Discrete And Topological Models In Molecular Biology

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Discrete and Topological Models in Molecular Biology

Author : Nataša Jonoska
Publisher : Springer Science & Business Media
ISBN 13 : 3642401937
Total Pages : 522 pages
Book Rating : 4.6/5 (424 download)

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Book Synopsis Discrete and Topological Models in Molecular Biology by : Nataša Jonoska

Download or read book Discrete and Topological Models in Molecular Biology written by Nataša Jonoska and published by Springer Science & Business Media. This book was released on 2013-12-23 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.

Mathematical Models in Biology

Author : Elizabeth Spencer Allman
Publisher : Cambridge University Press
ISBN 13 : 9780521525862
Total Pages : 388 pages
Book Rating : 4.5/5 (258 download)

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Book Synopsis Mathematical Models in Biology by : Elizabeth Spencer Allman

Download or read book Mathematical Models in Biology written by Elizabeth Spencer Allman and published by Cambridge University Press. This book was released on 2004 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: This introductory textbook on mathematical biology focuses on discrete models across a variety of biological subdisciplines. Biological topics treated include linear and non-linear models of populations, Markov models of molecular evolution, phylogenetic tree construction, genetics, and infectious disease models. The coverage of models of molecular evolution and phylogenetic tree construction from DNA sequence data is unique among books at this level. Computer investigations with MATLAB are incorporated throughout, in both exercises and more extensive projects, to give readers hands-on experience with the mathematical models developed. MATLAB programs accompany the text. Mathematical tools, such as matrix algebra, eigenvector analysis, and basic probability, are motivated by biological models and given self-contained developments, so that mathematical prerequisites are minimal.

Algebraic and Discrete Mathematical Methods for Modern Biology

Author : Raina Robeva
Publisher : Academic Press
ISBN 13 : 0128012714
Total Pages : 383 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Algebraic and Discrete Mathematical Methods for Modern Biology by : Raina Robeva

Download or read book Algebraic and Discrete Mathematical Methods for Modern Biology written by Raina Robeva and published by Academic Press. This book was released on 2015-05-09 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by experts in both mathematics and biology, Algebraic and Discrete Mathematical Methods for Modern Biology offers a bridge between math and biology, providing a framework for simulating, analyzing, predicting, and modulating the behavior of complex biological systems. Each chapter begins with a question from modern biology, followed by the description of certain mathematical methods and theory appropriate in the search of answers. Every topic provides a fast-track pathway through the problem by presenting the biological foundation, covering the relevant mathematical theory, and highlighting connections between them. Many of the projects and exercises embedded in each chapter utilize specialized software, providing students with much-needed familiarity and experience with computing applications, critical components of the "modern biology" skill set. This book is appropriate for mathematics courses such as finite mathematics, discrete structures, linear algebra, abstract/modern algebra, graph theory, probability, bioinformatics, statistics, biostatistics, and modeling, as well as for biology courses such as genetics, cell and molecular biology, biochemistry, ecology, and evolution. Examines significant questions in modern biology and their mathematical treatments Presents important mathematical concepts and tools in the context of essential biology Features material of interest to students in both mathematics and biology Presents chapters in modular format so coverage need not follow the Table of Contents Introduces projects appropriate for undergraduate research Utilizes freely accessible software for visualization, simulation, and analysis in modern biology Requires no calculus as a prerequisite Provides a complete Solutions Manual Features a companion website with supplementary resources

Topology in Molecular Biology

Author : Michael I. Monastyrsky
Publisher : Springer
ISBN 13 : 9783540234074
Total Pages : 238 pages
Book Rating : 4.2/5 (34 download)

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Book Synopsis Topology in Molecular Biology by : Michael I. Monastyrsky

Download or read book Topology in Molecular Biology written by Michael I. Monastyrsky and published by Springer. This book was released on 2006-10-23 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Models and Modeling in the Sciences

Author : Stephen M. Downes
Publisher : Routledge
ISBN 13 : 1317298063
Total Pages : 115 pages
Book Rating : 4.3/5 (172 download)

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Book Synopsis Models and Modeling in the Sciences by : Stephen M. Downes

Download or read book Models and Modeling in the Sciences written by Stephen M. Downes and published by Routledge. This book was released on 2020-07-09 with total page 115 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biologists, climate scientists, and economists all rely on models to move their work forward. In this book, Stephen M. Downes explores the use of models in these and other fields to introduce readers to the various philosophical issues that arise in scientific modeling. Readers learn that paying attention to models plays a crucial role in appraising scientific work. This book first presents a wide range of models from a number of different scientific disciplines. After assembling some illustrative examples, Downes demonstrates how models shed light on many perennial issues in philosophy of science and in philosophy in general. Reviewing the range of views on how models represent their targets introduces readers to the key issues in debates on representation, not only in science but in the arts as well. Also, standard epistemological questions are cast in new and interesting ways when readers confront the question, "What makes for a good (or bad) model?" All examples from the sciences and positions in the philosophy of science are presented in an accessible manner. The book is suitable for undergraduates with minimal experience in philosophy and an introductory undergraduate experience in science. Key features: The book serves as a highly accessible philosophical introduction to models and modeling in the sciences, presenting all philosophical and scientific issues in a nontechnical manner. Students and other readers learn to practice philosophy of science by starting with clear examples taken directly from the sciences. While not comprehensive, this book introduces the reader to a wide range of views on key issues in the philosophy of science.

ReCombinatorics

Author : Dan Gusfield
Publisher : MIT Press
ISBN 13 : 0262324482
Total Pages : 601 pages
Book Rating : 4.2/5 (623 download)

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Book Synopsis ReCombinatorics by : Dan Gusfield

Download or read book ReCombinatorics written by Dan Gusfield and published by MIT Press. This book was released on 2014-07-11 with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt: Combinatorial structure and algorithms for deducing genetic recombination history, represented by ancestral recombination graphs and other networks, and their role in the emerging field of phylogenetic networks. In this book, Dan Gusfield examines combinatorial algorithms to construct genealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs). The algorithms produce networks (or information about networks) that serve as hypotheses about the true genealogical history of observed biological sequences and can be applied to practical biological problems. Phylogenetic trees have been the traditional means to represent evolutionary history, but there is a growing realization that networks rather than trees are often needed, most notably for recent human history. This has led to the development of ARGs in population genetics and, more broadly, to phylogenetic networks. ReCombinatorics offers an in-depth, rigorous examination of current research on the combinatorial, graph-theoretic structure of ARGs and explicit phylogenetic networks, and algorithms to reconstruct or deduce information about those networks. ReCombinatorics, a groundbreaking contribution to the emerging field of phylogenetic networks, connects and unifies topics in population genetics and phylogenetics that have traditionally been discussed separately and considered to be unrelated. It covers the necessary combinatorial and algorithmic background material; the various biological phenomena; the mathematical, population genetic, and phylogenetic models that capture the essential elements of these phenomena; the combinatorial and algorithmic problems that derive from these models; the theoretical results that have been obtained; related software that has been developed; and some empirical testing of the software on simulated and real biological data.

Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology

Author : Hamid R Arabnia
Publisher : Morgan Kaufmann
ISBN 13 : 0128042591
Total Pages : 594 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology by : Hamid R Arabnia

Download or read book Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology written by Hamid R Arabnia and published by Morgan Kaufmann. This book was released on 2016-03-25 with total page 594 pages. Available in PDF, EPUB and Kindle. Book excerpt: Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology: Systems and Applications covers the latest trends in the field with special emphasis on their applications. The first part covers the major areas of computational biology, development and application of data-analytical and theoretical methods, mathematical modeling, and computational simulation techniques for the study of biological and behavioral systems. The second part covers bioinformatics, an interdisciplinary field concerned with methods for storing, retrieving, organizing, and analyzing biological data. The book also explores the software tools used to generate useful biological knowledge. The third part, on systems biology, explores how to obtain, integrate, and analyze complex datasets from multiple experimental sources using interdisciplinary tools and techniques, with the final section focusing on big data and the collection of datasets so large and complex that it becomes difficult to process using conventional database management systems or traditional data processing applications. Explores all the latest advances in this fast-developing field from an applied perspective Provides the only coherent and comprehensive treatment of the subject available Covers the algorithm development, software design, and database applications that have been developed to foster research

Machine Learning and Knowledge Discovery in Databases

Author : Michele Berlingerio
Publisher : Springer
ISBN 13 : 3030109283
Total Pages : 866 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Machine Learning and Knowledge Discovery in Databases by : Michele Berlingerio

Download or read book Machine Learning and Knowledge Discovery in Databases written by Michele Berlingerio and published by Springer. This book was released on 2019-01-22 with total page 866 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three volume proceedings LNAI 11051 – 11053 constitutes the refereed proceedings of the European Conference on Machine Learning and Knowledge Discovery in Databases, ECML PKDD 2018, held in Dublin, Ireland, in September 2018. The total of 131 regular papers presented in part I and part II was carefully reviewed and selected from 535 submissions; there are 52 papers in the applied data science, nectar and demo track. The contributions were organized in topical sections named as follows: Part I: adversarial learning; anomaly and outlier detection; applications; classification; clustering and unsupervised learning; deep learningensemble methods; and evaluation. Part II: graphs; kernel methods; learning paradigms; matrix and tensor analysis; online and active learning; pattern and sequence mining; probabilistic models and statistical methods; recommender systems; and transfer learning. Part III: ADS data science applications; ADS e-commerce; ADS engineering and design; ADS financial and security; ADS health; ADS sensing and positioning; nectar track; and demo track.

Algebraic and Combinatorial Computational Biology

Author : Raina Robeva
Publisher : Academic Press
ISBN 13 : 0128140690
Total Pages : 434 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Algebraic and Combinatorial Computational Biology by : Raina Robeva

Download or read book Algebraic and Combinatorial Computational Biology written by Raina Robeva and published by Academic Press. This book was released on 2018-10-08 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Algebraic and Combinatorial Computational Biology introduces students and researchers to a panorama of powerful and current methods for mathematical problem-solving in modern computational biology. Presented in a modular format, each topic introduces the biological foundations of the field, covers specialized mathematical theory, and concludes by highlighting connections with ongoing research, particularly open questions. The work addresses problems from gene regulation, neuroscience, phylogenetics, molecular networks, assembly and folding of biomolecular structures, and the use of clustering methods in biology. A number of these chapters are surveys of new topics that have not been previously compiled into one unified source. These topics were selected because they highlight the use of technique from algebra and combinatorics that are becoming mainstream in the life sciences. Integrates a comprehensive selection of tools from computational biology into educational or research programs Emphasizes practical problem-solving through multiple exercises, projects and spinoff computational simulations Contains scalable material for use in undergraduate and graduate-level classes and research projects Introduces the reader to freely-available professional software Supported by illustrative datasets and adaptable computer code

Integer Linear Programming in Computational and Systems Biology

Author : Dan Gusfield
Publisher : Cambridge University Press
ISBN 13 : 1108386253
Total Pages : 431 pages
Book Rating : 4.1/5 (83 download)

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Book Synopsis Integer Linear Programming in Computational and Systems Biology by : Dan Gusfield

Download or read book Integer Linear Programming in Computational and Systems Biology written by Dan Gusfield and published by Cambridge University Press. This book was released on 2019-06-13 with total page 431 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integer linear programming (ILP) is a versatile modeling and optimization technique that is increasingly used in non-traditional ways in biology, with the potential to transform biological computation. However, few biologists know about it. This how-to and why-do text introduces ILP through the lens of computational and systems biology. It uses in-depth examples from genomics, phylogenetics, RNA, protein folding, network analysis, cancer, ecology, co-evolution, DNA sequencing, sequence analysis, pedigree and sibling inference, haplotyping, and more, to establish the power of ILP. This book aims to teach the logic of modeling and solving problems with ILP, and to teach the practical 'work flow' involved in using ILP in biology. Written for a wide audience, with no biological or computational prerequisites, this book is appropriate for entry-level and advanced courses aimed at biological and computational students, and as a source for specialists. Numerous exercises and accompanying software (in Python and Perl) demonstrate the concepts.

Mathematical Congress of the Americas

Author : Jimmy Petean
Publisher : American Mathematical Soc.
ISBN 13 : 1470423103
Total Pages : 214 pages
Book Rating : 4.4/5 (74 download)

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Book Synopsis Mathematical Congress of the Americas by : Jimmy Petean

Download or read book Mathematical Congress of the Americas written by Jimmy Petean and published by American Mathematical Soc.. This book was released on 2016-01-25 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the proceedings of the First Mathematical Congress of the Americas, held from August 5-9, 2013, in Guanajuato, México. With the participation of close to 1,000 researchers from more than 40 countries, the meeting set a benchmark for mathematics in the two continents. The papers, written by some of the plenary and invited speakers, as well as winners of MCA awards, cover new developments in classic topics such as Hopf fibrations, minimal surfaces, and Markov processes, and provide recent insights on combinatorics and geometry, isospectral spherical space forms, homogenization on manifolds, and Lagrangian cobordism, as well as applications to physics and biology.

Logical Modeling of Cellular Processes: From Software Development to Network Dynamics

Author : Matteo Barberis
Publisher : Frontiers Media SA
ISBN 13 : 2889459837
Total Pages : 340 pages
Book Rating : 4.8/5 (894 download)

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Book Synopsis Logical Modeling of Cellular Processes: From Software Development to Network Dynamics by : Matteo Barberis

Download or read book Logical Modeling of Cellular Processes: From Software Development to Network Dynamics written by Matteo Barberis and published by Frontiers Media SA. This book was released on 2019-08-16 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical models have become invaluable tools for understanding the intricate dynamic behavior of complex biochemical and biological systems. Among computational strategies, logical modeling has been recently gaining interest as an alternative approach to address network dynamics. Due to its advantages, including scalability and independence of kinetic parameters, the logical modeling framework is becoming increasingly popular to study the dynamics of highly interconnected systems, such as cell cycle progression, T cell differentiation and gene regulation. Novel tools and standards have been developed to increase the interoperability of logical models, which can now be employ to respond a variety of biological questions. This Research Topic brings together the most recent and cutting-edge approaches in the area of logical modeling including, among others, novel biological applications, software development and model analysis techniques.

Big Data and Differential Privacy

Author : Nii O. Attoh-Okine
Publisher : John Wiley & Sons
ISBN 13 : 1119229057
Total Pages : 271 pages
Book Rating : 4.1/5 (192 download)

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Book Synopsis Big Data and Differential Privacy by : Nii O. Attoh-Okine

Download or read book Big Data and Differential Privacy written by Nii O. Attoh-Okine and published by John Wiley & Sons. This book was released on 2017-05-12 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive introduction to the theory and practice of contemporary data science analysis for railway track engineering Featuring a practical introduction to state-of-the-art data analysis for railway track engineering, Big Data and Differential Privacy: Analysis Strategies for Railway Track Engineering addresses common issues with the implementation of big data applications while exploring the limitations, advantages, and disadvantages of more conventional methods. In addition, the book provides a unifying approach to analyzing large volumes of data in railway track engineering using an array of proven methods and software technologies. Dr. Attoh-Okine considers some of today’s most notable applications and implementations and highlights when a particular method or algorithm is most appropriate. Throughout, the book presents numerous real-world examples to illustrate the latest railway engineering big data applications of predictive analytics, such as the Union Pacific Railroad’s use of big data to reduce train derailments, increase the velocity of shipments, and reduce emissions. In addition to providing an overview of the latest software tools used to analyze the large amount of data obtained by railways, Big Data and Differential Privacy: Analysis Strategies for Railway Track Engineering: • Features a unified framework for handling large volumes of data in railway track engineering using predictive analytics, machine learning, and data mining • Explores issues of big data and differential privacy and discusses the various advantages and disadvantages of more conventional data analysis techniques • Implements big data applications while addressing common issues in railway track maintenance • Explores the advantages and pitfalls of data analysis software such as R and Spark, as well as the ApacheTM Hadoop® data collection database and its popular implementation MapReduce Big Data and Differential Privacy is a valuable resource for researchers and professionals in transportation science, railway track engineering, design engineering, operations research, and railway planning and management. The book is also appropriate for graduate courses on data analysis and data mining, transportation science, operations research, and infrastructure management. NII ATTOH-OKINE, PhD, PE is Professor in the Department of Civil and Environmental Engineering at the University of Delaware. The author of over 70 journal articles, his main areas of research include big data and data science; computational intelligence; graphical models and belief functions; civil infrastructure systems; image and signal processing; resilience engineering; and railway track analysis. Dr. Attoh-Okine has edited five books in the areas of computational intelligence, infrastructure systems and has served as an Associate Editor of various ASCE and IEEE journals.

Language, Life, Limits

Author : Arnold Beckmann
Publisher : Springer
ISBN 13 : 3319080199
Total Pages : 424 pages
Book Rating : 4.3/5 (19 download)

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Book Synopsis Language, Life, Limits by : Arnold Beckmann

Download or read book Language, Life, Limits written by Arnold Beckmann and published by Springer. This book was released on 2014-06-05 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 10th Conference on Computability in Europe, CiE 2014, held in Budapest, Hungary, in June 2014. The 42 revised papers presented were carefully reviewed and selected from 78 submissions and included together with 15 invited papers in this proceedings. The conference had six special sessions: computational linguistics, bio-inspired computation, history and philosophy of computing, computability theory, online algorithms and complexity in automata theory.

Software Technologies: Applications and Foundations

Author : Paolo Milazzo
Publisher : Springer
ISBN 13 : 3319502301
Total Pages : 491 pages
Book Rating : 4.3/5 (195 download)

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Book Synopsis Software Technologies: Applications and Foundations by : Paolo Milazzo

Download or read book Software Technologies: Applications and Foundations written by Paolo Milazzo and published by Springer. This book was released on 2016-11-29 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains the thoroughly refereed technical papers presented in six workshops collocated with the International Conference on Software Technologies: Applications and Foundations, STAF 2016, held in Vienna, Austria, in July 2016. The six workshops whose papers are included in this volume are: DataMod, GCM, HOFM, MELO, SEMS, and VeryComp. The 33 full and 3 short papers presented were carefully reviewed and selected from 53 submissions. They focus on practical and foundational advances in software technology covering a wide range of aspects including formal foundations of software technology, testing and formal analysis, graph transformations and model transformations, model driven engineering, and tools.

Visions of DNA Nanotechnology at 40 for the Next 40

Author : Nataša Jonoska
Publisher : Springer Nature
ISBN 13 : 9811998914
Total Pages : 442 pages
Book Rating : 4.8/5 (119 download)

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Book Synopsis Visions of DNA Nanotechnology at 40 for the Next 40 by : Nataša Jonoska

Download or read book Visions of DNA Nanotechnology at 40 for the Next 40 written by Nataša Jonoska and published by Springer Nature. This book was released on 2023-07-04 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book provides a unique and state-of-the-art view on DNA nanotechnology with an eye toward future developments. Intended as a tribute to Nadrian C. Seeman, who founded the field of DNA nanotechnology, the content is an exciting mixture of technical and non-technical material, reviews, tutorials, perspectives, new findings, and open questions. The book aims to inspire current researchers to sit back and think about the big picture, while also enticing new researchers to enter the field. Most of all, the book captures voices from a unique moment in time: 40 years after the publication of the first paper that envisioned DNA nanotechnology. From this vantage point, what are the untold stories, the unspoken concerns, the underlying fundamental issues, the overlooked opportunities, and the unifying grand challenges? What will help us see more clearly, see more creatively, or see farther? What is transpiring right now that could pave the way for the future? To address these questions, leading researchers have contributed 22 chapters, grouped into five sections: perspectives, chemistry and physics, structures, biochemical circuits, and spatial systems. This book will be an important reference point in the field of DNA nanotechnology, both for established researchers looking to take stock of the field and its future, and for newcomers such as graduate students and researchers in other fields who are beginning to appreciate the power and applicability of its methods.

Infobiotics

Author : Vincenzo Manca
Publisher : Springer Science & Business Media
ISBN 13 : 3642362230
Total Pages : 395 pages
Book Rating : 4.6/5 (423 download)

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Book Synopsis Infobiotics by : Vincenzo Manca

Download or read book Infobiotics written by Vincenzo Manca and published by Springer Science & Business Media. This book was released on 2013-03-12 with total page 395 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book presents topics in discrete biomathematics. Mathematics has been widely used in modeling biological phenomena. However, the molecular and discrete nature of basic life processes suggests that their logic follow principles that are intrinsically based on discrete and informational mechanisms. The ultimate reason of polymers, as key element of life, is directly based on the computational power of strings, and the intrinsic necessity of metabolism is related to the mathematical notion of multiset. The switch of the two roots of bioinformatics suggests a change of perspective. In bioinformatics, the biologists ask computer scientists to assist them in processing biological data. Conversely, in infobiotics mathematicians and computer scientists investigate principles and theories yielding new interpretation keys of biological phenomena. Life is too important to be investigated by biologists alone, and though computers are essential to process data from biological laboratories, many fundamental questions about life can be appropriately answered by a perspicacious intervention of mathematicians, computer scientists, and physicists, who will complement the work of chemists, biochemists, biologists, and medical investigators. The volume is organized in seven chapters. The first part is devoted to research topics (Discrete information and life, Strings and genomes, Algorithms and Biorhythms, Life Strategies), the second one to mathematical backgrounds (Numbers and Measures, Languages and Grammars, Combinations and Chances).