Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)

Rating:
Summary: Excellent survey of the field
Review: An excellent survey for anyone contemplating doing research in this area. The authors make a special effort to identify the open research problems, what has been done to date and what there is very little of. This book will bridge the gap for anyone with a background in Molecular Biology that wants to build computer models for cellular and genetic activities. It is especially focused on gene regulation, but also covers other modeling areas such as diffusion. In reading this book, you will appreciatge both the good start this field is off to, but also the long way to go before a complete cell can be modeled. A great area to do pioneering work.

Rating:
Summary: it's about time!!!
Review: For many years, biologists have been accumulating descriptions of biological "parts" with an almost complete lack of a framework for understanding how those parts might really work together. This book represents the first and so far only example I have seen of an effort to describe modeling techniques that are right now being developed to construct such a framework. There are other books on "computational biology", but most of them are focused only on measuring and comparing different strands of molecules -- this book describes how computational techniques are starting to be applied to actually trying to understand how those molecules work together to generate life. On the outside jacket of the book, Bruce Alberts, President of the National Academy of Science, AND the guy whose book on molecular biology I had to buy for a lot of money when I was in college, describes the authors of this book as being "Brave". I would say it is an introduction to a "Brave New World". This has to be where biology is going -- Each of the chapters are written by different people, and as such there is some variation in readability. I also wish that the color illustrations were part of the chapter they refer to instead of being grouped in the middle. But most of the chapters start with enough of an overview to be understandable to anyone with a decent background in biology. And WOW -- biology is going to get much more exciting!! Oh one other thing -- the art on the inside of the jacket is wonderful - especially in contrast to the black cover with its standard diagram of metabolism -- I wonder if there is a message there :-) .

Rating:
Summary: Excellent survey of the field
Review: For many years, biologists have been accumulating descriptions of biological "parts" with an almost complete lack of a framework for understanding how those parts might really work together. This book represents the first and so far only example I have seen of an effort to describe modeling techniques that are right now being developed to construct such a framework. There are other books on "computational biology", but most of them are focused only on measuring and comparing different strands of molecules -- this book describes how computational techniques are starting to be applied to actually trying to understand how those molecules work together to generate life. On the outside jacket of the book, Bruce Alberts, President of the National Academy of Science, AND the guy whose book on molecular biology I had to buy for a lot of money when I was in college, describes the authors of this book as being "Brave". I would say it is an introduction to a "Brave New World". This has to be where biology is going -- Each of the chapters are written by different people, and as such there is some variation in readability. I also wish that the color illustrations were part of the chapter they refer to instead of being grouped in the middle. But most of the chapters start with enough of an overview to be understandable to anyone with a decent background in biology. And WOW -- biology is going to get much more exciting!! Oh one other thing -- the art on the inside of the jacket is wonderful - especially in contrast to the black cover with its standard diagram of metabolism -- I wonder if there is a message there :-) .

Rating:
Summary: Informative, but not information I can use
Review: Regulatory networks are central to every aspect of computational biology. Determining what they are, and what genes, proteins, and post-translational modifications interact is a major and exciting field of study.

I just didn't come away from this book with that excitement. I was hoping for more about the large-scale regulation networks, but these papers go down to the quantum mechanics of interactions between pairs of molecules. I appreciate that the exact interactions matter, and that computation is probably the only way to examine some kinds of interactions (e.g. the ones in lethal mutations). It's just not what I think of as a "network."

I was also hoping for some more specifics about the computation techniques. There were some interesting insights here. For example, I never thought about the similarities between steady state chemical equilibrium and steady state Markov model behavior before, but the formalisms have striking similarities. I was also interested in some of the information-based measures for determining how well a model represents a system. I learned that the statistical assumptions behind normal chemical "equilibrium" break down at the scale of bacteria - instead, presence or absence of individual molecules matters more. Still, those were isolated kinds of facts and never came together into a whole for me.

The range of views was worthwhile. On the whole, though, the models all seemed very low-level to me, probably not well suited to handling more than a few dozen interactions, and the computation specifics were not always explicit. I'm still looking for a book with more information that I can apply directly.