CSC 121
Computers and Scientific Thinking
Fall 2005
Computers in Biology
and Bioinformatics
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Biology
biology is roughly defined as "the study of life"
it is concerned with the characteristics and behaviors of organisms, how species
and individuals come into existence, and the interactions they have with each
other and with the environment (en.wikipedia.org/wiki/Biology)
biology encompasses a broad spectrum of academic fields that are often
viewed as independent disciplines
ecology and evolutionary biology study life at the habitat or population level
developmental biology and genetics study life at organism level
physiology, anatomy, and histology study life at the multicellular level
cell biology studies life at the cellular level
molecular biology, biochemistry, and molecular genetics study life at the atomic
and molecular level
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Impact of Computers
the history of biology dates as far back as the rise of various civilization
while computers are relatively new, they have had a monumental impact on
biological research
3 examples of impact:
1. computer technology is rapidly advancing the tools of scientific research
2. computer models are being used to study complex systems
3. computers are being used to store, process, and analyze large collections of
biological data
note: this list is in no way exhaustive
many aspects of biology and computer science are converging
biology researchers must be savvy computer users and even programmers
computer scientists must be able to solve interdisciplinary problems
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Technology Tools/Resources
many of the traditional tools of biological research are integrating computer
technology
e.g., the confocal microscope
invented by Marvin Minsky (computer science pioneer)
works by focusing a laser on a dyed sample and
measuring the fluorescent light emitted
can be used to build up a 3-D model of a sample, stored on
a computer
e.g., DNA Microarrays to measure the expression levels of genes
the Internet and the Web allow researchers to
share data and publications
speeds the dissemination of information and
the advancement of science
e.g., PubMed, from the National Library of
Medicine
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System Modeling
as computer memory and processing power has increased, it has become
possible to model complex biological systems in software
can attempt to discern natural laws or behaviors by observing the model under
varying conditions
e.g., models of plant or seashell growth
e.g., the evolution of cooperative behavior in species, such as bird flocking
can predict the effects of actions over long periods
e.g., the effects of automobile emissions on global warming
e.g., the effects of increased fishing on worldwide fishery stocks
can avoid infeasible, unethical, or costly experimentation
e.g., predict the toxicity of a new drug based on a chemical/biological model as opposed
to animal testing
e.g., study brain trauma using a neural network model
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Ecosystem Modeling
in the late 1960s, John Conway showed that a simple
model of an environment could produce complex and
interesting behavior
the environment is modeled as a 2-D grid of cells
a cell can be alive (contain an organism) or dead
simple rules model evolution
1. a dead cell becomes alive in the next generation if it has exactly
3 neighbors
2. a living cell survives in the next generation if it has 2 or 3
neighbors
Conway's ideas have been extended to a variety
of ecosystems
here, different colored cells denote different
organisms (sharks & fish)
other systems have modeled:
the growth of viruses
the spread of infectious diseases in a
population
the behavior of an ant colony 6
Bioinformatics
perhaps the biggest impact of computers in biology is in storing, accessing,
and processing large amounts of biological data
the new field of bioinformatics bridges biology and computer science (or
informatics, as it is known in Europe)
broad definition of bioinformatics: the use of computer science techniques to
solve biological problems
narrower but common definition: the application of computer science techniques
to the representation and processing of biological data
as research tools advance, biologists are generating enormous amount of
data
a single experiment with genetic material can produce thousands or millions of
data points
computational and statistical tools are needed to analyze and understand such
volumes of data
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DNA Overview
DNA is the genetic blue-print of life
made of nucleotides with four bases (A, T, G, C),
organized in a double-helix
the two strands match A+T and C+G base pairs
can think of DNA as encoding information in base 4
a gene is a region of DNA that encodes the
chemical structure of a protein
it is currently believed that there are 20,000-
30,000 different genes in human DNA
roughly 3 billion base pairs
"If our strands of DNA were stretched out in a line, the 46 chromosomes making
up the human genome would extend more than six feet. If the ... length of the 100
trillion cells could be stretched out, it would be ... over 113 billion miles. That is
enough material to reach to the sun and back 610 times." [Source: Centre for
Integrated Genomics]
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DNA RNA Proteins
in cell division,
the two strands of DNA are split
each strand is paired with free
nucleotides in the nucleus to
complete copies of the original
DNA
each cell gets a complete set of
the DNA
in mapping DNA to proteins,
the DNA strands are split and
copied into mRNA (using the same
bases except U replaces T)
this mRNA is then "read" by a
ribosome to build the specified
protein
proteins are commonly
represented using a 20 letter
alphabet (for the different types of
amino acids)
see www.dnai.org/a/index.html for a
series of online animations
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DNA Replication
DNA replication and transcription are basically information processing on a
biological level
if errors occur in the reading or replication of DNA information, then mutations
and diseases are the result
fortunately, DNA replication and transcription are INCREDIBLY reliable
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Bioinformatics Tools
many tools are available for searching and manipulating genetic sequences
e.g., the GeneBoy program (www.dnai.org/geneboy)
demonstrates DNA RNA transformations
analyzes the composition of a sequence
searches for specific patterns in the sequence
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DNA Databases and Tools
often, the source or
purpose of a DNA
sequence can be
determined by
comparing it with
documented genetic
material
several large
databases are
available online
tools for visualizing
and/or searching the
databases are also
available
e.g., the Ensemble site
(www.ensembl.org)
contains visualizations
of the human genome
and other DNA
sequences
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GenBank
the GenBank public
repository of DNA and
RNA sequence data
contains
partial or complete
genomes for more
than 165,000
organisms
more than 1 trillion
bases of sequence
data
roughly 3 million new
DNA sequences are
added per month
the database can be
accessed and searched
using various tools at
www.ncbi.nlm.nih.gov
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BLAST Search
Jurassic Park example
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Bioinformatics in the News
Researchers at the University of Bath have won a £261,000 grant to use the
latest software to produce a blueprint of a designer drug that could stop
influenza and some other diseases from replicating in humans.
UCSD biochemists have developed a computer program that helps explain a
long-standing mystery: how the same proteins can play different roles in a
wide range of cellular processes, including those leading to immune
responses and cancer.
Blue Gene is an IBM Research project dedicated to exploring the frontiers in
supercomputing: in computer architecture, in the software required to
program and control massively parallel systems, and in the use of
computation to advance our understanding of important biological
processes such as protein folding.
will utilize 65,536 processors working in parallel
will be able to perform 360 trillion operations/sec (greater than the total
computing power of the world's current 500 most powerful supercomputers)
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