Short Description:
Now available in print at Amazon.com and via the OSU Press! Data Dashboard

Long Description:
A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts: Introduction to Unix/Linux: The command-line is the “natural environment” of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful “pipe” operator for file and data manipulation. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.

Word Count: 111597

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Digital accessibility skills are in high demand, as the world becomes more aware of barriers in digital content that prevent some people from participating in a digital society. These are essential skills for web developers, and essential knowledge for organizations that want to ensure their web content is reaching the broadest audience possible.

Unlike some other textbooks, this one does not follow a top-down narrative. Rather it has the flow of a conversation, with backtracking. We will often build up programs incrementally, just as a pair of programmers would. We will include mistakes, not because I don’t know the answer, but because this is the best way for you to learn. Including mistakes makes it impossible for you to read passively: you must instead engage with the material, because you can never be sure of the veracity of what you’re reading.

The main programming language used in this book is Racket. Like with all operating systems, however, Racket actually supports a host of programming languages, so you must tell Racket which language you’re programming in.

This textbook has been used in classes at: Brown University, Cal Poly, Columbus State University, Northeastern University, NYU, Reed College, UC-San Diego, UC-Santa Cruz, University of Rhode Island, University of Utah, Westmont College, Williams College, and Worcester Polytechnic Institute.

New Edition! The goal of this book is to provide an Informatics-oriented introduction to programming. The primary difference between a computer science approach and the Informatics approach taken in this book is a greater focus on using Python to solve data analysis problems common in the world of Informatics.

This text is a free introductory text that introduces MS Access and relational database design. The motivation is to support a second-year course on database systems which, to the student, is either a service course providing an introduction to database concepts, or, as a prerequisite for more advanced study in the field.

The Shallow and the Deep is a collection of lecture notes that offers an accessible introduction to neural networks and machine learning in general. However, it was clear from the beginning that these notes would not be able to cover this rapidly changing and growing field in its entirety. The focus lies on classical machine learning techniques, with a bias towards classification and regression. Other learning paradigms and many recent developments in, for instance, Deep Learning are not addressed or only briefly touched upon.

Biehl argues that having a solid knowledge of the foundations of the field is essential, especially for anyone who wants to explore the world of machine learning with an ambition that goes beyond the application of some software package to some data set. Therefore, The Shallow and the Deep places emphasis on fundamental concepts and theoretical background. This also involves delving into the history and pre-history of neural networks, where the foundations for most of the recent developments were laid. These notes aim to demystify machine learning and neural networks without losing the appreciation for their impressive power and versatility.

Qualitative and Quantitative Approaches

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Spec is the default UI framework for Pharo. To build UI’s in Spec existing widgets or even complete UI’s are reused and configured to form a new UI.

This book first shows the basics of Spec and how it enables reuse of UIs. It then treats UI layout in detail before moving on to explaining the management of windows. Some of the more advanced widgets are also discussed as well as the dynamic features of Spec. Lastly, the book also contains a chapter with tips and tricks.

This is a text that covers the standard topics in a sophomore-level course in discrete mathematics: logic, sets, proof techniques, basic number theory, functions, relations, and elementary combinatorics, with an emphasis on motivation. It explains and clarifies the unwritten conventions in mathematics, and guides the students through a detailed discussion on how a proof is revised from its draft to a final polished form. Hands-on exercises help students understand a concept soon after learning it. The text adopts a spiral approach: many topics are revisited multiple times, sometimes from a different perspective or at a higher level of complexity. The goal is to slowly develop students’ problem-solving and writing skills.

Squeak is a modern open-source development environment for the classic Smalltalk-80 programming language. Despite being the first purely object-oriented language and environment, Smalltalk is in many ways still far ahead of its successors in promoting a vision of an environment where everything is an object, and anything can change at run-time.

Short Description:
This text is meant as a case study and companion text to many Systems Analysis & Design textbooks used in undergraduate Management Information Systems (MIS), Business Information Systems (BIS) and Computer Information Systems (CIS) programs. The US counts about 1,300 (undergraduate + graduate) such programs (Mandiwalla et al., 2016). These texts typically contain short descriptions of technologies which give students some sense of what these technologies are used for, but do not provide much context or reflection on why these technologies might or might not be applied and what such applications actually amount to in real life. As a consequence, students, having worked their way through these textbooks and associated courses will have had little exposure to the reasoning which must take place when making choices between these technologies and to what goes into combining them into working and successful system architectures. It is our hope that this Tale of Two Systems (pun very much intended) will help mitigate this problem a little. The first edition of this publication is available: A Tale of Two Systems (first edition). Data dashboard

Long Description:
This is the story of a web-based information system rebuild. The system in question is www.teachengineering.org, a digital library of K-12 engineering curriculum that was built from the ground up with established technology and which for 13 years enjoyed lasting support from its growing user community and its sponsors. These 13 years, however, cover the period during which smart phones and tablets became commonplace, during which the Internet of Things started replacing the Semantic Web, during which NoSQL databases made their way out of the research labs and into everyday development shops, during which we collectively started moving IT functions and services into ‘the cloud,’ and during which computing performance doubled a few times, yet again. During this same period, TeachEngineering’s user base grew from a few hundred to more than 3 million users annually, its collection size quadrupled, it went through several user interface renewals, and significant functionality was added while having an exemplary service record, and it enjoyed continued financial support from its sponsors.

Yet, although the system architecture could probably have survived a while longer, it started to become clear that with the newer technologies, better and newer services could be developed faster and at lower cost, that moving most of its functionality into the cloud would both boost performance and lower maintenance cost, and that the system’s resource and code footprint could be significantly reduced by rebuilding it on a different architecture, with different and more modern technology.

In this monograph we provide a side-by-side of this rebuild. We lay out the choices made in the old architecture —we refer to it as TE 1.0— and compare and contrast them with the choices made for TE 2.0. We explain why both the 1.0 and 2.0 choices were made and discuss the advantages and disadvantages associated with them.

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El nivel académico que pretende abordar el libro es en las diferentes licenciaturas e ingenierías que consideren tópicos en el área de interacción humano computadora, así como los posgrados relacionados con la temática. El libro describe diferentes tipos de interacción que pueden ofrecer las aplicaciones interactivas donde a través de la interfaz gráfica es posible guiar y hacer fácil la tarea del usuario. Así pues, el lector puede encontrar diferentes trabajos que especifican desde los requerimientos del usuario hasta el diseño, programación y evaluación de distintas aplicaciones interactivas.

The book is appropriately comprehensive, covering the basics as well as interesting and important applications of Bayesian methods.

This book is about complexity science, data structures and algorithms, intermediate programming in Python, and the philosophy of science. This book focuses on discrete models, which include graphs, cellular automata, and agent-based models. They are often characterized by structure, rules and transitions rather than by equations. They tend to be more abstract than continuous models; in some cases there is no direct correspondence between the model and a physical system.

The examples and supporting code for this book are in Python. You should know core Python and you should be familiar with object-oriented features, at least using objects if not defining your own. If you are not already familiar with Python, you might want to start with my other book, Think Python, which is an introduction to Python for people who have never programmed, or Mark Lutz’s Learning Python, which might be better for people with programming experience.

Data structures and algorithms are among the most important inventions of the last 50 years, and they are fundamental tools software engineers need to know. But in my opinion, most of the books on these topics are too theoretical, too big, and too bottom-up:

*Too theoretical: Mathematical analysis of algorithms is based on simplifying assumptions that limit its usefulness in practice. Many presentations of this topic gloss over the simplifications and focus on the math. In this book I present the most practical subset of this material and eliminate the rest.

*Too big: Most books on these topics are at least 500 pages, and some are more than 1000. By focusing on the topics I think are most useful for software engineers, I kept this book under 250 pages.

*Too bottom-up: Many data structures books focus on how data structures work (the implementations), with less about how to use them (the interfaces). In this book, I go “top down”, starting with the interfaces. Readers learn to use the structures in the Java Collections Framework before getting into the details of how they work.

Finally, many present this material out of context and without motivation: it’s just one damn data structure after another!

I try to alleviate the boredom by organizing the topics around an application—web search—that uses data structures extensively, and is an interesting and important topic in its own right.

This application also motivates some topics that are not usually covered in an introductory data structures class, including persistent data structures, with Redis, and streaming algorithms.

I have made difficult decisions about what to leave out, but I have made some compromises. I include a few topics that most readers will never use, but that they might be expected to know, possibly in a technical interview. For these topics, I present both the conventional wisdom as well as my reasons to be skeptical.

This book also presents basic aspects of software engineering practice, including version control and unit testing. Each chapter ends with an exercise that allows readers to apply what they have learned. Each exercise includes automated tests that check the solution. And for most exercises, I present my solution at the beginning of the next chapter.

This book is intended for college students in computer science and related fields, as well as professional software engineers, people training in software engineering, and people preparing for technical interviews.

I assume that the reader knows Java at an intermediate level, but I explain some Java features along the way, and provide pointers to supplementary material.

People who have read Think Java or Head First Java are prepared for this book.

Think Java is an introduction to Java programming for beginners. It is tailored for students preparing for the Computer Science Advanced Placement (AP) Exam, but it is for anyone who wants to learn Java.

The goal of this book is to teach you to think like a computer scientist. This way of thinking combines some of the best features of mathematics, engineering, and natural science. Like mathematicians, computer scientists use formal languages to denote ideas (specifically computations). Like engineers, they design things, assembling components into systems and evaluating tradeoffs among alternatives. Like scientists, they observe the behavior of complex systems, form hypotheses, and test predictions.

Think Raku is an introduction to computer science and programming intended for people with little or no experience.

This aim of this book is not primarily to teach Raku, but instead to teach the art of programming, using the Raku language. After having completed this book, you should hopefully be able to write programs to solve relatively difficult problems in Raku, but my main aim is to teach computer science, software programming, and problem solving rather than solely to teach the Raku language itself.

Think Raku is a free book available under a Creative Commons license. Readers are free to copy and distribute the text; they are also free to modify it, which allows them to adapt the book to different needs, and to help develop new material.