinity. Docking and mapping find application in drug discovery which involves docking-based screening of millions of drug candidates for a given protein target; mapping helps identify the site on the protein where the binding is likely to occur, thus limiting the docking-based search to a small region. Both docking and binding site mapping are computationally very demanding, requiring many hours to days on a serial processor. This makes it impractical for biologists to run them interactively on their desktop computers; production docking and mapping programs typically run in batch on large clusters. In this dissertation, we present the FPGA and CPU based acceleration of the production molecular docking program PIPER and the production binding site mapping program FTMap, enabling desktop based molecular modeling solutions which are fast and cost effective as well as more power efficient. The proposed FPGA-docking algorithms achieve multi-hundred-fold speedup of the code that represents over 95% of the original run-time, resulting in 36x overall speedup for small molecule docking. For effective docking of large molecules, we propose CPU accelerated docking algorithms which result in an overall speedup of 18x. The acceleration of mapping computations on FPGAs and CPUs poses further challenges for two reasons: the process is iterative, with relatively little computation per iteration, and a large fraction of the computation is serial. We address these issues on the FPGAs by creating highly customized, deeply pipelined processors. On GPUs, we introduce two new data structures that enable effective parallelization. The result using the GPUs is 6x to 28x speedup on different parts of the algorithm, with an overall speedup for FTMap of 13x. The FPGA-accelerated algorithms obtain 42x performance improvements on the core computations, resulting in an overall speedup of 30x. Many of the proposed algorithms and hardware structures are general and can vii be applied to a variety of other applications, both in the field of molecular modeling as well as other domains such as object recognition, n-body simulations and full-field biomechanics deformation and strain-measurement.
Book Synopsis Proceedings of the 5th International Workshop on OpenCL. by : Simon McIntosh-Smith
Download or read book Proceedings of the 5th International Workshop on OpenCL. written by Simon McIntosh-Smith and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Boost C++ Libraries by : Boris Schäling
Download or read book The Boost C++ Libraries written by Boris Schäling and published by Boris Schäling. This book was released on with total page 720 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of The Boost C++ Libraries introduces 72 Boost libraries that provide a wide range of useful capabilities. They help you manage memory and process strings more easily. They provide containers and other data structures that go well beyond what the standard library offers. They make it easy to build platform-independent network applications. Simply put, these 72 libraries greatly expand your C++ toolbox. The second edition contains more than 430 examples. All examples are as short as possible, but they are complete, so you can compile and run them as is. They show you what the Boost libraries offer and give you a head start on using the libraries in your own applications. The goal of this book is to increase your efficiency as a C++ developer and to simplify software development with C++. The Boost libraries introduced in this book will help you write less code with fewer bugs and finish projects faster. You code will be more concise and self-explanatory and more easily adapted when requirements change. The second edition is based on the Boost libraries 1.55.0 and 1.56.0 with the latter version having been released in August 2014. The examples are based on C++11 and have been tested with Visual Studio 2013, GCC 4.8 and Clang 3.3 on various platforms. For Boost libraries which were incorporated into the C++11 standard library, differences between Boost and the standard library are highlighted. The Boost libraries are one of the most important and influential open source C++ libraries. Their source code is available under a permissive free software license. Several Boost libraries have been incorporated into the C++11 standard library. The Boost libraries are developed and supported by the Boost community - a worldwide developer community with a strong interest in pushing C++ boundaries further.
Book Synopsis High Performance Computing by : Michela Taufer
Download or read book High Performance Computing written by Michela Taufer and published by Springer. This book was released on 2016-10-05 with total page 710 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes revised selected papers from 7 workshops that were held in conjunction with the ISC High Performance 2016 conference in Frankfurt, Germany, in June 2016. The 45 papers presented in this volume were carefully reviewed and selected for inclusion in this book. They stem from the following workshops: Workshop on Exascale Multi/Many Core Computing Systems, E-MuCoCoS; Second International Workshop on Communication Architectures at Extreme Scale, ExaComm; HPC I/O in the Data Center Workshop, HPC-IODC; International Workshop on OpenPOWER for HPC, IWOPH; Workshop on the Application Performance on Intel Xeon Phi – Being Prepared for KNL and Beyond, IXPUG; Workshop on Performance and Scalability of Storage Systems, WOPSSS; and International Workshop on Performance Portable Programming Models for Accelerators, P3MA.
Book Synopsis Deep Learning in Biology and Medicine by : Davide Bacciu
Download or read book Deep Learning in Biology and Medicine written by Davide Bacciu and published by World Scientific Publishing Europe Limited. This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology, medicine and biochemistry have become data-centric fields for which Deep Learning methods are delivering groundbreaking results. Addressing high impact challenges, Deep Learning in Biology and Medicine provides an accessible and organic collection of Deep Learning essays on bioinformatics and medicine. It caters for a wide readership, ranging from machine learning practitioners and data scientists seeking methodological knowledge to address biomedical applications, to life science specialists in search of a gentle reference for advanced data analytics.With contributions from internationally renowned experts, the book covers foundational methodologies in a wide spectrum of life sciences applications, including electronic health record processing, diagnostic imaging, text processing, as well as omics-data processing. This survey of consolidated problems is complemented by a selection of advanced applications, including cheminformatics and biomedical interaction network analysis. A modern and mindful approach to the use of data-driven methodologies in the life sciences also requires careful consideration of the associated societal, ethical, legal and transparency challenges, which are covered in the concluding chapters of this book.
Book Synopsis Parallel Computing by : Christian Bischof
Download or read book Parallel Computing written by Christian Bischof and published by IOS Press. This book was released on 2008 with total page 824 pages. Available in PDF, EPUB and Kindle. Book excerpt: ParCo2007 marks a quarter of a century of the international conferences on parallel computing that started in Berlin in 1983. The aim of the conference is to give an overview of the developments, applications and future trends in high-performance computing for various platforms.
Book Synopsis High-Performance Modelling and Simulation for Big Data Applications by : Joanna Kołodziej
Download or read book High-Performance Modelling and Simulation for Big Data Applications written by Joanna Kołodziej and published by Springer. This book was released on 2019-03-25 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications.
Book Synopsis Systems Biology by : Lilia Alberghina
Download or read book Systems Biology written by Lilia Alberghina and published by Springer Science & Business Media. This book was released on 2007-10-04 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: For life to be understood and disease to become manageable, the wealth of postgenomic data now needs to be made dynamic. This development requires systems biology, integrating computational models for cells and organisms in health and disease; quantitative experiments (high-throughput, genome-wide, living cell, in silico); and new concepts and principles concerning interactions. This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies. The benefits for industry, such as the new network-based drug-target design validation, and testing, are also presented.
Book Synopsis Special Topics in Information Technology by : Barbara Pernici
Download or read book Special Topics in Information Technology written by Barbara Pernici and published by Springer Nature. This book was released on 2019-10-01 with total page 135 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book presents nine outstanding doctoral dissertations in Information Technology from the Department of Electronics, Information and Bioengineering, Politecnico di Milano, Italy. Information Technology has always been highly interdisciplinary, as many aspects have to be considered in IT systems. The doctoral studies program in IT at Politecnico di Milano emphasizes this interdisciplinary nature, which is becoming more and more important in recent technological advances, in collaborative projects, and in the education of young researchers. Accordingly, the focus of advanced research is on pursuing a rigorous approach to specific research topics starting from a broad background in various areas of Information Technology, especially Computer Science and Engineering, Electronics, Systems and Controls, and Telecommunications. Each year, more than 50 PhDs graduate from the program. This book gathers the outcomes of the nine best theses defended in 2018-19 and selected for the IT PhD Award. Each of the nine authors provides a chapter summarizing his/her findings, including an introduction, description of methods, main achievements and future work on the topic. Hence, the book provides a cutting-edge overview of the latest research trends in Information Technology at Politecnico di Milano, presented in an easy-to-read format that will also appeal to non-specialists.
Book Synopsis Bibliography of Publications by : George Washington University. Human Resources Research Office
Download or read book Bibliography of Publications written by George Washington University. Human Resources Research Office and published by . This book was released on 1965 with total page 42 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Software Tools and Algorithms for Biological Systems by : Hamid Arabnia
Download or read book Software Tools and Algorithms for Biological Systems written by Hamid Arabnia and published by Springer Science & Business Media. This book was released on 2011-03-23 with total page 776 pages. Available in PDF, EPUB and Kindle. Book excerpt: “Software Tools and Algorithms for Biological Systems" is composed of a collection of papers received in response to an announcement that was widely distributed to academicians and practitioners in the broad area of computational biology and software tools. Also, selected authors of accepted papers of BIOCOMP’09 proceedings (International Conference on Bioinformatics and Computational Biology: July 13-16, 2009; Las Vegas, Nevada, USA) were invited to submit the extended versions of their papers for evaluation.
Book Synopsis Intelligent Computing and Innovation on Data Science by : Sheng-Lung Peng
Download or read book Intelligent Computing and Innovation on Data Science written by Sheng-Lung Peng and published by Springer Nature. This book was released on 2020-05-14 with total page 796 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers both basic and high-level concepts relating to the intelligent computing paradigm and data sciences in the context of distributed computing, big data, data sciences, high-performance computing and Internet of Things. It is becoming increasingly important to develop adaptive, intelligent computing-centric, energy-aware, secure and privacy-aware systems in high-performance computing and IoT applications. In this context, the book serves as a useful guide for industry practitioners, and also offers beginners a comprehensive introduction to basic and advanced areas of intelligent computing. Further, it provides a platform for researchers, engineers, academics and industrial professionals around the globe to showcase their recent research concerning recent trends. Presenting novel ideas and stimulating interesting discussions, the book appeals to researchers and practitioners working in the field of information technology and computer science.
Book Synopsis Computer Architecture and Security by : Shuangbao Paul Wang
Download or read book Computer Architecture and Security written by Shuangbao Paul Wang and published by John Wiley & Sons. This book was released on 2013-01-10 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first book to introduce computer architecture for security and provide the tools to implement secure computer systems This book provides the fundamentals of computer architecture for security. It covers a wide range of computer hardware, system software and data concepts from a security perspective. It is essential for computer science and security professionals to understand both hardware and software security solutions to survive in the workplace. Examination of memory, CPU architecture and system implementation Discussion of computer buses and a dual-port bus interface Examples cover a board spectrum of hardware and software systems Design and implementation of a patent-pending secure computer system Includes the latest patent-pending technologies in architecture security Placement of computers in a security fulfilled network environment Co-authored by the inventor of the modern Computed Tomography (CT) scanner Provides website for lecture notes, security tools and latest updates
Book Synopsis Methods in Systems Biology by : Daniel Jameson
Download or read book Methods in Systems Biology written by Daniel Jameson and published by Academic Press. This book was released on 2011-09-26 with total page 775 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology is a term used to describe a number of trends in bioscience research and a movement that draws on those trends. This volume in the Methods in Enzymology series comprehensively covers the methods in systems biology. With an international board of authors, this volume is split into sections that cover subjects such as machines for systems biology, protein production and quantification for systems biology, and enzymatic assays in systems biology research. This volume in the Methods in Enzymology series comprehensively covers the methods in systems biology With an international board of authors, this volume is split into sections that cover subjects such as machines for systems biology, protein production and quantification for systems biology, and enzymatic assays in systems biology research
Book Synopsis Proceedings of Integrated Intelligence Enable Networks and Computing by : Krishan Kant Singh Mer
Download or read book Proceedings of Integrated Intelligence Enable Networks and Computing written by Krishan Kant Singh Mer and published by Springer Nature. This book was released on 2021-04-23 with total page 975 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents best selected research papers presented at the First International Conference on Integrated Intelligence Enable Networks and Computing (IIENC 2020), held from May 25 to May 27, 2020, at the Institute of Technology, Gopeshwar, India (Government Institute of Uttarakhand Government and affiliated to Uttarakhand Technical University). The book includes papers in the field of intelligent computing. The book covers the areas of machine learning and robotics, signal processing and Internet of things, big data and renewable energy sources.
Book Synopsis Mathematics of Bioinformatics by : Matthew He
Download or read book Mathematics of Bioinformatics written by Matthew He and published by John Wiley & Sons. This book was released on 2011-03-16 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematics of Bioinformatics: Theory, Methods, and Applications provides a comprehensive format for connecting and integrating information derived from mathematical methods and applying it to the understanding of biological sequences, structures, and networks. Each chapter is divided into a number of sections based on the bioinformatics topics and related mathematical theory and methods. Each topic of the section is comprised of the following three parts: an introduction to the biological problems in bioinformatics; a presentation of relevant topics of mathematical theory and methods to the bioinformatics problems introduced in the first part; an integrative overview that draws the connections and interfaces between bioinformatics problems/issues and mathematical theory/methods/applications.
Download or read book WITS 2020 written by Saad Bennani and published by Springer Nature. This book was released on 2021-07-21 with total page 1139 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents peer-reviewed articles from the 6th International Conference on Wireless Technologies, Embedded and Intelligent Systems (WITS 2020), held at Fez, Morocco. It presents original research results, new ideas and practical lessons learnt that touch on all aspects of wireless technologies, embedded and intelligent systems. WITS is an international conference that serves researchers, scholars, professionals, students and academicians looking to foster both working relationships and gain access to the latest research results. Topics covered include Telecoms & Wireless Networking Electronics & Multimedia Embedded & Intelligent Systems Renewable Energies.
