they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

I wouldn't use this as my primary book, 27 May 2008
I felt the first few chapters were really geared towards newcomers to 2D/3D Maths and so every topic in the earlier chapters were covered very slowly and in detail. However, as I progressed through the chapters I noticed the authors had started accelerating through the topics at a quicker pace and I was left somewhat confused and so I had to research many of the topics from other resources.

One thing I really didn't like about the book was that the exercises were left to be done at the end of each chapter. The problem with this approach was that some chapters expanded across many pages packed with information you needed to know and thus, like a traditional maths book I would have liked to practice a few questions after each topic and not after a whole chapter.

Not sure who would find this useful, 21 Apr 2008
Sure the book starts off with really really simple maths, using 1d and 2d maths for a springboard. It slowly eases into vector and matrix maths, all described fairly run of the mill. So far so good.

Reading further on into geometric principles and intersections it becomes apparent that the author seems to have forgotten all about the first half of the book and is quickly rambling on using terms and symbols not previously referred to and thus will more than likely lose anyone without a mathematics degree.

Most of the articles here are locatable on the internet if you know how to use a search engine, and described in a much more user friendly way.

3D Maths for mathematicians, 21 Aug 2007
I bought this book thinking it would explain 3D maths to me, a programmer, but instead found it better suited to mathematicians who want to understand vectors and matrices.
There is virtually no pseudocode in the book, and only around 50 pages out of 400 cover 3D graphics in practice, and then in little depth.
The only people who will get anything from this book are people with a degree in Computer Science (and they will probably know 3D maths already).



Highly recommended, 28 Apr 2005
I love this book, and it has payed off very well for me.
The author has a remarkable skill to explain even the most difficult subjects in a way that everyone understands. For example, The Cartesian coordinate system is abstracted to a system of roads.
However, this simplification is not an issue for intermediate/advanced programmers or math students. All topics are provided with formulas and concise material; making this book good for everyone.
Topics covered (but not limited to) vectors, coordination systems, dot-product, cross-product, quaternions, matrices, Auler-angles, bsp-trees, screen projection, culling, bounding-boxes (and a load of other intersection tests).

Still I missed something. The author(s) also covers gourad shading, texture mapping and several other techniques, but they don't go into depth. Different lighting models were given a formula at best, which fortunately is good enough for me. Just don't expect the book to be API-specific or contain information about rendering methods.
The source code which came with the book compiled, but looks awful and very messy. The source code works very well as a reference, but it you are buying the book mainly for the code; don't. I hope they'll update their source code from the webpage soon.

Conclusion: This is a very good book to start with. It contains all the linear algebra math you'll need to start with 3D-programming, and is explained remarkably well. Yet the simplification is nevertheless no con for non-beginners, which will probably use this book as a reference laying on their desktop at all times :-)

Exceptionally good book, 25 Feb 2004
The authors of this book is a game programmer and a professor of Computer Science. This team is excellent!

The game programmer has alot of focus on making the material understandable, and the professor has focus on the mathematically correct semantics. Unlike other books, that teaches game programming (of which many have an author with his strength on either field), this book has the right blend of understandable text parred with the right mathematical semantics.

Furthermore the text is supported by code, so if you are shaky on some of the math, you can see the implementation in C++ code.

As a total math newbie, this book helped me alot, and today I understand totally and in detail what is going on in my 3D programming.

An ABSOLUTE MUST, if you want to learn 3D on top level.

they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

I wouldn't use this as my primary book, 27 May 2008
I felt the first few chapters were really geared towards newcomers to 2D/3D Maths and so every topic in the earlier chapters were covered very slowly and in detail. However, as I progressed through the chapters I noticed the authors had started accelerating through the topics at a quicker pace and I was left somewhat confused and so I had to research many of the topics from other resources.

One thing I really didn't like about the book was that the exercises were left to be done at the end of each chapter. The problem with this approach was that some chapters expanded across many pages packed with information you needed to know and thus, like a traditional maths book I would have liked to practice a few questions after each topic and not after a whole chapter.

Not sure who would find this useful, 21 Apr 2008
Sure the book starts off with really really simple maths, using 1d and 2d maths for a springboard. It slowly eases into vector and matrix maths, all described fairly run of the mill. So far so good.

Reading further on into geometric principles and intersections it becomes apparent that the author seems to have forgotten all about the first half of the book and is quickly rambling on using terms and symbols not previously referred to and thus will more than likely lose anyone without a mathematics degree.

Most of the articles here are locatable on the internet if you know how to use a search engine, and described in a much more user friendly way.

3D Maths for mathematicians, 21 Aug 2007
I bought this book thinking it would explain 3D maths to me, a programmer, but instead found it better suited to mathematicians who want to understand vectors and matrices.
There is virtually no pseudocode in the book, and only around 50 pages out of 400 cover 3D graphics in practice, and then in little depth.
The only people who will get anything from this book are people with a degree in Computer Science (and they will probably know 3D maths already).



Highly recommended, 28 Apr 2005
I love this book, and it has payed off very well for me.
The author has a remarkable skill to explain even the most difficult subjects in a way that everyone understands. For example, The Cartesian coordinate system is abstracted to a system of roads.
However, this simplification is not an issue for intermediate/advanced programmers or math students. All topics are provided with formulas and concise material; making this book good for everyone.
Topics covered (but not limited to) vectors, coordination systems, dot-product, cross-product, quaternions, matrices, Auler-angles, bsp-trees, screen projection, culling, bounding-boxes (and a load of other intersection tests).

Still I missed something. The author(s) also covers gourad shading, texture mapping and several other techniques, but they don't go into depth. Different lighting models were given a formula at best, which fortunately is good enough for me. Just don't expect the book to be API-specific or contain information about rendering methods.
The source code which came with the book compiled, but looks awful and very messy. The source code works very well as a reference, but it you are buying the book mainly for the code; don't. I hope they'll update their source code from the webpage soon.

Conclusion: This is a very good book to start with. It contains all the linear algebra math you'll need to start with 3D-programming, and is explained remarkably well. Yet the simplification is nevertheless no con for non-beginners, which will probably use this book as a reference laying on their desktop at all times :-)

Exceptionally good book, 25 Feb 2004
The authors of this book is a game programmer and a professor of Computer Science. This team is excellent!

The game programmer has alot of focus on making the material understandable, and the professor has focus on the mathematically correct semantics. Unlike other books, that teaches game programming (of which many have an author with his strength on either field), this book has the right blend of understandable text parred with the right mathematical semantics.

Furthermore the text is supported by code, so if you are shaky on some of the math, you can see the implementation in C++ code.

As a total math newbie, this book helped me alot, and today I understand totally and in detail what is going on in my 3D programming.

An ABSOLUTE MUST, if you want to learn 3D on top level.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

I wouldn't use this as my primary book, 27 May 2008
I felt the first few chapters were really geared towards newcomers to 2D/3D Maths and so every topic in the earlier chapters were covered very slowly and in detail. However, as I progressed through the chapters I noticed the authors had started accelerating through the topics at a quicker pace and I was left somewhat confused and so I had to research many of the topics from other resources.

One thing I really didn't like about the book was that the exercises were left to be done at the end of each chapter. The problem with this approach was that some chapters expanded across many pages packed with information you needed to know and thus, like a traditional maths book I would have liked to practice a few questions after each topic and not after a whole chapter.

Not sure who would find this useful, 21 Apr 2008
Sure the book starts off with really really simple maths, using 1d and 2d maths for a springboard. It slowly eases into vector and matrix maths, all described fairly run of the mill. So far so good.

Reading further on into geometric principles and intersections it becomes apparent that the author seems to have forgotten all about the first half of the book and is quickly rambling on using terms and symbols not previously referred to and thus will more than likely lose anyone without a mathematics degree.

Most of the articles here are locatable on the internet if you know how to use a search engine, and described in a much more user friendly way.

3D Maths for mathematicians, 21 Aug 2007
I bought this book thinking it would explain 3D maths to me, a programmer, but instead found it better suited to mathematicians who want to understand vectors and matrices.
There is virtually no pseudocode in the book, and only around 50 pages out of 400 cover 3D graphics in practice, and then in little depth.
The only people who will get anything from this book are people with a degree in Computer Science (and they will probably know 3D maths already).



Highly recommended, 28 Apr 2005
I love this book, and it has payed off very well for me.
The author has a remarkable skill to explain even the most difficult subjects in a way that everyone understands. For example, The Cartesian coordinate system is abstracted to a system of roads.
However, this simplification is not an issue for intermediate/advanced programmers or math students. All topics are provided with formulas and concise material; making this book good for everyone.
Topics covered (but not limited to) vectors, coordination systems, dot-product, cross-product, quaternions, matrices, Auler-angles, bsp-trees, screen projection, culling, bounding-boxes (and a load of other intersection tests).

Still I missed something. The author(s) also covers gourad shading, texture mapping and several other techniques, but they don't go into depth. Different lighting models were given a formula at best, which fortunately is good enough for me. Just don't expect the book to be API-specific or contain information about rendering methods.
The source code which came with the book compiled, but looks awful and very messy. The source code works very well as a reference, but it you are buying the book mainly for the code; don't. I hope they'll update their source code from the webpage soon.

Conclusion: This is a very good book to start with. It contains all the linear algebra math you'll need to start with 3D-programming, and is explained remarkably well. Yet the simplification is nevertheless no con for non-beginners, which will probably use this book as a reference laying on their desktop at all times :-)

Exceptionally good book, 25 Feb 2004
The authors of this book is a game programmer and a professor of Computer Science. This team is excellent!

The game programmer has alot of focus on making the material understandable, and the professor has focus on the mathematically correct semantics. Unlike other books, that teaches game programming (of which many have an author with his strength on either field), this book has the right blend of understandable text parred with the right mathematical semantics.

Furthermore the text is supported by code, so if you are shaky on some of the math, you can see the implementation in C++ code.

As a total math newbie, this book helped me alot, and today I understand totally and in detail what is going on in my 3D programming.

An ABSOLUTE MUST, if you want to learn 3D on top level.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Resistance is futile - read this book, 03 May 2002
In this book of panoramic scope Hayles considers no less than the fate of the human race. In a rich and detailed discussion ranging from the science fiction of Greg Bear and Philip K. Dick to the science of Norbert Wiener's cybernetics and Claude Shannon's information theory, Hayles traces the changing conception of human consciousness and claims that a great many of us are already posthuman. A posthuman is someone who has been reconstructed in some sense, either physically or mentally, such that he or she exceeds, or believes they can exceed, the boundaries of a human. About ten percent of Americans can be considered cyborgs in the technical sense by virtue of having some kind of artificial implant - these people would qualify as posthuman since they have compensated for some limitation of their bodies through technological augmentation. However, Hayles claims that to be posthuman no prosthesis is necessary, simply the way in which we think about ourselves as conscious agents needs to change. The advent of Shannon's information theory has led to the modern convention of treating information as if it were entirely non-physical. If this idea is applied to the information in our heads - that is, the collection of memories that make each of us unique - then we quickly arrive at the conclusion that our consciousness can be uploaded into a computer, decanted into a robot-body, or even backed-up onto computer disk, giving us eternal life.

This is the story of how information lost its body and it is an idea which is now well established in Western culture and technology. Yet, Hayles believes it to be misguided. Any informational pattern, be it pebbles on the beach or electrons whizzing across the internet, must have a physical embodiment to exist. The importance of embodiment is also being discovered in fields such as neurology and experimental robotics. A surprisingly large amount of the information processing essential for being a responsive agent in the world goes on in body parts such as nerves, the spine and the proprioception of joints - our powerful human consciousness is a relatively recent add-on.

Hayles argues that future posthumans will not be the ethereal information-beings of much of current science fiction, but they will certainly have a much more intimate relationship with computers than we do today. In terms of information flows, a collection of humans and computers contains no boundaries between one and the next. As computers approach the complexity of our bodies and information becomes more important to our work and leisure, humans and computers will become more compatible with each other and there will be an increasing potential for one to collapse into the other. Whether this is to the detriment or betterment of humanity represents a cross-roads which urgently needs to be addressed. Hayles is well aware that technology issues such as these currently concern relatively few people - the majority of the world's population has yet to make their first phone call. Yet, now is precisely when such issues need to be aired before our posthuman futures are set in stone as either assimilated components in a vast machine or as free agents with powerful human-integrated technology at our disposal.

Stunning tour de "force" ! Hayles burns up brain circuits!, 03 Mar 1999
Read this book to see how an American writes in that obtuse French post-modern style. She covers the psybernetic/media territory from 1943 to 1999 the best I've ever seen. Zig-zags from Gregory Bateson & Alan Turing on to William Gibson and covers the very interesting idea that "information" probably does not exist like we generally think of it...a la Franciso Varela. Most importantly, She retreives Embodiment as the fundamental ground of all consciousness..that no feature of consciousness is ever not physical and even "information"-bits & bytes on/in the 'Net... cyber"space" is always embodied in servers/fiber optic lines/memory storage magnetic fields,etc.

Brief review in AMERICAN SCIENTIST, Mar-Apr 1999, p.178, 18 Feb 1999
HOW WE BECAME POSTHUMAN by N. Katherine Hayles (Chicago, $18, paper) explores the relation between the computer revolution and our changing ideas of what it means to be a human being. Her pet theme: how information became an entity in itself, divorced from the material that carries it, in both science and literature. Norbert Wiener meets P.K. Dick. (p. 178)

they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

I wouldn't use this as my primary book, 27 May 2008
I felt the first few chapters were really geared towards newcomers to 2D/3D Maths and so every topic in the earlier chapters were covered very slowly and in detail. However, as I progressed through the chapters I noticed the authors had started accelerating through the topics at a quicker pace and I was left somewhat confused and so I had to research many of the topics from other resources.

One thing I really didn't like about the book was that the exercises were left to be done at the end of each chapter. The problem with this approach was that some chapters expanded across many pages packed with information you needed to know and thus, like a traditional maths book I would have liked to practice a few questions after each topic and not after a whole chapter.

Not sure who would find this useful, 21 Apr 2008
Sure the book starts off with really really simple maths, using 1d and 2d maths for a springboard. It slowly eases into vector and matrix maths, all described fairly run of the mill. So far so good.

Reading further on into geometric principles and intersections it becomes apparent that the author seems to have forgotten all about the first half of the book and is quickly rambling on using terms and symbols not previously referred to and thus will more than likely lose anyone without a mathematics degree.

Most of the articles here are locatable on the internet if you know how to use a search engine, and described in a much more user friendly way.

3D Maths for mathematicians, 21 Aug 2007
I bought this book thinking it would explain 3D maths to me, a programmer, but instead found it better suited to mathematicians who want to understand vectors and matrices.
There is virtually no pseudocode in the book, and only around 50 pages out of 400 cover 3D graphics in practice, and then in little depth.
The only people who will get anything from this book are people with a degree in Computer Science (and they will probably know 3D maths already).



Highly recommended, 28 Apr 2005
I love this book, and it has payed off very well for me.
The author has a remarkable skill to explain even the most difficult subjects in a way that everyone understands. For example, The Cartesian coordinate system is abstracted to a system of roads.
However, this simplification is not an issue for intermediate/advanced programmers or math students. All topics are provided with formulas and concise material; making this book good for everyone.
Topics covered (but not limited to) vectors, coordination systems, dot-product, cross-product, quaternions, matrices, Auler-angles, bsp-trees, screen projection, culling, bounding-boxes (and a load of other intersection tests).

Still I missed something. The author(s) also covers gourad shading, texture mapping and several other techniques, but they don't go into depth. Different lighting models were given a formula at best, which fortunately is good enough for me. Just don't expect the book to be API-specific or contain information about rendering methods.
The source code which came with the book compiled, but looks awful and very messy. The source code works very well as a reference, but it you are buying the book mainly for the code; don't. I hope they'll update their source code from the webpage soon.

Conclusion: This is a very good book to start with. It contains all the linear algebra math you'll need to start with 3D-programming, and is explained remarkably well. Yet the simplification is nevertheless no con for non-beginners, which will probably use this book as a reference laying on their desktop at all times :-)

Exceptionally good book, 25 Feb 2004
The authors of this book is a game programmer and a professor of Computer Science. This team is excellent!

The game programmer has alot of focus on making the material understandable, and the professor has focus on the mathematically correct semantics. Unlike other books, that teaches game programming (of which many have an author with his strength on either field), this book has the right blend of understandable text parred with the right mathematical semantics.

Furthermore the text is supported by code, so if you are shaky on some of the math, you can see the implementation in C++ code.

As a total math newbie, this book helped me alot, and today I understand totally and in detail what is going on in my 3D programming.

An ABSOLUTE MUST, if you want to learn 3D on top level.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Resistance is futile - read this book, 03 May 2002
In this book of panoramic scope Hayles considers no less than the fate of the human race. In a rich and detailed discussion ranging from the science fiction of Greg Bear and Philip K. Dick to the science of Norbert Wiener's cybernetics and Claude Shannon's information theory, Hayles traces the changing conception of human consciousness and claims that a great many of us are already posthuman. A posthuman is someone who has been reconstructed in some sense, either physically or mentally, such that he or she exceeds, or believes they can exceed, the boundaries of a human. About ten percent of Americans can be considered cyborgs in the technical sense by virtue of having some kind of artificial implant - these people would qualify as posthuman since they have compensated for some limitation of their bodies through technological augmentation. However, Hayles claims that to be posthuman no prosthesis is necessary, simply the way in which we think about ourselves as conscious agents needs to change. The advent of Shannon's information theory has led to the modern convention of treating information as if it were entirely non-physical. If this idea is applied to the information in our heads - that is, the collection of memories that make each of us unique - then we quickly arrive at the conclusion that our consciousness can be uploaded into a computer, decanted into a robot-body, or even backed-up onto computer disk, giving us eternal life.

This is the story of how information lost its body and it is an idea which is now well established in Western culture and technology. Yet, Hayles believes it to be misguided. Any informational pattern, be it pebbles on the beach or electrons whizzing across the internet, must have a physical embodiment to exist. The importance of embodiment is also being discovered in fields such as neurology and experimental robotics. A surprisingly large amount of the information processing essential for being a responsive agent in the world goes on in body parts such as nerves, the spine and the proprioception of joints - our powerful human consciousness is a relatively recent add-on.

Hayles argues that future posthumans will not be the ethereal information-beings of much of current science fiction, but they will certainly have a much more intimate relationship with computers than we do today. In terms of information flows, a collection of humans and computers contains no boundaries between one and the next. As computers approach the complexity of our bodies and information becomes more important to our work and leisure, humans and computers will become more compatible with each other and there will be an increasing potential for one to collapse into the other. Whether this is to the detriment or betterment of humanity represents a cross-roads which urgently needs to be addressed. Hayles is well aware that technology issues such as these currently concern relatively few people - the majority of the world's population has yet to make their first phone call. Yet, now is precisely when such issues need to be aired before our posthuman futures are set in stone as either assimilated components in a vast machine or as free agents with powerful human-integrated technology at our disposal.

Stunning tour de "force" ! Hayles burns up brain circuits!, 03 Mar 1999
Read this book to see how an American writes in that obtuse French post-modern style. She covers the psybernetic/media territory from 1943 to 1999 the best I've ever seen. Zig-zags from Gregory Bateson & Alan Turing on to William Gibson and covers the very interesting idea that "information" probably does not exist like we generally think of it...a la Franciso Varela. Most importantly, She retreives Embodiment as the fundamental ground of all consciousness..that no feature of consciousness is ever not physical and even "information"-bits & bytes on/in the 'Net... cyber"space" is always embodied in servers/fiber optic lines/memory storage magnetic fields,etc.

Brief review in AMERICAN SCIENTIST, Mar-Apr 1999, p.178, 18 Feb 1999
HOW WE BECAME POSTHUMAN by N. Katherine Hayles (Chicago, $18, paper) explores the relation between the computer revolution and our changing ideas of what it means to be a human being. Her pet theme: how information became an entity in itself, divorced from the material that carries it, in both science and literature. Norbert Wiener meets P.K. Dick. (p. 178)

If you are an evolutinary biologist or ecologist and you want to get into modelling buy this book., 29 Nov 2008
This is an excellent and very comprehensive text written in a biologist friendly style but that still delivers almost all of the maths you are ever likely to need in mathematical biology.

Books like Edelstein-Keshet and Murray are written from a much more mathematical background and tend to use notation and concepts that are hard for non-mathematicians to grasp. Maths phobia is a serious barrier to biologists entering the field, where we need biological as well as mathematical insight.

This book introduces the mathemtical concepts as they are needed by way of a series of primers. The rest of the book is filled with examples that concentrate on the biology rather than the mathematical techniques. There are also chapters that explain the methods of model building and the reasoning behind model building.

For me this is a perfect graduate level or third year undergraduate level text.

they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

I wouldn't use this as my primary book, 27 May 2008
I felt the first few chapters were really geared towards newcomers to 2D/3D Maths and so every topic in the earlier chapters were covered very slowly and in detail. However, as I progressed through the chapters I noticed the authors had started accelerating through the topics at a quicker pace and I was left somewhat confused and so I had to research many of the topics from other resources.

One thing I really didn't like about the book was that the exercises were left to be done at the end of each chapter. The problem with this approach was that some chapters expanded across many pages packed with information you needed to know and thus, like a traditional maths book I would have liked to practice a few questions after each topic and not after a whole chapter.

Not sure who would find this useful, 21 Apr 2008
Sure the book starts off with really really simple maths, using 1d and 2d maths for a springboard. It slowly eases into vector and matrix maths, all described fairly run of the mill. So far so good.

Reading further on into geometric principles and intersections it becomes apparent that the author seems to have forgotten all about the first half of the book and is quickly rambling on using terms and symbols not previously referred to and thus will more than likely lose anyone without a mathematics degree.

Most of the articles here are locatable on the internet if you know how to use a search engine, and described in a much more user friendly way.

3D Maths for mathematicians, 21 Aug 2007
I bought this book thinking it would explain 3D maths to me, a programmer, but instead found it better suited to mathematicians who want to understand vectors and matrices.
There is virtually no pseudocode in the book, and only around 50 pages out of 400 cover 3D graphics in practice, and then in little depth.
The only people who will get anything from this book are people with a degree in Computer Science (and they will probably know 3D maths already).



Highly recommended, 28 Apr 2005
I love this book, and it has payed off very well for me.
The author has a remarkable skill to explain even the most difficult subjects in a way that everyone understands. For example, The Cartesian coordinate system is abstracted to a system of roads.
However, this simplification is not an issue for intermediate/advanced programmers or math students. All topics are provided with formulas and concise material; making this book good for everyone.
Topics covered (but not limited to) vectors, coordination systems, dot-product, cross-product, quaternions, matrices, Auler-angles, bsp-trees, screen projection, culling, bounding-boxes (and a load of other intersection tests).

Still I missed something. The author(s) also covers gourad shading, texture mapping and several other techniques, but they don't go into depth. Different lighting models were given a formula at best, which fortunately is good enough for me. Just don't expect the book to be API-specific or contain information about rendering methods.
The source code which came with the book compiled, but looks awful and very messy. The source code works very well as a reference, but it you are buying the book mainly for the code; don't. I hope they'll update their source code from the webpage soon.

Conclusion: This is a very good book to start with. It contains all the linear algebra math you'll need to start with 3D-programming, and is explained remarkably well. Yet the simplification is nevertheless no con for non-beginners, which will probably use this book as a reference laying on their desktop at all times :-)

Exceptionally good book, 25 Feb 2004
The authors of this book is a game programmer and a professor of Computer Science. This team is excellent!

The game programmer has alot of focus on making the material understandable, and the professor has focus on the mathematically correct semantics. Unlike other books, that teaches game programming (of which many have an author with his strength on either field), this book has the right blend of understandable text parred with the right mathematical semantics.

Furthermore the text is supported by code, so if you are shaky on some of the math, you can see the implementation in C++ code.

As a total math newbie, this book helped me alot, and today I understand totally and in detail what is going on in my 3D programming.

An ABSOLUTE MUST, if you want to learn 3D on top level.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Resistance is futile - read this book, 03 May 2002
In this book of panoramic scope Hayles considers no less than the fate of the human race. In a rich and detailed discussion ranging from the science fiction of Greg Bear and Philip K. Dick to the science of Norbert Wiener's cybernetics and Claude Shannon's information theory, Hayles traces the changing conception of human consciousness and claims that a great many of us are already posthuman. A posthuman is someone who has been reconstructed in some sense, either physically or mentally, such that he or she exceeds, or believes they can exceed, the boundaries of a human. About ten percent of Americans can be considered cyborgs in the technical sense by virtue of having some kind of artificial implant - these people would qualify as posthuman since they have compensated for some limitation of their bodies through technological augmentation. However, Hayles claims that to be posthuman no prosthesis is necessary, simply the way in which we think about ourselves as conscious agents needs to change. The advent of Shannon's information theory has led to the modern convention of treating information as if it were entirely non-physical. If this idea is applied to the information in our heads - that is, the collection of memories that make each of us unique - then we quickly arrive at the conclusion that our consciousness can be uploaded into a computer, decanted into a robot-body, or even backed-up onto computer disk, giving us eternal life.

This is the story of how information lost its body and it is an idea which is now well established in Western culture and technology. Yet, Hayles believes it to be misguided. Any informational pattern, be it pebbles on the beach or electrons whizzing across the internet, must have a physical embodiment to exist. The importance of embodiment is also being discovered in fields such as neurology and experimental robotics. A surprisingly large amount of the information processing essential for being a responsive agent in the world goes on in body parts such as nerves, the spine and the proprioception of joints - our powerful human consciousness is a relatively recent add-on.

Hayles argues that future posthumans will not be the ethereal information-beings of much of current science fiction, but they will certainly have a much more intimate relationship with computers than we do today. In terms of information flows, a collection of humans and computers contains no boundaries between one and the next. As computers approach the complexity of our bodies and information becomes more important to our work and leisure, humans and computers will become more compatible with each other and there will be an increasing potential for one to collapse into the other. Whether this is to the detriment or betterment of humanity represents a cross-roads which urgently needs to be addressed. Hayles is well aware that technology issues such as these currently concern relatively few people - the majority of the world's population has yet to make their first phone call. Yet, now is precisely when such issues need to be aired before our posthuman futures are set in stone as either assimilated components in a vast machine or as free agents with powerful human-integrated technology at our disposal.

Stunning tour de "force" ! Hayles burns up brain circuits!, 03 Mar 1999
Read this book to see how an American writes in that obtuse French post-modern style. She covers the psybernetic/media territory from 1943 to 1999 the best I've ever seen. Zig-zags from Gregory Bateson & Alan Turing on to William Gibson and covers the very interesting idea that "information" probably does not exist like we generally think of it...a la Franciso Varela. Most importantly, She retreives Embodiment as the fundamental ground of all consciousness..that no feature of consciousness is ever not physical and even "information"-bits & bytes on/in the 'Net... cyber"space" is always embodied in servers/fiber optic lines/memory storage magnetic fields,etc.

Brief review in AMERICAN SCIENTIST, Mar-Apr 1999, p.178, 18 Feb 1999
HOW WE BECAME POSTHUMAN by N. Katherine Hayles (Chicago, $18, paper) explores the relation between the computer revolution and our changing ideas of what it means to be a human being. Her pet theme: how information became an entity in itself, divorced from the material that carries it, in both science and literature. Norbert Wiener meets P.K. Dick. (p. 178)

If you are an evolutinary biologist or ecologist and you want to get into modelling buy this book., 29 Nov 2008
This is an excellent and very comprehensive text written in a biologist friendly style but that still delivers almost all of the maths you are ever likely to need in mathematical biology.

Books like Edelstein-Keshet and Murray are written from a much more mathematical background and tend to use notation and concepts that are hard for non-mathematicians to grasp. Maths phobia is a serious barrier to biologists entering the field, where we need biological as well as mathematical insight.

This book introduces the mathemtical concepts as they are needed by way of a series of primers. The rest of the book is filled with examples that concentrate on the biology rather than the mathematical techniques. There are also chapters that explain the methods of model building and the reasoning behind model building.

For me this is a perfect graduate level or third year undergraduate level text.

Phylogenetic trees made wrong, 21 Jul 2008
This is a how-to manual and with that all is said. If you really believe you can make a proper phylogenetic tree without understanding basic concepts of molecular evolution, you 've got it all wrong. The author spices his book with his own experiences, without giving details. This is like just believing your teacher because he is your teacher. Unfortunately the book is full with half-truths. The author encourages NOT to go profound since errors in the alignments will typically not affect tree architecture. And so on and so on.

Actually, I think it is a shame this book is published. With this book you will indeed produce trees within minutes, but quite sure: most of them are all wrong.

Furthermore, the author completely ignores Phylip. No matter how you look at it, you cannot ignore Phylip. This is probably just to advertise the software for which this How-to was written, Mega (also not the best choice). Typically most of these packges come with free how-to's. Please ignore this book.

Extraordinarily good, compact and value for money, 03 Jun 2008
Shortly after I got the second edition, I got the third. Within the covers of this slim volume is all the information you will need to generate the most elaborate hypotheses you may dare to venture on the basis of all the hard work you may have put into obtaining a data set of protein or DNA sequences.

The chapters are clearly laid out and this is a cook book - you can follow the instructions chapter by chapter using freely available software that it recommends. All the way from organizing your data, making an alignment and turning this into a simple tree, to computing genetic distances and finally producing trees by Baysian Inference or Maximum Likelihood.

Within certain relevant chapters are essays explaining the mathematical bases of tree building, models employed and the various kinds of trees and how they are built up - chapters on Trees, Neighbour Joining, Maximum Parsimony, Maximum Likelihood, Baysian Inference and there are downloadable programs that work fine as per the instructions like Fas2PhyNex which instantly transforms your Fasta file format into a Phylip and Nexus format. This book is a treasure trove of such packages and the simplest available descriptions of the sort of work you're up to at a level suitable for beginners and those with background (tells it to you straight without dumbing down). Those who go through your conclusions later may admire you for your profound understanding of the subject, on the basis of this book.

I feel the book could have tackled the following issues more clearly: 1. Establishing genetic distances for publications, uncorrected vs corrected - this book gives information on how to establish distances using the P distance model and the pairwise deletion option in MEGA - but I had to read further before realising it was sort of all there - but perhaps not emphasised enough (descriptions of new species frequently give uncorrected genetic distances at least). 2. Whether data from two different sequences for the same taxa should be combined to create a single data set for tree building, and when or when not to think about this (you can also make separate trees and combine them consensually). 3. What to do about gaps in the data - for example, I had several intact sequences of around 1kbp but a few were only 600bp - what problems would the shorter sequences cause? In the event, I had full and truncated data sets and trees for comparison. I found that having the odd short sequence was not too problematic - or at least, that's how it appeared.

This book is almost perfect, but it should be supplemented if you're a beginner (as with many books). I strongly recommend - Bioinformatics for Dummies. Using Bioinformatics, I realised that making alignments in T-coffee was better than using the MEGA multiple alignment system in terms of ironing out any errors that may be fiddly to correct by hand.

For information, whereas PHYML was superb for ML trees, I actually found that the ALRT bootstrap implementation just failed several times and went to use the traditional method. In a similar vein, I found the older versions of PHYML more effective that the latest, given sometimes the latest versions just did not deliver the goods.

I found that the author to be totally perspicacious and helpful and he has struggled so we don't have to. He has been wise to create such a slim volume - to paraphrase from the Seven Pillars of Wisdom by TE Lawrence - A Triumph. With a little supplementary reading (as this book recommends, do read the bits of the Mr Bayes Manual and take other pointers into account) the book is a gem - well worth the small cost and saving in Library space. I certainly look forward to future editions without begging for them as this book is so good.

Followed it fairly religiously and I will owe my upcoming award of a PhD in part to this helpful manual/friend.

good introductory 'recipe' book, 25 Apr 2008
Contrary to the review left by another reader, the third edition of this book uses MEGA4 (freely available) to illustrate the practical examples. Although the background theory to models is at best rudimentary, this is a really nice and easy introduction for complete beginners to the practical aspects of phylogenetic tree construction.

Phylogenetic trees made difficult !!, 29 Aug 2005
I am really disappointed about this book. I bought it originally because I wanted to learn the basic principles of making phylogenetic trees. My background about this subject was very shallow and the title of this book was very tempting. However, when i started to read through its chapters, I was not impressed. The first chapter is describing how to prepare multiple alignements, which I already knew about and I would also expect all molecular biologists to know very well. The second chapter is describing the use of "a commercially available software" called PAUP in making phylogenetic trees. Although I could understand from the author's description of the software that it is very efficient in doing the job, I totally disagree with this choice for two reasons. Firstly, it is not a freely availale software that anybody can use and I don't think that the time-limited copy of the software available with the book will be useful for frequent long-term users. So. you will have to purchase it at some stage. Secondly, it works best on Macintosh and only accessible through tedious command lines on PCs. So, make sure that you own a Mac before thinking of using this piece of software, otherwise your life will not be easy! The third chapter is only for advanced users. The last chapter is dealing with other options for using the software under windows and a very short description for a free online software called Phylip; to be honest it didn't find it particularly useful. Nevertheless, there are some informative boxes throught the book about the background behind the applications done by the software. I think the beauty of this book was spoiled by the choice of the software which constitutes the main body of the book.

they say on the title "an excellent book for beginners and occasional practioners", 19 Jun 2007
... and I agree. This is a book for molecular biologist who want to analyse their data using bioinformatics tools. I would prefer Baxevanis/Oullette "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins", however, if this is too expensive for you than this "Bioinformatics for Dummies" is the second best choice. Layout and index is a bit more confused but it covers most stuff you will need.

A word of warning: if you want to learn how the programs work, you have to look for a different type of book, e.g. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by R. Durbin, Sean R. Eddy, Anders Krogh, and Graeme Mitchison or "Algorithmic Aspects of Bioinformatics" by Hans-Joachim Bockenhauer and Dirk Bongartz.

Clear and informative, 26 Dec 2005
So much of the information is this field (and indeed some of the applications which have been developed) seems almost intentially convoluted and difficult to understand. This book gives a very good overview of some of the more common programs that one will need to use if one is starting bioinformatics research in a way that is practical and easy understand. Despite the title, the authors have done some good work in the field (I use Notredame's T-Coffee alignment program often) and are credible authorities in this area.

I wouldn't use this as my primary book, 27 May 2008
I felt the first few chapters were really geared towards newcomers to 2D/3D Maths and so every topic in the earlier chapters were covered very slowly and in detail. However, as I progressed through the chapters I noticed the authors had started accelerating through the topics at a quicker pace and I was left somewhat confused and so I had to research many of the topics from other resources.

One thing I really didn't like about the book was that the exercises were left to be done at the end of each chapter. The problem with this approach was that some chapters expanded across many pages packed with information you needed to know and thus, like a traditional maths book I would have liked to practice a few questions after each topic and not after a whole chapter.

Not sure who would find this useful, 21 Apr 2008
Sure the book starts off with really really simple maths, using 1d and 2d maths for a springboard. It slowly eases into vector and matrix maths, all described fairly run of the mill. So far so good.

Reading further on into geometric principles and intersections it becomes apparent that the author seems to have forgotten all about the first half of the book and is quickly rambling on using terms and symbols not previously referred to and thus will more than likely lose anyone without a mathematics degree.

Most of the articles here are locatable on the internet if you know how to use a search engine, and described in a much more user friendly way.

3D Maths for mathematicians, 21 Aug 2007
I bought this book thinking it would explain 3D maths to me, a programmer, but instead found it better suited to mathematicians who want to understand vectors and matrices.
There is virtually no pseudocode in the book, and only around 50 pages out of 400 cover 3D graphics in practice, and then in little depth.
The only people who will get anything from this book are people with a degree in Computer Science (and they will probably know 3D maths already).



Highly recommended, 28 Apr 2005
I love this book, and it has payed off very well for me.
The author has a remarkable skill to explain even the most difficult subjects in a way that everyone understands. For example, The Cartesian coordinate system is abstracted to a system of roads.
However, this simplification is not an issue for intermediate/advanced programmers or math students. All topics are provided with formulas and concise material; making this book good for everyone.
Topics covered (but not limited to) vectors, coordination systems, dot-product, cross-product, quaternions, matrices, Auler-angles, bsp-trees, screen projection, culling, bounding-boxes (and a load of other intersection tests).

Still I missed something. The author(s) also covers gourad shading, texture mapping and several other techniques, but they don't go into depth. Different lighting models were given a formula at best, which fortunately is good enough for me. Just don't expect the book to be API-specific or contain information about rendering methods.
The source code which came with the book compiled, but looks awful and very messy. The source code works very well as a reference, but it you are buying the book mainly for the code; don't. I hope they'll update their source code from the webpage soon.

Conclusion: This is a very good book to start with. It contains all the linear algebra math you'll need to start with 3D-programming, and is explained remarkably well. Yet the simplification is nevertheless no con for non-beginners, which will probably use this book as a reference laying on their desktop at all times :-)

Exceptionally good book, 25 Feb 2004
The authors of this book is a game programmer and a professor of Computer Science. This team is excellent!

The game programmer has alot of focus on making the material understandable, and the professor has focus on the mathematically correct semantics. Unlike other books, that teaches game programming (of which many have an author with his strength on either field), this book has the right blend of understandable text parred with the right mathematical semantics.

Furthermore the text is supported by code, so if you are shaky on some of the math, you can see the implementation in C++ code.

As a total math newbie, this book helped me alot, and today I understand totally and in detail what is going on in my 3D programming.

An ABSOLUTE MUST, if you want to learn 3D on top level.

Brings strands of knowledge together, 11 Oct 2008
My science background is well out-of-date. In this book I can find several half understood concepts brought together, well explained and illuminating each other to an amazing extent. It's really rather exciting!

A great introductory book, 25 Jun 2004
This is an excellent introduction to this up-and-coming field. Bioinformatics one of many fields that is inherently inter-disciplinary, with biologists coming in and needing to learn computer science, and computer scientists coming in and needing to learn biology. I think that the book is very useful for both groups. I have a computer science background and did not find any of the biology overly difficult. So I highly recommend it for anyone, from the undergraduate to the postrgraduate or professional.

The book covers all of the major topics in bioinformatics, and touches on several of the minor ones. There are 5 long chapters:
Chapter 1 Introduction: introduces the basics of the field, describing the basics of data archiving, the WWW, computers and computer programming, biological classification and nomenclature, phylogenetic relationships and use of sequences, PSI-BLAST, and protein structure.
Chapter 2 Genome organization and evolution: genomics and proteomics, methods of genetic information transmission, genes and genomes, SNPs, genome evolution.
Chapter 3 Archives and information retrieval: this contains a detailed discussion of various databases and how to interact with them.
Chapter 4 Alignments and phylogenetic trees: this vast majority of this chapter covers many aspects of the important area of sequence alignment, including BLAST and HMMs. Then it has short sections on phylogeny and phylogenetic trees, again covering the basics.
Chapter 5 Protein structure and drug discovery: this starts with protein folding, and deals with hydrophobicity, structural alignments, DALI, and then evolution, classification and prediction of protein structures and function. Finally it touches on drug discovery in this context.

One of the nice things about this book is the code samples, written in the bioinformatician's favorite language, Perl. These are printed and discussed in the book, but then also available on the web site that is associated with the book, so you don't have to type it in yourself. In addition to the programs, the website also has graphics from the book, many of which rotate so you can see them from different positions (can't get that in a book!). It also has the web links mentioned in the book, so you can explore them more conveniently than having to flip through the book and type the URLs in.

An excellent beginner's guide to bioinformatics, 27 Apr 2002
This is a superb introduction to the subject of bioinformatics. It is very well written, and for the first time (thanks to this book) I can understand what hidden Markov models are about. It invites comparison with another book of the same name, namely "Introduction to Bioinformatics" by Attwood and Parry-Smith. The book by Lesk has two advantages (three, I suppose, if you include the fact that it is a more recent publication): it uses everyday, non-biological analogies to explain many of the concepts that are otherwise difficult to grasp, and it also covers molecular modelling.

Advanced undergraduate students tackling bioinformatics for the first time, or research students whose experience of bioinformatics is limited to the odd BLAST search and surfing through genomes, will find this book a must have. You will wonder how you ever got by without it.

Resistance is futile - read this book, 03 May 2002
In this book of panoramic scope Hayles considers no less than the fate of the human race. In a rich and detailed discussion ranging from the science fiction of Greg Bear and Philip K. Dick to the science of Norbert Wiener's cybernetics and Claude Shannon's information theory, Hayles traces the changing conception of human consciousness and claims that a great many of us are already posthuman. A posthuman is someone who has been reconstructed in some sense, either physically or mentally, such that he or she exceeds, or believes they can exceed, the boundaries of a human. About ten percent of Americans can be considered cyborgs in the technical sense by virtue of having some kind of artificial implant - these people would qualify as posthuman since they have compensated for some limitation of their bodies through technological augmentation. However, Hayles claims that to be posthuman no prosthesis is necessary, simply the way in which we think about ourselves as conscious agents needs to change. The advent of Shannon's information theory has led to the modern convention of treating information as if it were entirely non-physical. If this idea is applied to the information in our heads - that is, the collection of memories that make each of us unique - then we quickly arrive at the conclusion that our consciousness can be uploaded into a computer, decanted into a robot-body, or even backed-up onto computer disk, giving us eternal life.

This is the story of how information lost its body and it is an idea which is now well established in Western culture and technology. Yet, Hayles believes it to be misguided. Any informational pattern, be it pebbles on the beach or electrons whizzing across the internet, must have a physical embodiment to exist. The importance of embodiment is also being discovered in fields such as neurology and experimental robotics. A surprisingly large amount of the information processing essential for being a responsive agent in the world goes on in body parts such as nerves, the spine and the proprioception of joints - our powerful human consciousness is a relatively recent add-on.

Hayles argues that future posthumans will not be the ethereal information-beings of much of current science fiction, but they will certainly have a much more intimate relationship with computers than we do today. In terms of information flows, a collection of humans and computers contains no boundaries between one and the next. As computers approach the complexity of our bodies and information becomes more important to our work and leisure, humans and computers will become more compatible with each other and there will be an increasing potential for one to collapse into the other. Whether this is to the detriment or betterment of humanity represents a cross-roads which urgently needs to be addressed. Hayles is well aware that technology issues such as these currently concern relatively few people - the majority of the world's population has yet to make their first phone call. Yet, now is precisely when such issues need to be aired before our posthuman futures are set in stone as either assimilated components in a vast machine or as free agents with powerful human-integrated technology at our disposal.

Stunning tour de "force" ! Hayles burns up brain circuits!, 03 Mar 1999
Read this book to see how an American writes in that obtuse French post-modern style. She covers the psybernetic/media territory from 1943 to 1999 the best I've ever seen. Zig-zags from Gregory Bateson & Alan Turing on to William Gibson and covers the very interesting idea that "information" probably does not exist like we generally think of it...a la Franciso Varela. Most importantly, She retreives Embodiment as the fundamental ground of all consciousness..that no feature of consciousness is ever not physical and even "information"-bits & bytes on/in the 'Net... cyber"space" is always embodied in servers/fiber optic lines/memory storage magnetic fields,etc.

Brief review in AMERICAN SCIENTIST, Mar-Apr 1999, p.178, 18 Feb 1999
HOW WE BECAME POSTHUMAN by N. Katherine Hayles (Chicago, $18, paper) explores the relation between the computer revolution and our changing ideas of what it means to be a human being. Her pet theme: how information became an entity in itself, divorced from the material that carries it, in both science and literature. Norbert Wiener meets P.K. Dick. (p. 178)

If you are an evolutinary biologist or ecologist and you want to get into modelling buy this book., 29 Nov 2008
This is an excellent and very comprehensive text written in a biologist friendly style but that still delivers almost all of the maths you are ever likely to need in mathematical biology.

Books like Edelstein-Keshet and Murray are written from a much more mathematical background and tend to use notation and concepts that are hard for non-mathematicians to grasp. Maths phobia is a serious barrier to biologists entering the field, where we need biological as well as mathematical insight.

This book introduces the mathemtical concepts as they are needed by way of a series of primers. The rest of the book is filled with examples that concentrate on the biology rather than the mathematical techniques. There are also chapters that explain the methods of model building and the reasoning behind model building.

For me this is a perfect graduate level or third year undergraduate level text.

Phylogenetic trees made wrong, 21 Jul 2008
This is a how-to manual and with that all is said. If you really believe you can make a proper phylogenetic tree without understanding basic concepts of molecular evolution, you 've got it all wrong. The author spices his book with his own experiences, without giving details. This is like just believing your teacher because he is your teacher. Unfortunately the book is full with half-truths. The author encourages NOT to go profound since errors in the alignments will typically not affect tree architecture. And so on and so on.

Actually, I think it is a shame this book is published. With this book you will indeed produce trees within minutes, but quite sure: most of them are all wrong.

Furthermore, the author completely ignores Phylip. No matter how you look at it, you cannot ignore Phylip. This is probably just to advertise the software for which this How-to was written, Mega (also not the best choice). Typically most of these packges come with free how-to's. Please ignore this book.

Extraordinarily good, compact and value for money, 03 Jun