Preface
A contemporary biomedical investigation is akin to a triathlon: multiple challenges lying ahead before reaching the final destination. Contestants are competing with other but at the same time with their own limitations. A biomedical investigation consists of at least three distinct challenges to be overcome:
1. Formulate hypotheses and investigational strategies.
2. Conduct experiments using sophisticated technology platforms and adequate materials and samples.
All these challenges require a high concentration of expertise to overcome them. Although the literature offers comprehensive references and success stories, young investigators are still frustrated by the enormous amount of detail scattered throughout the many sources. The last mile of data analysis is particularly difficult to overcome. A scientist needs to dive into a deluge of complex, heterogeneous and non-linear data, remove noise, boil down the content, delineate the underlying yet obscure picture, and painstakingly piece together the fragmented pieces of the picture into an integral whole. This stage critically determines the overall value of the investigation. An insightful overview of essential knowledge would be very helpful to any young investigator, for them to accomplish their projects on time in this very competitive race.
Bioinformatics is the employment of various information technologies, together with mathematics and statistics, for accomplishing biomedical investigations. This book aims to guide young investigators and clinical practitioners during their biomedical research, releasing them from the heavy burden of trying to remember all the details from the extensive literature, by concentrating on essential knowledge, skills, success stories and available resources of bioinformatics. The content of this book is designed to be 20% theory (mostly in Chapter 1) and 80% on practical problem solving skills. Theoretical discussions are aimed at a deeper comprehension of computational methods. If they wish, readers can skip these parts and directly seek practical solutions. After reading this book, they will be able to use resources efficiently, select adequate tools for their study, and also collaborate with colleagues to design new tools when current tools fall short of their needs.
Integrated or specialized biomedical information databases, as well as associated software and tools, have been contributed by the generous bioinformatics community worldwide. These invaluable resources are largely accessible on the web. This book will enable readers to take advantage of these resources efficiently and effectively. A succinct description of useful resources is presented in each chapter. Some of the software is designed to handle tasks of heavy computational burdens. Others are lightweight versions, which offer convenient and handy solutions for viewing experimental data on a personal computer.
However, because of their constantly evolving nature, this book is not intended to serve as a user manual with step-by-step usage instructions of these software and databases, but will provide the key concepts, names, keywords and references of these resources rather than specific web links. With such information to hand, readers will be able to locate the most up-to-date version of resources using web search engines such as Google. For example, readers can locate the HapMap Genome Browser website (introduced in Chapter 2) simply by searching the phrase "HapMap Genome Browser" using Google.
How to use this book
There are a variety of ways to read this book. Readers can go through the text of each chapter, from head to toe, to obtain a comprehensive overview. Or alternatively, they can jump directly to the take home messages section, and then decide which subsections contain the solution to their current problem. One other way is to jump directly to the case studies to see how the tools are used in real examples. Finally, if the reader already has specific needs of bioinformatic resources, they can go to the boxes directly to check those available.
Of course, if what is covered in the book is still not enough, the reader can always check the citations within the text for further reading, or use key words to search the internet for the latest developments.