Biology Reference
In-Depth Information
Strings
; Setubal and Medianas,
Introduction to Computational Molecular
Biology
.
91. Waterman,
Introduction
.
92. Altman, “Editorial,” 549.
93. Altman, “Editorial,” 550.
94. Expectation maximization is a statistical method; Monte Carlo meth-
ods come from physics, as we have seen; simulated annealing is a probabilistic
simulation; dynamic programming was originally invented in the context of
systems analysis; cluster analysis is a kind of statistical data analysis; neural
networks are simulations based on the brain; genetic algorithms are simula-
tions based on evolution; Bayesian inference is a statistical method based on
Bayes's theorem; stochastic context-free grammars are probabilistic models of
behavior.
95. Taylor, “Bioinformatics: Jobs Galore.”
96. Black and Stephan, “Bioinformatics: Recent Trends,” i.
97.
Nature
, “Post-genomic Cultures.”
98.
Nature
, “Post-genomic Cultures.”
99. Butler, “Are You Ready for the Revolution?,” 758.
100. Roos, “Bioinformatics,” 1260
101. Butler, “Are You Ready for the Revolution?,” 760.
102. Knight, “Bridging the Culture Gap,” 244.
Chapter Two
1. These controversies can also be seen in disagreement over the origins of
bioinformatics: should it be dated to the fi rst attempts at systematically orga-
nizing biological data, the fi rst paper databases, the fi rst computer databases,
the fi rst networked databases, or the fi rst algorithms for data analysis?
2. Usually the word “data” refers to
any
set of numbers or facts that are
operated on in order to draw an inference or conclusion, regardless of context.
Such a defi nition is inappropriate here because bioinformatics is so tightly
bound to computational practices that make data what they are for their
biological users.
3. For this project, I made no attempt to gain direct access to corporate
spaces. However, over the course of many interviews with current and former
private-sector employees, I managed to build up a reasonably detailed picture
of work in corporate bioinformatics. There are also a few companies that are
exclusively devoted to bioinformatics (for example, IntelliGenetics and Panther
Informatics).
4. Throughout the topic, i rst names appearing alone are pseudonyms.
Where fi rst and last names are given, this indicates the use of an individual's
real name.
5. For example, the paper announcing the sequencing of the honeybee in
2006 had over 300 authors from 90 institutions. Indeed, authorship had to
be broken down into overall project leadership (2), principal investigators (2),
community coordination (7), annotation section leaders (12), caste develop-
ment and reproduction (14), EST sequencing (8), brain and behavior (42),
