Before You Begin
Part I: Text Files
1. Getting Set Up
2. Regular Expressions: Powerful Search & Replace
3. Exploring the Flexibility of Regular Expressions
Part II: The Shell
4. Command-line Operations: The Shell
5. Handling Text in the Shell
6. Scripting with the Shell
Part III: Programming
7. Components of Programming
8. Beginning Python Programming
9. Decisions and Loops
10. Reading and Writing Files
11. Merging Files
12. Modules and Libraries
13. Debugging Strategies
Part IV: Combining Methods
14. Selecting and Combining Tools
15. Relational Databases
16. Advanced Shell and Pipelines
Part V: Graphics
17. Graphical Concepts
18. Working with Vector Art
19. Working with Pixel Images
Part VI: Advanced Topics
20. Working on Remote Computers
21. Installing Software
22. Electronics: Interacting with the Physical World
Appendices
Steven H.D. Haddock is a Research Scientist at the Monterey Bay
Aquarium Research Institute and adjunct Associate Professor at the
University of California, Santa Cruz, studying bioluminescence and
biodiversity of gelatinous zooplankton. He started programming in
BASIC on an Apple ][ and began his undergraduate studies in
engineering before deciding to change fields. He took this
programming background with him to his graduate studies in
Marine
Biology, where he quickly realized the advantages that computing
skills offered and felt compelled to help foster these abilities in
others. He has developed many utilities and devices for research,
including instruments
to monitor bioluminescence from fireflies, a freezer monitoring
system, a web-based conference registration database, and a PCR
calculator for smartphones. In addition to teaching invertebrate
zoology and writing a booklet to teach the technique of blue-water
scuba diving, he has given tutorials in computing to students and
administrators. His interest in education extends to his
Bioluminescence Web Page (http://lifesci.ucsb.edu/~biolum/) and the
Jellywatch.org citizen-science website
(www.jellywatch.org).
Casey W. Dunn, a Professor at Yale University, does research that
has a large computational component but always in conjunction with
work in the field and lab. His first interest in computers stemmed
from building electronics, and he further developed his
computational skills working in Silicon Valley while an
undergraduate. As his data sets grew larger and larger during grad
school and his postdoc, he found himself reaching back to his
computer background more often. In the
course of his own research and helping other biologists with their
computational challenges, he became concerned about the mismatch
between training opportunities and the real day-to-day
computational problems biologists
face. In addition to teaching invertebrate biology, evolution, and
development, his educational activities include the websites
siphonophores.org and creaturecast.org. Dr. Dunn is the recipient
of the National Science Foundation's 2011 Alan T. Waterman Award,
recognizing an outstanding young researcher in any field of science
or engineering supported by NSF.
"Practical Computing for Biologists is a clear guide to methods
that unlock the power of the personal computer. Although the
breadth of subjects covered is certainly an asset of this volume,
what really makes the book stand out is how well the authors
clearly describe each technique and its applicability to biological
sciences. It is a great launching point for any necessary further
investigation of computational techniques."
--Matthew Aiello-Lammens, The Quarterly Review of Biology
"The book covers a wide range of subjects that truly justifies the
title of 'practical computing.' In addition to the usual
programming-related topics, it also includes a thorough
introduction to the programming environment, approaches to
combining different programs together, a description of the basic
text manipulation tools such as regular expressions, and even an
introduction to dealing with digital art and images. As such the
book is great value for the
money, being at least three books in one."
--Olga G. Troyanskaya, Cell
"My copy of Practical Computing for Biologists arrived last week,
and I've been very impressed. It is a well-written, well-paced
guide to basic computing skills for scientists and engineers of all
stripes (not just biologists). It is beautifully produced:
full-color printing and great graphical design make this book a joy
to read. If I ever do turn Software Carpentry into a book, I might
skip the topics PCB covers and just tell people to go and buy
it."
--Greg Wilson, software-carpentry.org
"When considering my research and use of time, this book has been
the most important book I've read in the last year, and perhaps the
last decade. Striking a perfect balance by guiding you through
tutorials and nudging your own self-exploration, the book has just
enough guided direction to not annoy or overwhelm. It has helped
(and is still helping) me to do what I was doing before, but more
efficiently."
--Cyme & Cystidium
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