# Textbook Overview

### What is bioinformatics?

Formally speaking, bioinformatics is the application of
mathematics and computer science methodology to solve problems
in biology, and in particular, molecular biology. A central
goal of *Bioinformatics for Biologists* is therefore to
convey why these inherited methods are so vital to a thorough
understanding of molecular biology.

As biologists learn more about the nature of life on the molecular level, they discover more and more life processes that require a surprising level of structure. The canonical example of such a process is that of DNA replication, in which an organism's "genetic code" is reproduced. Simply the word "code" implies that mathematics is at hand, and certainly that is the case: the structure of DNA is based upon the ordering of only four nucleotide bases!

Therefore, a number of questions immediately arise. How can we interpret this genetic code? Assuming we can interpret the code, can we use it to identify the sources of disease? What happens if a mistake is made in DNA replication? Biologists are still far from answering these questions, but what is certain is that without a rigorous grounding in mathematics and computer science, attempting to comprehend the mystery of molecular life is a failed endeavor.

*Bioinformatics for Biologists* will therefore consider
several distinct problems that arise in the course of
mainstream biological research, as well as the
computational methods that biologists have borrowed in order
to attack them.

### What is this book?

This book is aimed to convey fundamentals of
bioinformatics to life science students and researchers. It aims to
communicate the computational ideas behind key methods in bioinformatics to
readers without formal college-level computational education. It is not a
"recipe book": it focuses on the *computational ideas* and avoids technical
explanation on running bioinformatics programs or searching databases. Our
experience and strong belief are that once the computational ideas are
grasped, students will be able to use existing bioinformatics tools more
effectively, and can utilize their understanding to advance their research
goals by envisioning new computational goals and communicating better with
computational scientists. The book consists of self-contained chapters each
introducing a basic computational method in bioinformatics along with the
biological problems the method is aimed to solve. Review questions follow
each chapter. An accompanying website containing teaching materials,
presentations, questions and updates will be of help to students as well as
educators.

### Who is the audience for the book?

The book is aimed at life-science undergraduates; it does not assume that the reader has a background in mathematics and computer science, but rather introduces mathematical concepts as they are needed. The book is also appropriate for graduate students and researchers in life science and for medical students. Each chapter can be studied individually and used individually in class or for independent reading.

### What is in the book?

Each chapter describes the biological motivation for a problem and then outlines a computational approach to addressing the problem. Chapters can be read separately, as each introduces any needed computational background beyond basic college-level knowledge.

The range of biological topics addressed is quite broad:
it includes evolution, genomes, regulatory networks, phylogeny and more. The
computational techniques used are also diverse, from probability and graphs,
combinatorics and statistics to algorithms and complexity. However, we made
an effort to keep the material accessible and avoid complex computational
details (those can be filled in by the interested reader using the
references). **Figure 1** aims to show for each chapter the biological topics it
touches upon and the computational areas involved in the analysis.

**Figure 1:** The connections between biological and computational
topics for each chapter. The nodes in the middle are chapters, and edges
connect each chapter to the biological topics it covers (right) and to the
computational topic it introduces (left).

The pedagogical approach, the style, the length, and the depth of the introduced mathematical concepts vary greatly from chapter to chapter. Moreover, even the notation and computational framework describing the same mathematical concepts (e.g., graph theory) across different chapters may vary. As computer scientists say, this is not a bug but a feature: we provided the contributors with complete freedom in selecting the approach that fits their pedagogical goal the best. Indeed, there is no consensus yet on how to introduce computer science to biologists and we feel it is important to see how leading bioinformaticians address the same pedagogical challenge.

### How will this book develop?

"Bioinformatics for Biologists" is an *Open Book Project*:
we welcome all educators to contribute to the future editions of the book.
We envision introduction of computational culture to the biological
education as an ever expanding and self-organizing process: starting from
the second edition, we will work towards unifying the notation and the
pedagogical framework based on the students' and instructors' feedback.
Meanwhile the educators have an option of selecting the specific
self-contained chapters they like for the courses they teach.

### How should I use this book?

Since chapters are self-contained, each chapter can be studied or taught individually and chapters can be followed in any order. One can select to cover, for example, a sample of topics from each of the five biological themes in order to obtain a broader view, or cover completely one of the themes for a deeper concentration. Review questions that follow each chapter are helpful to assimilate the material. Additional resources available at the website will be helpful to teachers in preparing their lectures and to students in deeper and broader learning.