What is 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:

Focus isn`t everything.

Do things smarter and save work.

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