domingo, 9 de agosto de 2009

Python para Bio Informáticos :D

Noticias de Python Argentina... Sebastian Bassi
Aca está el anuncio del libro "Python for Bioinformatics", el anuncio está en inglés porque ese es el idioma del libro.
PyAr y sus integrantes figuran en los agradecimientos :)

"Python for Bioinformatics"
ISBN 1584889292

This book introduces programming concepts to life science researchers,
bioinformaticians, support staff, students, and everyone who is
interested in applying programming to solve biologically-related
problems. Python is the chosen programming language for this task
because it is both powerful and easy-to-use.

It begins with the basic aspects of the language (like data types and
control structures) up to essential skills on today's bioinformatics
tasks like building web applications, using relational database
management systems, XML and version control. There is a chapter
devoted to Biopython ( since it can be used for most
of the tasks related to bioinformatics data processing.

There is a section with applications with source code, featuring
sequence manipulation, filtering vector contamination, calculating DNA
melting temperature, parsing a genbank file, inferring splicing sites,
and more.

There are questions at the end of every chapter and odd numbered
questiona are answered in an appendix making this text suitable for
classroom use.

This book can be used also as a reference material as it includes
Richard Gruet's Python Quick Reference, and the Python Style Guide.

DVD: The included DVD features a virtual machine with a special
edition of DNALinux, with all the programs and complementary files
required to run the scripts commented in the book. All scripts can be
tweaked to fit a particular configuration. By using a pre-configured
virtual machine the reader has access to the same development
environment than the author, so he can focus on learning Python. All
code is also available at the where ## is the code
number, for example:

I've been working on this book for more than two years testing the
examples under different setups and working to make the code
compatible for most versions of Python, Biopython and operating
systems. Where there is code that only works with a particular
dependency, this is clearly noted.

Finally, I want to highlight that non-bioinformaticians out there can
use this book as an introduction to bioinformatics by starting with
the included "Diving into the Gene Pool with BioPython" (by Zachary
Voase and published originally in Python Magazine).

Linux for Bioinformatics
DNALinux is a Virtual Machine with bioinformatic software preinstalled. NEW: Python for Bioinformatics (Py4Bio) edition. Go to download page.

Python for Bioinformatics (Chapman & Hall/Crc Mathematical & Computational Biology) (Paperback)
Product Description
Programming knowledge is often necessary for finding a solution to a biological problem. Based on the author’s experience working for an agricultural biotechnology company, Python for Bioinformatics helps scientists solve their biological problems by helping them understand the basics of programming. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language.
The book begins with a very basic introduction that teaches the principles of programming. It then introduces the Biopython package, which can be useful in solving life science problems. The next section covers sophisticated tools for bioinformatics, including relational database management systems and XML. The last part illustrates applications with source code, such as sequence manipulation, filtering vector contamination, calculating DNA melting temperature, parsing a genbank file, inferring splicing sites, and more. The appendices provide a wealth of supplementary information, including instructions for installing Python and Biopython and a Python language and style guide.

By incorporating examples in biology as well as code fragments throughout, the author places a special emphasis on practice, encouraging readers to experiment with the code. He shows how to use Python and the Biopython package for building web applications, genomic annotation, data manipulation, and countless other applications.

About the Author
Sebastian Bassi is the leader of the DNALinux bioinformatics distribution and member of the developer team for Biopython. He is currently providing bioinformatics support for the tomato mitochondrial genome sequencing project, which is part of the Latin America Solanaceae Genome Project (LAT-SOL).

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