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Bioinformatics
Publisher’s information Comments
Bioinformatics Using Computational Intelligence Paradigms
Edited by U. Sieffert, L. C. Jain, and P. Schwiezer
March 14, 2005
Springer
ISBN 3540229019
Introduction to Mathematical Methods in Bioinformatics
by Alexander Isaev
July 27, 2004
Springer
ISBN 3540219730

The book’s chapters are:

  1. Introduction: Biological sequences
  2. Sequence alignment
  3. Markov chains and hidden markov models
  4. Protein folding
  5. Phylogenetic reconstruction
  6. Elements of probability theory
  7. Significance of sequence alignment scores
  8. Elements of statistics
  9. Substitution matrices
Molecular Modeling and Simulation
by Tamar Schlick
2002
Springer
Structural Bioinformatics
Philip E. Bourne and Helge Weissig, editors
ISBN 0471201995
The Ten Most Wanted Solutions in Bioinformatics
by Anna Tramontano
Chapman & Hall/CRC
ISBN 1-58488-491-6

Good introductory book on protein bioinformatics. Available at Boston University’s Science Library.

Biology
Publisher’s information Comments
Protein Structure and Function
by Gregory A. Petsko and Dagmar Ringe
2003
ISBN 0878936637
Systems Biology in Practice
by E. Klipp
2005
Weinheim: Wiley-VCH
ISBN 9783527310784

Available at Boston University’s Science Library.

C, C++, and Objective-C
Publisher’s information Comments
Beginning Mac OS X Programming
by Michael Trent and Drew McCormack
July 2005
Wrox
ISBN 0-7645-7399-3
C++ and Object-Oriented Numeric Computing for Scientists and Engineers
by Yeng
Springer
The Mac OS X Xcode 2 Book
by Cohen and Cohen
Object-Oriented Neural Networks in C++
by Joey Rogers
1997
Academic Press

Contains C++ source code for building neural nets.

Programming in C
3rd Edition
by Stephen G. Kochan
2005
SAMS Publishing
ISBN 0-672-32666-3

Covers C99. Available at Boston University’s Science Library.

Programming in Objective-C
by Stephen G. Kochan
2004
ISBN 0-672-32586-1

A highly-recommended book for learning Objective C for programming for Mac OS X.

Xcode Tools Sinsei A print and electronic book that covers the Xcode tools provided with Mac OS X.
Computing
Publisher’s information Comments
Scientific Parallel Computing
by L. Ridgway Scott, Terry Clark, and Babak Bagheri
2005
Princeton University Press
ISBN 0-691-11935-X

Available at Boston University’s Science Library.

Sourcebook of Parallel Computing
by Jack Dongarra et al.
2003
Morgan Kaufmann Publishers
ISBN 1-55860-871-0

Available at Boston University’s Science Library.

Database Management Systems
Publisher’s information Comments
SQL Cookbook
by Athony Molinaro
December 2005
O'Reilly
ISBN 0-596-00976-3

Simon P. Chappell has contributed a review to slashdot.org.

The book’s chapters are:

  1. Retrieving Records
  2. Sorting Query Results
  3. Working with Multiple Tables
  4. Inserting, Updating, Deleting
  5. Metadata Queries
  6. Working with Strings
  7. Working with Numbers
  8. Date Arithmetic
  9. Date Manipulation
  10. Working with Ranges
  11. Advanced Searching
  12. Reporting and Warehousing
  13. Hierarchical Queries
  14. Odds ’n’ Ends
Perl
Publisher’s information Comments
Advanced Perl Programming
2nd edition
by Simon Cozens
June 2005
O’Reilly
ISBN 0-596-00456-7

This looks like a wonderful resource for advanced Perl programmers. The book’s chapters are:

  1. Advanced techniques
  2. Parsing techniques
  3. Templating tools
  4. Objects, databases, and applications
  5. Natural language tools
  6. Perl and Unicode
  7. POE
  8. Testing
  9. Inline extensions
  10. Fun with Perl
Higher Order Perl: Transforming Programs with Programs
by Mark Jason Dominus
March 14, 2005
Morgan Kaufman
ISBN 1558607013
This book teaches the reader how to use functional programming techniques, LISP-like programming approaches that are not familiar to people who learned programming using the C-like languages.
Perl CookBook
2nd Edition
by Tom Christiansen and Nathan Torkington
August 2003
O’Reilly
ISBN 0-596-00313-7

I own the first edition of this book, which is getting a bit dated.

Perl Hacks
by chromatic, Damian Conway, and Curtis “Ovid” Poe
May 2006
O'Reilly
ISBN 0-596-52674-1

This new book contains 101 hacks. The book’s chapters are:

  1. Productivity Hacks
  2. User Interaction
  3. Data Munging
  4. Working with Modules
  5. Object Hacks
  6. Debugging
  7. Developer Tricks
  8. Know Thy Code
  9. Expand Your Perl Foo
Perl Testing: A Developer’s Notebook
by Ian Langworth and chromatic
July 14, 2005
O’Reilly Media, Inc.
ISBN 0596100922
This book teaches the reader how to use Perl’s test suites. This is especially important when writing Perl modules that will be distributed to others.
Statistics and Data Analysis
Publisher’s information Comments
Analysis of Variance in Experimental Design
by Harold R. Lindman
1992
Springer-Verlag, New York
ISBN 0-387-97571-3

A good book on the level of Boston University’s course CAS MA 416. Unfortunately, this book is out of print. Available in Boston University’s Science Library.

Bootstrap Methods and Their Application
by A. C. Davison and D. V. Hinkley
1997
Cambridge University Press
ISBN 0521574714

Five-star rating at amazon.com. The code from this book was used as the basis for the boot package for R.

Graphics of Large Data Sets: Visualizing a Million
by Antony Unwin, Martin Theus, and Heike Hofmann
July 10, 2006
Springer
ISBN 0387329064
This book will be published in the summer of 2006. It shows how to visualize large data sets in ways that help the analyst make sense of them.
Linear Models with R
by Julian J. Faraway
July 26, 2004
Chapman & Hall/CRC
ISBN 1584884258

The book’s chapters are:

  1. Introduction
  2. Estimation
  3. Inference
  4. Diagnostics
  5. Problems with the predictors
  6. Problems with the error
  7. Transformation
  8. Variable selection
  9. Shrinkage methods
  10. Statistical strategy and model uncertainty
  11. Insurance redlining—a complete example
  12. Missing data
  13. Analysis of covariance
  14. One-way analysis of variance
  15. Factorial designs
  16. Block designs
Mixed-Effects Models in S and S-PLUS
by Jose C. Pinheiro and Douglas M. Bates
April 2, 2002
Springer
ISBN 0387989579

This book provides complete coverage of the nlme package for nonlinear and linear mixed effects models using the S language.

R Graphics
by Paul Murrell
2005
Chapman & Hall/CRC
ISBN 158488486X

This book is devoted to creating graphics using R. The book covers traditional R graphics and the more sophisticated grid graphics, including the lattice package. The author provides his own web page devoted to the book. Some interesting commentary on R, prompted by the announcement of this book, is available at Statistical Modeling, Causal Inference, and Social Science blog at Columbia University.

Self-Organizing Maps
3rd Edition
by Teuvo Kohonen
2001

This difficult book will take a lot of time to absorb. Available at Boston University’s Science Library.

Statistical Methods: The Geometric Approach
by David J. Saville and Graham R. Wood
1991
Springer-Verlag
ISBN 0-387-97517-9

Out of print. Available in Boston University’s Science Library.