Modeling Biomolecular Site Dynamics Methods and Protocols
This volume covers a variety of topics related to the practice of rule-based modeling, a type of mathematical modeling useful for studying biomolecular site dynamics. There is an emphasis on software tools and detailed descriptions of techniques. The chap
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William S. Hlavacek Editor
Modeling Biomolecular Site Dynamics Methods and Protocols
METHODS
IN
MOLECULAR BIOLOGY
Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes: http://www.springer.com/series/7651
Modeling Biomolecular Site Dynamics Methods and Protocols
Edited by
William S. Hlavacek Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
Editor William S. Hlavacek Theoretical Biology and Biophysics Group Theoretical Division Los Alamos National Laboratory Los Alamos, NM, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-9100-6 ISBN 978-1-4939-9102-0 (eBook) https://doi.org/10.1007/978-1-4939-9102-0 Library of Congress Control Number: 2019935573 © Springer Science+Business Media, LLC, part of Springer Nature 2019 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Humana Press imprint is published by the registered company Springer Science+Business Media, LLC, part of Springer Nature. The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A.
Foreword As both computational systems biologists and users of rule-based modeling software, we are privileged to be able to introduce this volume of Methods in Molecular Biology, which is focused on rule-based modeling languages and the growing ecosystem of related tools. We would like to acknowledge that the editor of this volume, Bill Hlavacek, is also a member of both communities, and he is one of the original developers of rule-based modeling methodologies for the study of cellular information processing. We were generously given an invitation by Bill to write the foreword to this volume and will thus focus primarily on introducing the motivation for and general use cases of
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