The Python Shell
In This Chapter You Will Learn
Story: Calculating the G of ATP Hydrolysis
What Do the Commands Mean?
"... a significant step forward ... The book is cleverly
designed to cover a wide range of subjects in a pleasant,
easy-to-follow sequence of chapters. These have been carefully
prepared so that the minimum level of interdependence is kept,
making it possible to begin working at virtually any level without
falling into intricate cross-references. A beginner will find the
first chapters quite welcoming while a person with medium or even
high levels of programming experience can easily find a suitable
entry point in the middle.
The book is written using an entertaining style that pushes the reader into a naturally built engaging experience ... the authors have chosen a collection of underlying subject areas that cover a very wide variety of interests, ensuring that mixed audiences are kept engaged. In that sense, the content becomes adaptable to the wide diversity of learners that are found in today's communities of specialised biologists.
... also usable as a reference guide, due to the richness of its worked examples that will prove valuable as seeds for code development for programmers at any level. ... as a single book to support learning Python for problem solvers in the life sciences, this book is certainly a very smart choice. It is also ready for creative teachers to develop more in the same direction."
-Pedro L. Fernandes, Instituto Gulbenkian de Ciencia
"Having read Managing Your Biological Data with
Python brings back memories of the times I started writing
my first lines of code nearly a decade ago. As a beginning
structural biologist without any coding experience, this book would
have been a welcome companion to quickly get me started on my
bioinformatical projects with Python. It is this, often pragmatic,
attitude scientists have towards programming that makes Python the
language of choice for many. A clear syntax, powerful build-in
functions and a lively ecosystem of user contributed modules allow
you to do advanced things with only little lines of code.
The book introduces you to the basic principles of programming in Python using the many build-in functions. It does so using practical examples that you can start using right away in your day-to-day research.
Python's modular design principles could even be seen in the organization of this book. If you have never written a line of code in your life, the first chapters are indispensable to teach you basic coding principles but if you have some experience, you can safely skip these. I would however, recommend to read the ones introducing the build-in functions. It never hurts to refresh your memory on the many powerful build-ins Python actually has; I certainly forgot about one or two of them. Working your way through the first chapters will help you get comfortable with Python and lay the foundation for writing more advanced programs in the remaining chapters. These chapters introduce some of the powerful community contributed Python modules that make your life as a biologist a whole lot easier. Again, the example code introducing these modules is of high practical value and together with the coding recipes in the `cookbook' chapter they provide a solid blueprint for you to build your own code upon.
I'm confident that reading Managing Your Biological Data with Python will quickly allow you to get the most out of your data and start answering those trilling scientific questions you have, and do all of that while having fun. "
-Marc van Dijk, Structural biologist, bioinformaticien, and eScience entrepreneur, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
"For many biologists faced with computational challenges, Python
has become the language of choice, due to its power, elegance, and
simplicity. Managing Your Biological Data with
Python by Allegra Via et al. teaches Python using
biological examples and discusses important Python-driven
applications, such as PyMol and Biopython. The book is an excellent
resource for any biologist needing relevant programming
-Thomas Hamelryck, Associate Professor, Bioinformatics Center, University of Copenhagen, Denmark
"Biological data volumes are growing rapidly as high-throughput
technologies (e.g., DNA microarrays or DNA/RNA sequencing) improve.
Managing and analyzing biological data are becoming more demanding
and the application of programming techniques has simply become a
standard. Managing Your Biological Data with
Python is one of very few user-friendly books for
biologists. It is amazing how clearly authors explain the possible
applications of Python for data management (parsing data records,
filtering and sorting data) and data visualization (also using the
Python interface to R). The book also offers the description of
modular programming, which is simply excellent! It guides readers
from writing simple functions through writing classes to building
program pipelines-everything according to Python coding standards
and in an easy-to-follow way. This is absolutely the best book to
start learning Python. Intermediate Python users can use this book
to learn some new tricks that they could implement in their own
code. I can highly recommend this book to researchers, students,
and their lecturers."
-Dr. Barbara Uszczynska, Centre de Regulacio Genomica (CRG), Barcelona, Spain