PDF Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice

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I notice that you also registered on my blog, I am very sorry but I assumed your sign up was bogus as I had a spate of sign ups today, and your account was deleted. I think you are spot on with your observation. For some reason most of the recent bioinformatics books, particularly the expensive hardcover ones from CRC and Springer, are written by non-practitioners. By non-practitioners I mean professors who teach statistics, biological science or computer science, as opposed to software developers working in the field of bioinformatics.

The result has read like a cross-section of stodgy textbooks and research articles, with little in the way of practical code or analysis strategy. Others, as you mention, are "mildly bio-flavored" introductions to a programming language.


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I love technical books but with a couple exceptions Beginning Perl for Bioinformatics I have never felt bioinformatics books were worth the money. I am looking forward to reading Bioinformatics Programming Using Python.

I think it will be a good one. Some of the textbooks I have found useful for research, lecturing and project supervision in bioinformatics are:.

Let me preface that I have three big interests in my life: biology, computer science and sailing. It was about two of my interests: computer science and sailing. But after coming up with the basic idea for Healtheon, securing the initial seed money, and hiring the people to make it happen, Clark concentrated on the building of Hyperion , a sailboat with a foot mast at the time of her launch, she was the largest sloop ever build and the tallest mast ever built , whose functions are controlled by 25 SGI workstations.

As the title implies, Jim Clark is a restless man who was always looking for the new new thing , the next big breaktrough. Near the end of the book Michael Lewis tells about one of the new things of Jim Clarks radar, a new emerging field called bioinformatics. I remember sitting there in my chair, staring at that sentence and thinking "What!

I can combine both biology and computer science! The book with the ultimate triumvirate, where the three of my interest -biology, computer science and sailing- were combined, came later with the autobiography of Craig Venter, A life decoded , where he writes about the Global Ocean Sampling Expedition he undertook with his personal foot sailboat named the Sorcerer II. The expedition sampled water from Halifax, Nova Scotia to the Eastern Tropical Pacific while undertaking a two year circumnavigation.

The micro-organisms in the water were sequenced and the results were published , more then doubling the amount of genetic sequences available up to that point. It hasn't been mentioned yet but Algorithms on Strings, Tree's and Sequences is a fantastic book if you are looking to learn about sequence alignment. I've learnt pretty much everything from doing, i.

Introduction

There have been occasional programming books that I've used to bootstrap learning about a language especially if it was a major leap, say from procedural to object-oriented languages, or from standalone application programming to web scripting. Of the bioinformatics books mentioned so far, Durbin et al.

Good description of the problem, algorithms clearly explained, and pseudocode. Great stuff. Fly: An Experimental Life. Francis Ouellette.. Here's a different take to this question. My favorite book is the one that I could write - or the one that Ewan Birney or Lincoln Stein could write not that I am in their company.

In all seriousness, what I am getting at is a kind of interview that is not a digest of a career path but more like this is what I have used and developed in the field of Bioinformatics in response to these challenges with details and here is where I required assistance from colleagues who were expert in X or Y. My favourite bioinformatics book is a biology book Lewin's Genes X.

Of course it's not a bioinformatics book, but is very good for getting a good understanding of the biology. Bio-informatics is an interdisciplinary field and for me, it is the fascination of the related genetics that motivates me to analyse it. I see computer science as a means to better understand genetics. This book can provide the necessary insight into genetics required for good bioinformatics.

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I cannot read this from cover to cover, it's just too much information, but it provides different levels of detail. Even when reading only the headlines, one could learn something new. Maybe not so well suited for absolute beginners in genetics, and some biologists say it is superficial sometimes. Might be, but that I cannot judge, I just found the parts I read well understandable. There are of course lots of references rather many to "Cell". I have Genes VII A beautifully written and produced masterpiece. I tend to say that the problem with all these computer scientists and pure informaticians doing bioinformatics is that they don't even know what a gene is.

So, yes, it does make sense to at least have one book on your shelf that really tells you about genes. Taylor: A fantastic book particularly on protein structural bioinformatics. I think one book that a Person must have in addition to the large repertoire of above mentioned resources to stay afloat in Bioinformatics is the trimonthly edition of Wiley "Current Protocols in Bioinformatics".

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A Quick Guide for Developing Effective Bioinformatics Programming Skills

Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material.

I Working with Perl. II Working with Data.

Bioinformatics, Biocomputing and Perl: An Introduction

III Working with the Web. IV Working with Applications.

C Appendix C.