A Selection of Metaheuristics and Various Projects
Besides the algorithm design paradigms presented in the preceding chapters that have a clear theoretical foundation, various more or less well understood heuristics are applied to solve bioinformatics problems, often with astonishing good results. Though
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Volker Sperschneider
Bioinformatics Problem Solving Paradigms With contributions by Jana Sperschneider and Lena Scheubert
Volker Sperschneider University of Osnabrück Department of Mathematics and Computer Science Albrechtstr. 28 49076 Osnabrück Germany informatik.uni-osnabrueck.de Contributors: Lena Scheubert University of Osnabrück Department of Mathematics and Computer Science Albrechtstr. 28 49076 Osnabrück Germany
Jana Sperschneider The University of Western Australia School of Computer Science and Software Engineering 35 Stirling Highway Perth, WA 6009 Australia
ISBN 978-3-540-78505-7
e-ISBN 978-3-540-78506-4
DOI 10.1007/978-3-540-78506-4 Library of Congress Control Number: 2008930485 c 2008 Springer-Verlag Berlin Heidelberg This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, 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. Cover design: KuenkelLopka Werbeagentur, Heidelberg Printed on acid-free paper 9 8 7 6 5 4 3 2 1 springer.com
Dedicated to my family
Preface
What is this book good for? Imagine you are a computer scientist working in the bioinformatics area. Probably you will be a member of a highly interdisciplinary team consisting of biologists, chemists, mathematicians, computer scientists ranging from programmers to algorithm engineers, and eventually people from various further fields. A major problem within such interdisciplinary teams is always to find some common language, and, for each member of some discipline, to have profound knowledge of what are the notions, basic concepts and goals of the other participating disciplines, as well as of what they can contribute to the solution of ones own problems. This does, of course, not mean that a computer scientist should do the job of the biologist. Nevertheless, a computer scientist should be able to understand what a biologist deals with. On the other hand, the biologist should not do the computer scientists job, but should know what computer science and algorithm engineering might contribute to the solution of her/his problems, and also how problems should be stated in order for the computer scientist to understand them. This book primarily aims to show the potential that algorithm engineering offers for the solution of core bioinformatics problems. In this sense, it is oriented both towards biologists
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