Transcript Why teach a course in bioinformatics?

What is bioinformatics?
Answer:
It depends who you ask.
Various definitions:
• The science of using information to
understand biology.
• The science that uses computational
approaches to answer biological questions.
• The science of understanding the structure and
function of genes and proteins through
advanced, computer-aided statistical analysis.
• The marriage of biology and computer
science.
What skills should a
bioinformatician have?
• You should have fairly deep background in
molecular biology.
• You must understand the central dogma of
molecular biology.
• You should have experience with
programming.
• You should be comfortable working in a
command line computing environment.
2nd Opinion- Skills critical to
success:
• The ability to frame biological questions in a manner
understandable to computer scientists
• A thorough understanding of the problems addressed
in the bioinformatics field
• Database administration and programming skills
• Computer science and genomics expertise for analysis
of small- and large scale informatics problems
• The ability to filter information and extract possible
relationships between data sets
Put in simpler terms:
• You need to know some molecular biology
• You have to love computers
• It helps to like math
Important Point• Bioinformatics is a tool
and not an end in itself.
Why teach a course in
bioinformatics?
Part of answer:
Bioinformaticians are
needed.
From Science ‘next wave’*:
• Imagine a job fair with 50 high-tech companies
competing to recruit one of the handful of properly
qualified scientists who bothered to show up.
Sounds like a pie-in-the-sky dream, doesn't it? But
according to Victor Markovitz, vice president of
bioinformatics systems at Gene Logic Inc., this
actually happened at a recent biotech fair. And it is
more or less typical of the prevailing global job
market in bioinformatics and computational
biology, where there are many more headhunters
than heads.
• *10-29-00
From Nov. 2000:
• “There is a huge demand for people with
the combination of a master’s degree in
computer science and a Ph. D. in a life
science.”
Why now??
Easy Answer:
* The astronomical growth of
Genbank and The Protein Data
Bank!
Historical Perspective
The launch (late 1980s) of the Human
Genome Project was a decisive moment
in the development of bioinformatics.
More complex answer:
The way biology is done is
changing.
*one of goals of this course: to
illustrate the ways biology is
changing
Biology is scaling up.
•
•
Genetics lab don’t do things one gene at a time
anymore.
Genetics lab use a ‘Genomic Approach’.
*These types of large scale projects required, more
than anything, a change in mindset:
1. Focus isn't everything.
2. Do things smarter and save work.
3. Think big!
Today large molecular
biology projects are rarely
hypothesis driven
The projects are designed to generate
data.
Bioinformatics provides the tools to
obtain, store, and unravel the
information.
Collaborative projects require
centralized databases and
systematic methods for sharing
data.
• A good example is the C. elegans
genome project. This project has a
centralized website. Information is:
– Stored in a consistent format
– Linked in an informative manner
Transcription
=
RNA
synthesis
Translation
=
Protein
synthesis
. Knowledge is built by
constructing relations between
different kinds of data.
• SMD (Stanford Microarray Database)
stores raw and normalized data from
microarray experiments. The data for a
given gene is linked to a mass of
genetic information, including an
expression history for that entity, a
description of the associated protein,
chromosomal location, etc.
Data is a resource that can be mined.
• Beyond the initial project, data is still a
valuable resource . Results from
numerous research projects that might
themselves be of minimal significance,
can often be put together to make
generalizations or observations that
could be quite significant.
Bioinformatics is an applied
science.
• The human genome project is
fundamentally about information.
The current nucleotide database
contain about 16 x 109 bases (16
Gbp)
Killer App?
• “ . . . every researcher and
entrepreneur hopes to develop or
discover the next “killer app”- the one
application that will bring the world to
his or her door and provide funding for
R & D, marketing, and production.”
What might be the computer-enabled
‘killer app’ in bioinformatics?
• Common answer:
Personalized medicine. Instead of taking a
generic over-the-counter drug, a patient
would submit a tissue sample. The
person’s genome would be analyzed and
the appropriate compound(s) designed,
synthesized, and delivered.
Required for this scenario to be realized:
• Affordable microarray technology to determine a
person’s genetic profile
• Medically relevant information gathering- Tools to
match a patient’s genetic profile, predisposition for
specific disease, and current condition with efficacy
of specific drug-therapy options
• Custom drug synthesis based on the person’s
medical condition and genetic profile.
What questions can
biologist/bioinformaticists
answer?
• 1) How can we cure disease?
• 2) How can we prevent infection?
• 3) How can we produce enough
food to feed all of humanity?
Why teach a course in
bioinformatics?
Needed- Biologists who understand
enough computer science to utilize the full
power of available bioinformatics tools.
Needed- Computer scientists with enough
biology background to design and deploy
new bioinformatics tools.
Warning:
Bioinformatics is often dealing
with small units of large, complex
systems. Understanding the
interactions among the components
is critical to understanding the
system. Currently, biologist are
limited in their understanding.
From Chapter 1:
• Pairwise comparisons of biological
sequences is the foundation of most widely
used bioinformatics techniques.
• A high quality sequence match between
two full-length sequences may suggest . . .
There are now numerous
bioinformatics programs around
the country:
• B.S., M.S., and Ph.D.
• Bioinformatics - as a standalone
discipline, at least - will be
extinct by 2012
The End