Introduction to modeling for biosciences
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Introduction to modeling for biosciences
Introductionto Modeling for Biosciences4^ springerDavid J. Barnes • Dominique ChuIntroduction to Modeling for BiosciencesSpringerDavid J. Barnes Compu Introduction to modeling for biosciences uting Laboratory University of Kent Canterbury. Kent CT2 7NF UKd.j .barncs 0' kcnl.ac.ukDr. Dominique Chu Computing Laboratory University of Kent Canterbury. Kent CT2 7NF UKD. KCh u kcnl.ac.uke-ISBN 978-1-84996-326-8ISBN 978-1-84996-325-1DOI 10.1007/978-1-84996-326-8Springer London Dordrecht Heidelb Introduction to modeling for biosciences erg New YorkBritish Library Cataloguing in Publication DataA catalogue record for this book is available from the British LibraryLibrary of Congress CIntroduction to modeling for biosciences
ontrol -Number: 2010931520© Springer-Vcrlag London Limited 2010Apart from any fair dealing for the purposes of research or private study, or criticismIntroductionto Modeling for Biosciences4^ springerDavid J. Barnes • Dominique ChuIntroduction to Modeling for BiosciencesSpringerDavid J. Barnes Compu Introduction to modeling for biosciences m or by any means, with the prior permission in writing of the publishers, or in the case of reprographic repnxluction in accordance with the terms of licenses issued by the Copyright Licensing Agency. Enquiries concerning reproduction outside those terms should be sent co the publishers.The use of Introduction to modeling for biosciences registered names, trademarks, etc., in this publication docs not imply, even in the absence of a specific statement, that such names are exempt from tIntroduction to modeling for biosciences
he relevant laws and regulations and therefore free for general use.’rhe publisher makes no representation, express or implied, w ith regard Io the acIntroductionto Modeling for Biosciences4^ springerDavid J. Barnes • Dominique ChuIntroduction to Modeling for BiosciencesSpringerDavid J. Barnes Compu Introduction to modeling for biosciences over art by snailsnail('overdesign: Kiinkellxtpka GmbH. HeidelbergPrinted on acid-free paperSpringer is part of springer Scicncc+Busincss Media (www.springcr.com)David dedicates this book to Helen, Ben. (Hannah and John), John and SarahPrefaceIn this book we seek to provide a detailed introduction t Introduction to modeling for biosciences o a range of modeling techniques that are appropriate for modeling in biosciences. The book is primarily intended for bioscientists, but will be equalIntroduction to modeling for biosciences
ly useful for anybody wishing to start modeling in biosciences and related fields. The topics we discuss include agentbased models, stochastic modelinIntroductionto Modeling for Biosciences4^ springerDavid J. Barnes • Dominique ChuIntroduction to Modeling for BiosciencesSpringerDavid J. Barnes Compu Introduction to modeling for biosciences ce modeler. We recognise that modeling in science in general (and in biology, in particular) requires both skills (i.e., programming, developing algorithms. and solving equations) and techniques (i.e.. the ability to recognise what is important and needs to be represented in the model, and what can Introduction to modeling for biosciences and should be left out). In our experience with novice modelers we have noticed that: (i) both skill and technique are equally important: and (ii) botIntroduction to modeling for biosciences
h are normally lacking to some degree.The philosophy of this book, therefore, is to discuss both aspects—the technical side, and the side that concernIntroductionto Modeling for Biosciences4^ springerDavid J. Barnes • Dominique ChuIntroduction to Modeling for BiosciencesSpringerDavid J. Barnes Compu Introduction to modeling for biosciences if followed, will necessarily lead to a successful modeling result. Therefore, we have not provided a list of such rules. Instead, we adopt a practical approach which involves walking the reader through realistic and concrete modeling projects. In doing so, we highlight and comment on the process o Introduction to modeling for biosciences f abstracting the real system into a model. The motivation for this approach is that it is akin to apprenticeship, allowing the reader both to observeIntroduction to modeling for biosciences
practical expertise and to generate personal understanding and intuition, that will ultimately help them to formulate their own models.Included in thIntroductionto Modeling for Biosciences4^ springerDavid J. Barnes • Dominique ChuIntroduction to Modeling for BiosciencesSpringerDavid J. Barnes Compu Introduction to modeling for biosciences mphony agent modeling environment. Some of the chapters also include exercises to help the reader sharpen their understanding of the topics. The book is supported by a web site. http://www.cs.kent.ac.uk/imb/. that includes source code of many of the example models we discuss.Canterbury. UKDavid J. B Introduction to modeling for biosciences arnesDominique ChuviiIntroductionto Modeling for Biosciences4^ springerDavid J. Barnes • Dominique ChuIntroduction to Modeling for BiosciencesSpringerDavid J. Barnes CompuIntroductionto Modeling for Biosciences4^ springerDavid J. Barnes • Dominique ChuIntroduction to Modeling for BiosciencesSpringerDavid J. Barnes CompuGọi ngay
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