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Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools by Vince Buffalo
bioinformatics
biology
programming
science
Test-Driven Development: By Example
Kent Beck - 2002
While some fear is healthy (often viewed as a conscience that tells programmers to be careful!), the author believes that byproducts of fear include tentative, grumpy, and uncommunicative programmers who are unable to absorb constructive criticism. When programming teams buy into TDD, they immediately see positive results. They eliminate the fear involved in their jobs, and are better equipped to tackle the difficult challenges that face them. TDD eliminates tentative traits, it teaches programmers to communicate, and it encourages team members to seek out criticism However, even the author admits that grumpiness must be worked out individually! In short, the premise behind TDD is that code should be continually tested and refactored. Kent Beck teaches programmers by example, so they can painlessly and dramatically increase the quality of their work.
Thinking in Java
Bruce Eckel - 1998
The author's take on the essence of Java as a new programming language and the thorough introduction to Java's features make this a worthwhile tutorial. Thinking in Java begins a little esoterically, with the author's reflections on why Java is new and better. (This book's choice of font for chapter headings is remarkably hard on the eyes.) The author outlines his thoughts on why Java will make you a better programmer, without all the complexity. The book is better when he presents actual language features. There's a tutorial to basic Java types, keywords, and operators. The guide includes extensive source code that is sometimes daunting (as with the author's sample code for all the Java operators in one listing.) As such, this text will be most useful for the experienced developer. The text then moves on to class design issues, when to use inheritance and composition, and related topics of information hiding and polymorphism. (The treatment of inner classes and scoping will likely seem a bit overdone for most readers.) The chapter on Java collection classes for both Java Developer's Kit (JDK) 1.1 and the new classes, such as sets, lists, and maps, are much better. There's material in this chapter that you are unlikely to find anywhere else. Chapters on exception handling and programming with type information are also worthwhile, as are the chapters on the new Swing interface classes and network programming. Although it adopts somewhat of a mixed-bag approach, Thinking in Java contains some excellent material for the object-oriented developer who wants to see what all the fuss is about with Java.
Artificial Intelligence: A Guide for Thinking Humans
Melanie Mitchell - 2019
The award-winning author Melanie Mitchell, a leading computer scientist, now reveals AI’s turbulent history and the recent spate of apparent successes, grand hopes, and emerging fears surrounding it.In Artificial Intelligence, Mitchell turns to the most urgent questions concerning AI today: How intelligent—really—are the best AI programs? How do they work? What can they actually do, and when do they fail? How humanlike do we expect them to become, and how soon do we need to worry about them surpassing us? Along the way, she introduces the dominant models of modern AI and machine learning, describing cutting-edge AI programs, their human inventors, and the historical lines of thought underpinning recent achievements. She meets with fellow experts such as Douglas Hofstadter, the cognitive scientist and Pulitzer Prize–winning author of the modern classic Gödel, Escher, Bach, who explains why he is “terrified” about the future of AI. She explores the profound disconnect between the hype and the actual achievements in AI, providing a clear sense of what the field has accomplished and how much further it has to go.Interweaving stories about the science of AI and the people behind it, Artificial Intelligence brims with clear-sighted, captivating, and accessible accounts of the most interesting and provocative modern work in the field, flavored with Mitchell’s humor and personal observations. This frank, lively book is an indispensable guide to understanding today’s AI, its quest for “human-level” intelligence, and its impact on the future for us all.
Machine Learning for Absolute Beginners
Oliver Theobald - 2017
The manner in which computers are now able to mimic human thinking is rapidly exceeding human capabilities in everything from chess to picking the winner of a song contest. In the age of machine learning, computers do not strictly need to receive an ‘input command’ to perform a task, but rather ‘input data’. From the input of data they are able to form their own decisions and take actions virtually as a human would. But as a machine, can consider many more scenarios and execute calculations to solve complex problems. This is the element that excites companies and budding machine learning engineers the most. The ability to solve complex problems never before attempted. This is also perhaps one reason why you are looking at purchasing this book, to gain a beginner's introduction to machine learning. This book provides a plain English introduction to the following topics: - Artificial Intelligence - Big Data - Downloading Free Datasets - Regression - Support Vector Machine Algorithms - Deep Learning/Neural Networks - Data Reduction - Clustering - Association Analysis - Decision Trees - Recommenders - Machine Learning Careers This book has recently been updated following feedback from readers. Version II now includes: - New Chapter: Decision Trees - Cleanup of minor errors
Introduction to Computation and Programming Using Python
John V. Guttag - 2013
It provides students with skills that will enable them to make productive use of computational techniques, including some of the tools and techniques of "data science" for using computation to model and interpret data. The book is based on an MIT course (which became the most popular course offered through MIT's OpenCourseWare) and was developed for use not only in a conventional classroom but in in a massive open online course (or MOOC) offered by the pioneering MIT--Harvard collaboration edX.Students are introduced to Python and the basics of programming in the context of such computational concepts and techniques as exhaustive enumeration, bisection search, and efficient approximation algorithms. The book does not require knowledge of mathematics beyond high school algebra, but does assume that readers are comfortable with rigorous thinking and not intimidated by mathematical concepts. Although it covers such traditional topics as computational complexity and simple algorithms, the book focuses on a wide range of topics not found in most introductory texts, including information visualization, simulations to model randomness, computational techniques to understand data, and statistical techniques that inform (and misinform) as well as two related but relatively advanced topics: optimization problems and dynamic programming.Introduction to Computation and Programming Using Python can serve as a stepping-stone to more advanced computer science courses, or as a basic grounding in computational problem solving for students in other disciplines.
The Rails 3 Way
Obie Fernandez - 2010
"The Rails(TM) 3 Way"is the only comprehensive, authoritative guide to delivering production-quality code with Rails 3. Pioneering Rails expert Obie Fernandez and a team of leading experts illuminate the entire Rails 3 API, along with the idioms, design approaches, and libraries that make developing applications with Rails so powerful. Drawing on their unsurpassed experience and track record, they address the real challenges development teams face, showing how to use Rails 3 to maximize your productivity. Using numerous detailed code examples, the author systematically covers Rails 3 key capabilities and subsystems, making this book a reference that you will turn to again and again. He presents advanced Rails programming techniques that have been proven effective in day-to-day usage on dozens of production Rails systems and offers important insights into behavior-driven development and production considerations such as scalability. Dive deep into the Rails 3 codebase and discover why Rails is designed the way it is--and how to make it do what you want it to do.This book will help youLearn what's new in Rails 3 Increase your productivity as a web application developer Realize the overall joy in programming with Rails Leverage Rails' powerful capabilities for building REST-compliant APIs Drive implementation and protect long-term maintainability using RSpec Design and manipulate your domain layer using Active Record Understand and program complex program flows using Action Controller Master sophisticated URL routing concepts Use Ajax techniques via Rails 3 support for unobtrusive JavaScript Learn to extend Rails with popular gems and plugins, and how to write your own Extend Rails with the best third-party plug-ins and write your own Integrate email services into your applications with Action Mailer Improve application responsiveness with background processing Create your own non-Active Record domain classes using Active Model Master Rails' utility classes and extensions in Active Support
The Analysis of Biological Data
Michael C. Whitlock - 2008
To reach this unique audience, Whitlock and Schluter motivate learning with interesting biological and medical examples; they emphasize intuitive understanding; and they focus on real data. The book covers basic topics in introductory statistics, including graphs, confidence intervals, hypothesis testing, comparison of means, regression, and designing experiments. It also introduces the principles behind such modern topics as likelihood, linear models, meta-analysis and computer-intensive methods. Instructors and students consistently praise the book's clear and engaging writing, strong visualization techniques, and its variety of fascinating and relevant biological examples.
Programming Perl
Tom Christiansen - 1991
The first edition of this book, Programming Perl, hit the shelves in 1990, and was quickly adopted as the undisputed bible of the language. Since then, Perl has grown with the times, and so has this book.Programming Perl is not just a book about Perl. It is also a unique introduction to the language and its culture, as one might expect only from its authors. Larry Wall is the inventor of Perl, and provides a unique perspective on the evolution of Perl and its future direction. Tom Christiansen was one of the first champions of the language, and lives and breathes the complexities of Perl internals as few other mortals do. Jon Orwant is the editor of The Perl Journal, which has brought together the Perl community as a common forum for new developments in Perl.Any Perl book can show the syntax of Perl's functions, but only this one is a comprehensive guide to all the nooks and crannies of the language. Any Perl book can explain typeglobs, pseudohashes, and closures, but only this one shows how they really work. Any Perl book can say that my is faster than local, but only this one explains why. Any Perl book can have a title, but only this book is affectionately known by all Perl programmers as "The Camel."This third edition of Programming Perl has been expanded to cover version 5.6 of this maturing language. New topics include threading, the compiler, Unicode, and other new features that have been added since the previous edition.
Hackers: Heroes of the Computer Revolution
Steven Levy - 1984
That was before one pioneering work documented the underground computer revolution that was about to change our world forever. With groundbreaking profiles of Bill Gates, Steve Wozniak, MIT's Tech Model Railroad Club, and more, Steven Levy's Hackers brilliantly captured a seminal moment when the risk-takers and explorers were poised to conquer twentieth-century America's last great frontier. And in the Internet age, the hacker ethic-first espoused here-is alive and well.
Peopleware: Productive Projects and Teams
Tom DeMarco - 1987
The answers aren't easy -- just incredibly successful.
Python in a Nutshell
Alex Martelli - 2003
Demonstrates the programming language's strength as a Web development tool, covering syntax, data types, built-ins, the Python standard module library, and real world examples
JavaScript: The Definitive Guide
David Flanagan - 1996
This book is both an example-driven programmer's guide and a keep-on-your-desk reference, with new chapters that explain everything you need to know to get the most out of JavaScript, including:Scripted HTTP and Ajax XML processing Client-side graphics using the canvas tag Namespaces in JavaScript--essential when writing complex programs Classes, closures, persistence, Flash, and JavaScript embedded in Java applicationsPart I explains the core JavaScript language in detail. If you are new to JavaScript, it will teach you the language. If you are already a JavaScript programmer, Part I will sharpen your skills and deepen your understanding of the language.Part II explains the scripting environment provided by web browsers, with a focus on DOM scripting with unobtrusive JavaScript. The broad and deep coverage of client-side JavaScript is illustrated with many sophisticated examples that demonstrate how to:Generate a table of contents for an HTML document Display DHTML animations Automate form validation Draw dynamic pie charts Make HTML elements draggable Define keyboard shortcuts for web applications Create Ajax-enabled tool tips Use XPath and XSLT on XML documents loaded with Ajax And much morePart III is a complete reference for core JavaScript. It documents every class, object, constructor, method, function, property, and constant defined by JavaScript 1.5 and ECMAScript Version 3.Part IV is a reference for client-side JavaScript, covering legacy web browser APIs, the standard Level 2 DOM API, and emerging standards such as the XMLHttpRequest object and the canvas tag.More than 300,000 JavaScript programmers around the world have made this their indispensable reference book for building JavaScript applications."A must-have reference for expert JavaScript programmers...well-organized and detailed."-- Brendan Eich, creator of JavaScript
Bayes Theorem: A Visual Introduction For Beginners
Dan Morris - 2016
Bayesian statistics is taught in most first-year statistics classes across the nation, but there is one major problem that many students (and others who are interested in the theorem) face. The theorem is not intuitive for most people, and understanding how it works can be a challenge, especially because it is often taught without visual aids. In this guide, we unpack the various components of the theorem and provide a basic overview of how it works - and with illustrations to help. Three scenarios - the flu, breathalyzer tests, and peacekeeping - are used throughout the booklet to teach how problems involving Bayes Theorem can be approached and solved. Over 60 hand-drawn visuals are included throughout to help you work through each problem as you learn by example. The illustrations are simple, hand-drawn, and in black and white. For those interested, we have also included sections typically not found in other beginner guides to Bayes Rule. These include: A short tutorial on how to understand problem scenarios and find P(B), P(A), and P(B|A). For many people, knowing how to approach scenarios and break them apart can be daunting. In this booklet, we provide a quick step-by-step reference on how to confidently understand scenarios.A few examples of how to think like a Bayesian in everyday life. Bayes Rule might seem somewhat abstract, but it can be applied to many areas of life and help you make better decisions. It is a great tool that can help you with critical thinking, problem-solving, and dealing with the gray areas of life. A concise history of Bayes Rule. Bayes Theorem has a fascinating 200+ year history, and we have summed it up for you in this booklet. From its discovery in the 1700’s to its being used to break the German’s Enigma Code during World War 2, its tale is quite phenomenal.Fascinating real-life stories on how Bayes formula is used in everyday life.From search and rescue to spam filtering and driverless cars, Bayes is used in many areas of modern day life. We have summed up 3 examples for you and provided an example of how Bayes could be used.An expanded definitions, notations, and proof section.We have included an expanded definitions and notations sections at the end of the booklet. In this section we define core terms more concretely, and also cover additional terms you might be confused about. A recommended readings section.From The Theory That Would Not Die to a few other books, there are a number of recommendations we have for further reading. Take a look! If you are a visual learner and like to learn by example, this intuitive booklet might be a good fit for you. Bayesian statistics is an incredibly fascinating topic and likely touches your life every single day. It is a very important tool that is used in data analysis throughout a wide-range of industries - so take an easy dive into the theorem for yourself with a visual approach!If you are looking for a short beginners guide packed with visual examples, this booklet is for you.
SQL and Relational Theory: How to Write Accurate SQL Code
C.J. Date - 2009
On the other hand, if you're not well versed in the theory, you can fall into several traps. In SQL and Relational Theory, author C.J. Date demonstrates how you can apply relational theory directly to your use of SQL. With numerous examples and clear explanations of the reasoning behind them, you'll learn how to deal with common SQL dilemmas, such as:Should database access granted be through views instead of base tables? Nulls in your database are causing you to get wrong answers. Why? What can you do about it? Could you write an SQL query to find employees who have never been in the same department for more than six months at a time? SQL supports "quantified comparisons," but they're better avoided. Why? How do you avoid them? Constraints are crucially important, but most SQL products don't support them properly. What can you do to resolve this situation? Database theory and practice have evolved since Edgar Codd originally defined the relational model back in 1969. Independent of any SQL products, SQL and Relational Theory draws on decades of research to present the most up-to-date treatment of the material available anywhere. Anyone with a modest to advanced background in SQL will benefit from the many insights in this book.