WILEY SERIES IN MATHEMATICAL AND COMPUTATIONAL BIOLOGY
Editor-in-Chief
Simon Levin
Department of Ecology and Evolutionary Biology, Princeton University, USA
Associate Editors
Zvia Agur, Tel-Aviv University, Israel
Odo Diekmann, University of Utrecht, The Netherlands
Marcus Feldman, Stanford University, USA
Bryan Grenfell, Cambridge University, UK
Philip Maini, Oxford University, UK
Martin Nowak, Oxford University, UK
Karl Sigmund, University of Vienna, Austria
CHAPLAIN/SINGH/MCLACHLAN—On Growth and Form: Spatio-temporal Pattern Formation in Biology
CHRISTIANSEN—Population Genetics of Multiple Loci
CLOTE/BACKOFEN—Computational Molecular Biology: An Introduction
DIEKMANN/HEESTERBEEK—Mathematical Epidemiology of Infectious
Diseases: Model Building, Analysis and Interpretation
Reflecting the rapidly growing interest and research in the field of mathematical biology, this outstanding new book series
examines the integration of mathematical and computational methods into biological work. It also encourages the advancement
of theoretical and quantitative approaches to biology, and the development of biological organisation and function.
The scope of the series is broad, ranging from molecular structure and processes to the dynamics of ecosystems and the
biosphere, but unified through evolutionary and physical principles, and the interplay of processes across scales of biological
organisation.
Topics to be covered in the series include:
• Cell and molecular biology
• Functional morphology and physiology
• Neurobiology and higher function
• Immunology
• Epidemiology
• Ecological and evolutionary dynamics of interacting populations
A fundamental research tool, the Wiley Series in Mathematical and Computational Biology provides essential and invaluable
reading for biomathematicians and development biologists, as well as graduate students and researchers in mathematical biology
and epidemiology.
'A Byte of Python' is a book on programming using the Python language. It serves as a
tutorial or guide to the Python language for a beginner audience. If all you know about
computers is how to save text files, then this is the book for you.
This book is updated for the new Python 3.0 language. If you are looking for a tutorial
on the current Python 2.x version, please download the previous revision of the book
[5]
. On
the same note, if you're wondering whether to learn Python 2.x or 3.x, then read this article
by James Bennett
[6]
.
The files here are gzipped tar files of examples and exercise solutions
for the book Beginning Perl for Bioinformatics by James Tisdall, published
by O'Reilly & Associates in 2001.
All the code here is copyright (c) 2002 by James Tisdall.
If you have trouble downloading these files, contact [email protected]
MODULE
BeginPerlBioinfo.pm module containing subroutines from the text
You'll need the module BegPerlBioinfo.pm for most of the examples and exercises.
Place it in the same directory (or folder) as the programs you're trying to
run; if you'd prefer, other places to install the module can be found in the book
or in the Perl documentation.
EXAMPLES
The file begperlbio_examples.tar.gz contains all the numbered examples
from the book in ASCII format.
EXERCISES
The exercises are in a few different files:
Chapters 4 to 8: begperlbio_exercises_part1.tar.gz
Chapter 9: begperlbio_exercises_ch09.tar.gz
Chapter 10: begperlbio_exercises_ch10.tar.gz
Chapter 11: begperlbio_exercises_ch11.tar.gz
Chapter 12: begperlbio_exercises_ch12.tar.gz
I expect to post revised forms of these solutions, as readers find bugs or
improvements in the code. But I should remind you that since this is a book
for beginners, the code may promote clarity and simplicity to the detriment
of completeness, or robustness in the presence of unexpected input; this is
by design.
SEND ME YOUR SOLUTIONS
I also invite you to send in your favorite solutions to selected exercises.
After I've collected enough of them, I'll post some of them -- with due credit given --
in this place, for the dual purpose of encouraging your work, and for showing
how alternate solutions to a programming problem can all be "correct".
Thanks for your interest, and good luck with the material!
Sincerely,
Jim
Plant Proteomics Methods and Protocols
——————————————————————————
The aim of Plant Proteomics: Methods and Protocols is to present up-to-
date methods and protocols used by recognized scientists in the world of plant
proteomics. If this world was a very small one twenty-five years ago when the
first papers were published, it has since experienced exponential growth, and
in most countries around the world there are laboratories working on plant
proteomics.
Two-dimensional gel electrophoresis is still the basic method used, but it
has been improved greatly with IPG in the first dimension (Chapter 13) and
with new detection methods with fluorochromes (Chapters 14 and 15). Signifi-
cant progress has been achieved in protein extraction, which is particularly
difficult with plant tissues containing phenols, proteases, and other secondary
metabolites that interfere with proteins. Standard procedures have been opti-
mized (Chapters 1 and 2) for peculiar tissues (Chapters 3, 4, and 5) and cellular
compartments (Chapters 6 to 10). These methods rely on improvements made
in the solubilization of proteins from membranes (Chapters 11 and 12). Mass
spectrometry was a revolution that permitted the high throughput identifica-
tion of proteins separated by 2D gels (Chapters 19 and 20) but also from blue
native 1D gels (Chapters 27 and 28) despite the fact that Edman sequencing
can still be useful (Chapter 18). Associated with other techniques such as 2DLC
or LC of intact proteins, mass spectrometry also permits the identification of
polypeptides from complexes (Chapters 21 and 22). A rapidly expending area
of plant proteomics concerns the analysis of post translational modifications
and protein–protein relationships (Chapters 24 to 29). Finally, proteomics pro-
duces different kinds of data (qualitative and quantitative data, spectrometric
data) that must be organized in databases to be shared by the community (Chap-
ter 23) and statistic tools are necessary to analyze the abundance of data effi-
ciently (Chapters 16,17)
The authors contribute by explaining in full detail their experimental meth-
odology, either in the wet or in the dry lab, allowing a novice to successfully
undertake the described method. Experts in proteomics will also appreciate the
chapters dealing with approaches with which they are not familiar.
Hervé Thiellement
Michel Zivy
Catherine Damerval
Valérie Méchin
PREFACE
This book celebrates the importance of the question; it is not meant
to be a collection of facts or procedures. The writing of this book was
inspired by 16 years of queries from the research community.The con-
tributors and I have tried to meet two primary objectives:
• Enhance the reader’s ability to identify the critical elements of
any technique, reagent, or procedure, in order to address questions
for which documented answers might be unavailable.
• Clarify theory and practice that is taken for granted yet fre-
quently misapplied.
Why is this book organized as a series of questions? For one, the
researchers (and people in general) who greatly impress me are those
who when faced with a seemingly impassible dilemma, can identify the
question(s) that point the way to an eventual solution. Second, I’m
fairly certain that I was most useful to others when all I did was to
help them identify the questions that enabled them to solve their own
problems.
Who should read this book? I can only say that the contributing
authors, many of whom work within a technical support group or have
previously done so, were asked to compose their chapters based on
questions that they were chronically asked, or based on questions that
they wish had been asked by those requesting assistance.
What are the strategies for working with this book? While I’ve been
harping on the importance of the question, you might only have time
to locate an answer. For readers in search of quick information, you
might want to begin your search with a review of the index. A second
approach would be to review the tables of content at the beginning
of each chapter, which list the questions addressed within them.
I strongly recommend that at some point you read through a chapter
of interest, focusing only on the questions being asked and the sub-
headings contained in the answer.The authors and I would like to think
that this information and the questions they inspire will provide insight
and perspective to help you solve problems that go beyond the content
of this book.
So many friends, colleagues, and others who could have been clas-
sified as competitors gave selflessly to make this project a reality. It is
all too likely that someone will be forgotten, and to all those individ-
uals whose help I have not acknowledged, I sincerely apologize.
Among those that I remember are Peter Herzer, Billi Herzer, Martha
Booz,Alice Marcy, Bob Dunst, Mary Ann Fink, George Donzella, Kathie
Gorski, Lou Hosta, Claire Wheeler John Graziadei, Joseph Stencel, Phil
Franciskovich, Tom Myers, Holly Hogrefe, Carl Baker, John SantaLucia,
Patti Taranto, Phil Beckett (Cheers, me old mucker), Howard Coyer,
Anita Gradowski, David Remeta, Cica Minetti, Peter Chiang, Martha
Cole, Matt Szap, Barb Kaboard, Julie DeGregaro, and Paul Hoderlein
for the invaluable service they provided by reviewing manuscripts. I
am grateful to Terri Sunquist and colleagues at Promega Biotech for
data on RNA polymerases, Bengt Bjellqvist for data on agarose, to
Bjorn Lundgren for centrifugation data, to Bronwen Harvey and her
research team for providing intriguing hybridization data, to Carl Fuller
for sharing his contacts and enzyme expertise, and to Gene Stircak
for access to search services. I am especially grateful to my colleagues
at Amersham Pharmacia Biotech for their support, good wishes and
collective sense of humor.With such a talented group of supporters
and contributing authors, you can blame me for any inadequacies you
note within these pages.
There are probably innumerable people at John Wiley and Sons that
I should include, but I can only name a few. Ann Boyle and Virginia
Benson Chanda have my sincere gratitude for their roles in convert-
ing an idea into a publication. Special thanks go to my editor, Luna Han,
for her bottomless well of patience and professional guidance.
I wish I could thank my parents, Bernard and Florence, who urged
me to focus on learning, not test scores. I’m glad I can thank my wife
Sharon for her love and ability to ignore my mood swings during this
project, and my son Daniel, whose uncanny knack for getting me out
of bed before dawn hastened me to the finish line.
Alan Gerstein
This book will help you develop network applications with .NET, using either the C# or VB.NET programming language.
It covers everything you need to know about network programming in .NET, from basic get-started information, to a huge selection of advanced networking technologies that may have seemed like science fiction—until now. Whether you’re looking for a solution to a specific networking issue or for a general all-round knowledge of network application development, you’ll find it in this book!
