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This book offers a comprehensive introduction to using Mathematica and the Wolfram Language for Bioinformatics. The chapters build gradually from basic concepts and the introduction of the Wolfram Language and coding paradigms in Mathematica, to detailed worked examples derived from typical research applications using Wolfram Language code. The coding examples range from basic sequence analysis, accessing genomic databases, differential gene expression, and machine learning implementations to time series analysis of longitudinal omics experiments, multi-omics integration and building dynamic interactive bioinformatics tools using the Wolfram Language. The topics address the daily bioinformatics needs of a broad audience: experimental users looking to understand and visualize their data, beginner bioinformaticians acquiring coding expertise in providing biological research solutions, and practicing expert bioinformaticians working on omics who wish to expand their toolset to include the Wolfram Language.
This practical, example-driven introduction teaches the foundations of the Mathematica language so it can be applied to solving concrete problems.
This text presents mathematical biology as a field with a unity of its own, rather than only the intrusion of one science into another. The book focuses on problems of contemporary interest, such as cancer, genetics, and the rapidly growing field of genomics.
The massive research effort known as the Human Genome Project is an attempt to record the sequence of the three trillion nucleotides that make up the human genome and to identify individual genes within this sequence. While the basic effort is of course a biological one, the description and classification of sequences also lend themselves naturally to mathematical and statistical modeling. This short textbook on the mathematics of genome analysis presents a brief description of several ways in which mathematics and statistics are being used in genome analysis and sequencing. It will be of interest not only to students but also to professional mathematicians curious about the subject.
This richly illustrated third edition provides a thorough training in practical mathematical biology and shows how exciting mathematical challenges can arise from a genuinely interdisciplinary involvement with the biosciences. It has been extensively updated and extended to cover much of the growth of mathematical biology. From the reviews: ""This book, a classical text in mathematical biology, cleverly combines mathematical tools with subject area sciences."--SHORT BOOK REVIEWS
Enhance your data science programming and analysis with the Wolfram programming language and Mathematica, an applied mathematical tools suite. The book introduces you to the Wolfram programming language and its syntax, as well as the structure of Mathematica and its advantages and disadvantages. You’ll see how to use the Wolfram language for data science from a theoretical and practical perspective. Learning this language makes your data science code better because it is very intuitive and comes with pre-existing functions that can provide a welcoming experience for those who use other programming languages. You’ll cover how to use Mathematica where data management and mathematical computations are needed. Along the way you’ll appreciate how Mathematica provides a complete integrated platform: it has a mixed syntax as a result of its symbolic and numerical calculations allowing it to carry out various processes without superfluous lines of code. You’ll learn to use its notebooks as a standard format, which also serves to create detailed reports of the processes carried out. What You Will Learn Use Mathematica to explore data and describe the concepts using Wolfram language commands Create datasets, work with data frames, and create tables Import, export, analyze, and visualize data Work with the Wolfram data repository Build reports on the analysis Use Mathematica for machine learning, with different algorithms, including linear, multiple, and logistic regression; decision trees; and data clustering The fundamentals of the Wolfram Neural Network Framework and how to build your neural network for different tasks How to use pre-trained models from the Wolfram Neural Net Repository Who This Book Is For Data scientists new to using Wolfram and Mathematica as a language/tool to program in. Programmers should have some prior programming experience, but can be new to the Wolfram language.
Accompanying the book, as with all TELOS sponsored publications, is an electronic component. In this case it is a DOS-Diskette produced by one of the coauthors, Paul Wellin. This diskette consists of Mathematica notebooks and packages which contain the codes for all examples and exercises in the book, as well as additional materials intended to extend many ideas covered in the text. It is of great value to teachers, students, and others using this book to learn how to effectively program with Mathematica .
This comprehensive, detailed reference provides readers with both a working knowledge of Mathematica in general and a detailed knowledge of the key aspects needed to create the fastest, shortest, and most elegant implementations possible. It gives users a deeper understanding of Mathematica by instructive implementations, explanations, and examples from a range of disciplines at varying levels of complexity. The three volumes -- Programming, Graphics, and Mathematics, total 3,000 pages and contain more than 15,000 Mathematica inputs, over 1,500 graphics, 4,000+ references, and more than 500 exercises. This first volume begins with the structure of Mathematica expressions, the syntax of Mathematica, its programming, graphic, numeric and symbolic capabilities. It then covers the hierarchical construction of objects out of symbolic expressions, the definition of functions, the recognition of patterns and their efficient application, program flows and program structuring, and the manipulation of lists. An indispensible resource for students, researchers and professionals in mathematics, the sciences, and engineering.
This book covers Mathematica® for beginners. An example-driven text covering a wide variety of applications, containing over 350 exercises with solutions available online.
An essential capacity of intelligence is the ability to learn. An artificially intelligent system that could learn would not have to be programmed for every eventuality; it could adapt to its changing environment and conditions just as biological systems do. Illustrating Evolutionary Computation with Mathematica introduces evolutionary computation to the technically savvy reader who wishes to explore this fascinating and increasingly important field. Unique among books on evolutionary computation, the book also explores the application of evolution to developmental processes in nature, such as the growth processes in cells and plants. If you are a newcomer to the evolutionary computation field, an engineer, a programmer, or even a biologist wanting to learn how to model the evolution and coevolution of plants, this book will provide you with a visually rich and engaging account of this complex subject.* Introduces the major mechanisms of biological evolution.* Demonstrates many fascinating aspects of evolution in nature with simple, yet illustrative examples.* Explains each of the major branches of evolutionary computation: genetic algorithms, genetic programming, evolutionary programming, and evolution strategies.* Demonstrates the programming of computers by evolutionary principles using Evolvica, a genetic programming system designed by the author.* Shows in detail how to evolve developmental programs modeled by cellular automata and Lindenmayer systems.* Provides Mathematica notebooks on the Web that include all the programs in the book and supporting animations, movies, and graphics.