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Python Programming for Biology

Python Programming for Biology

Python Programming for Biology
by Tim J. Stevens, Wayne Boucher

Do you have a biological question that could be readily answered by computational techniques, but little experience in programming? Do you want to learn more about the core techniques used in computational biology and bioinformatics? Written in an accessible style, this guide provides a foundation for both newcomers to computer programming and those interested in learning more about computational biology. The chapters guide the reader through: a complete beginners’ course to programming in Python, with an introduction to computing jargon; descriptions of core bioinformatics methods with working Python examples; scientific computing techniques, including image analysis, statistics and machine learning. This book also functions as a language reference written in straightforward English, covering the most common Python language elements and a glossary of computing and biological terms. This title will teach undergraduates, postgraduates and professionals working in the life sciences how to program with Python, a powerful, flexible and easy-to-use language.

 

; “> Many years ago we started programming in Python because we were working on a large computational biology project. In those days choosing Python was not nearly as common as it is today. Nonetheless things worked out well, and as our expertise grew it seemed only natural that we should run some elementary Python courses for the School of Biology at the University of Cambridge, where we were employed. The basis for those courses is what turned into the initial idea for this book. While there were many books about getting started with Python and some that were tailored to bioinformatics, we felt that there was still some room for what we wanted to put across. We began with the idea that we could write some chapters in relatively straightforward English that were aimed at biologists, who might be complete novices at programming, and have other sections that are useful to a more experienced programmer. Also, given that we didn’t consider ourselves to be typical bioinformaticians, we were thinking more broadly than just sequence-based informatics, though naturally such things would be included. We felt that although we
couldn’t anticipate all the requirements of a biological programmer there were nonetheless a number of key concepts and techniques which we could try to explain. The end result is hopefully a toolkit of ideas and examples which can be applied by biologists in a variety of situations.

Physics by Computer Programming of Physical Problems Using Mathematica and C

Physics by Computer

Physics by Computer Programming of Physical Problems Using Mathematica and C

Using computers to solve problems and model physical problems has fast become an integral part of undergraduate and graduate education in physics. This 3rd year undergraduate and subsequent graduate course is a supplement to courses in theoretical physics and develops problem-solving techniques using the computer. It makes use of the newest version of Mathematica (3.0) while still remaining compatible with older versions The programs using Mathematica 3.0 and C are written for both PCs and workstations, and the problems, source files, and graphic routines help students gain experience from the very beginning.

Nowadays the computer is an important tool in physics. The acquisition and analysis of extensive experimental data and the control of complex experiments are hardly imaginable without the use of computers. In theoretical
physics the computer has turned from a mere calculator to a comprehensive tool. Graphical displays, numerical and algebraic solutions of equations, and extensive simulations of microscopic models have become important methods for the exploration of the laws of physics.
The computer, however, is not just a tool, it also offers new perspectives and opens new areas of research. Until recently physicists generally described nature with differential equations; nowadays discrete algorithms are also used.
For some apparently simple physical models there are only numerical answers so far. We know universal laws that any high school student can reproduce on a pocket calculator, for which there is, however, no analytical theory (yet?).
In addition to this, the computer opens up new fields to physics: neural networks, combinatorial optimization, biological evolution, formation of fractal structures, and self-organized criticality are just some of the topics from the growing field of complex systems.
Almost every advanced undergraduate or graduate physics student uses a computer at one time or another. Nonetheless, computer training and the use of computers in teaching are still by no means the expected norm, but rather the exception. The literature in this field is correspondingly sparse.
The goal of our textbook is to contribute to filling this gap.
This book evolved out of lectures at the University of Wiirzburg, Germany, for physics majors after their fourth semester – those having completed the introductory coursework in theoretical physics. It is conceived as a text book in computational physics but may also serve as a supplement to the traditional physics classes in which the possibilities of computer use have so far been underutilized. We would like to show the reader how to solve physics problems using the computer. Experience with computers and computer languages is helpful, but not necessary, for we want to present an introduction and explain the first steps with computers and algorithms. This book does not contain many details about numerical mathematics, it does not offer a course on programming languages, nor does it teach advanced methods of
computer-oriented theoretical physics. It does, however, introduce numerous physics problems, some of which are at the cutting edge of research, and tries to solve them with simple algorithms.
One goal is to encourage our readers to do their own programming. Although a CD-ROM with finished programs is enclosed with the book, they are not meant as user-friendly experimental environments. We hope that instead they can be taken as a starting-point, and we encourage our readers to modify them, or better yet to rewrite them more efficiently. Exercises accompany every section of this introductory book.
We have received suggestions from many colleagues and students, to whom we wish to express our thanks. We would like especially to mention M. Biehl, H. Dietz, A. Engel, A. Freking, Th. Hahn, W. Hanke, G. Hildebrand, A. Jung, A. Karch, U. Krey, B. Lopez, J. Nestler, M. Opper, M. Schreckenberg, and D. Stauffer. Special thanks go to the following three people: Martin Liiders developed the program package Xgraphics, Martin Schroder wrote the section on Unix, and Ursula Eitelwein typed the manuscript of this book in UTEX.
Finally we would like to thank Martin Clajus for valuable suggestions in the course of translating this textbook into English.

Building Web Applications with ArcGIS

Building Web Applications with ArcGIS

Building Web Applications with ArcGIS
by Hussein Nasser

Building Web Applications with ArcGIS is a short book. Short books are hard to write, because I have to condense essential information into less than 150 pages. It is challenging to determine what is essential when you know a lot about a particular subject. The writer has to sacrifice of some content so that they can produce a quality title that readers can really benefit from.

ArcGIS is a suite of software, developed by Esri—Environmental Systems Research Institute. ArcGIS allows its users to view, edit, analyze, and work with geographic data. You can work with geographic data on desktop, web, or mobile. This book tackles the web development side of ArcGIS; it teaches the reader how to build web applications that can interact with ArcGIS.

I am very proud of this title. It is a special book because I have tried a new writing style I haven’t used before. This is the first book I have ever written that is purely based on a real-life project. As a reader, you act like a web development company where your clients hand you their requirements. Chapter by chapter you start building the application required by the client gradually: adding functionalities, studying their feasibility, and implementing accordingly. Not only will this teach you the basics of developments for ArcGIS, but it will also relate to your real-life projects as well.

I get bored when I read a book that is cluttered with methods and functions and I have to figure out when and where to use them. Some books give you examples disconnected from reality that you won’t ever encounter in your lifetime. This book is different, as each method you use, each library you add, contributes to a requirement requested by a client and it makes sense. You will read and say “yes, this is something my client would definitely request”.

About This Book

  • Learn how to design, build, and run high performance and interactive applications with the help of ArcGIS
  • Incorporate ArcGIS for Server services to allow end users to visualize, query, and edit GIS data using the ArcGIS JavaScript APIs
  • Step-by-step tutorial that teaches you how to design and customize a GIS web application from scratch

Who This Book Is For

If you are a GIS user or a web programmer, this book is for you. This book is also intended for all those who have basic web development knowledge with no prior experience of ArcGIS and are keen on venturing into the world of ArcGIS technology. The book will equip you with the skills to comfortably start your own ArcGIS web development project.

In Detail

ArcGIS allows users to create rich maps and applications that interact with services hosted on ArcGIS for Server and ArcGIS Online. This book will help you to understand the ArcGIS JavaScript API in a fun way while building a real-life project.

This book revolves around a fictional project called Bestaurants. The journey starts with a description of the project requirements before moving on to designing and sketching an interface of what the website will look like. Then, gradually with each chapter, you will add a single functionality until the full ArcGIS application is completed.

By the end of this book, you will have built an entire ArcGIS web application from scratch. An additional bonus appendix is included on how to build ArcGIS applications with ArcGIS Online–a new and extremely useful service offered by Esri.

Creating Beautiful Web Apps with Laravel 5.1

Laravel5.1Beauty

Creating Beautiful Web Apps with Laravel 5.1 by Chuck Heintzelman

This book has a different tone than my previous book. No lame attempts to be funny. (I
guess we all can’t be Dayle Rees.)
Laravel 5.1 Beauty goes through the process of creating, designing and coding a realworld application while focusing on the the architecture that makes Laravel the number one PHP framework available today.

What is the Application?
Throughout this book we’ll build a simple, clean and beautiful blogging application along with the administration required to maintain the blog.
My own Laravel blog, LaravelCoding.com, uses the same blogging application developed here.
Conventions Used This Book There are a few conventions used throughout this book.
Code is indented two spaces The standard indentation for PHP code is 4 spaces. Since this book is available in a
variety of eBook formats and some devices with small screens don’t have much horizontal space, code within this book is indented 2 spaces instead of 4 to save space.

for ($i = 1; $i <= 10; $i++) {
echo “I can count to $i\n”;
}
Lines that end with backslash (\) should be continued If you see any line ending with a backslash, that means the code should continue uninterrupted with text from the next line.
$ here_is_a_really_really_long_command that_has_a_long list of_arguments\
which should continue In the above line, even though two lines are shown you should type in everything, excluding the backlash into one line.
Be Careful of This One When you’re typing code and miss this it can cause an issue. When in doubt check the GitHub
l5beauty repository

Laravel 5 Essentials

Laravel haslaravel_5_essentials established itself as one of the most popular PHP frameworks over the past couple of years. Its popularity comes due to its ease of use, expressive syntax, and the number of components it has, allowing you to achieve practically any task in a modern PHP application. If you’ve not had the opportunity to dive into Laravel yet, then this book will be the perfect companion, as it covers the fundamentals Laravel is built on in a thorough yet easy-to-follow manner. To make this book your best learning source, we have covered integral topics such as preparing an environment for working with Laravel applications, creating your first Laravel application from start to finish, a tour of Laravel’s ORM Eloquent, and more advanced topics such as testing, user authentication, and security. Being one of the most interesting features in Laravel, we also cover an overview of Artisan, including descriptions of some of its tasks. Post this, we talk about testing and security. By the end of this book, you will be able to create robust PHP websites and web applications quickly and efficiently.

Learning Laravel’s Eloquent

Llearning_laravels_eloquentearning Laravel’s Eloquent starts off by taking you through setting up your first project and guiding you in creating a perfect Laravel environment. You will learn how to build the right database structure with the Migrations system and the Schema Builder class. Next, you will be introduced to the main element of Eloquent: the model. After treating the model as a single, isolated entity, you will learn how to create relations between them. You will be taken through organizing, filtering, and sorting your data with collections. You will then learn to enhance an application with new features using events and by creating new observers. Towards the end of the book, you will discover how to install, configure, and use the Eloquent ORM without Laravel. The book concludes by walking you through how to deal with complex problems and build advanced and flexible systems.

Getting Started with Laravel 4

getting_started_with_laravel_4PHP powers many of the largest websites on the planet. Yet, even though it was specifically created for the Web, its shortcomings never cease to frustrate developers. This is where a tool like Laravel comes in. Rather than reinventing the wheel, Laravel reuses tried and tested components and principles and bundles them to form a cohesive whole and makes PHP development enjoyable again. Getting Started with Laravel 4 is a practical and concise introduction to the Laravel PHP framework. It covers its fundamental concepts and presents the many features that will boost your productivity when developing web applications. After introducing the key concepts and installing Composer, you will build a CRUD application and add more features to it in each successive chapter.