Powerpoint for Bioinformatics course at CSULA

underlingbuddhaBiotechnology

Oct 2, 2013 (4 years and 1 month ago)

81 views

Welcome to Chem 434

Bioinformatics

March 25, 2008

Review of course prerequisites

Review of syllabus

Review of Bioinformatics Course website

Course objectives


Become proficient at using existing bioinformatics
software


Become familiar with bioinformatics databases


Write an algorithm that answers a specific
bioinformatics problem


Rationale for offering bioinformatics

1.
Need to understand how popular
bioinformatics algorithms operate (Clustal
W, BLAST, PSIPRED).

2.
A programming assignment gives a taste
of what it is like to be a developer.

Learning Goals of CSULA

Intro to Bioinformatics Course

Introduce software and databases currently used
by bioinformaticists

Introduce how data is organized. How data is
gathered and how it is annotated.

Introduce statistics of data analysis.

Introduce the concept of dynamic programming

Give an opportunity to create an algorithm that
analyzes sequence data

Analyze the primary literature in the field or
software company and improve writing skills.


Course logistics

Course Website
(
http://www.calstatela.edu/faculty/jmomand
/Bioinformaticscourse.html
)


Syllabus


Power point presentations


Homework assignments


In
-
class Workshop


References

Definition of Bioinformatics


Use of computers to catalog and organize
biological information into meaningful entities.

Bioinformatics is Multidisciplinary

Computer

Science

Math

Statistics

Structural

Biology

Phylogenetics

Drug Design

Genomics

Molecular

Life Sciences

Unknown Function

How much of the genome is defined?

How is Bioinformatics Used?

Experimental proof is still the

“Gold Standard”.

Bioinformatics isn’t going to replace

lab work anytime soon

Bioinformatics is used to help “focus”

the experiments of the benchtop scientist

Useful textbooks on the subject

Beginning Python: From Novice

to Professional, Apress 2005


ISBN:
159059519X

Basis of molecular life sciences

Hierarchy of relationships (some exceptions):

Genome

Gene 1

Gene 3

Gene 2

Gene X

Protein 1

Protein 2

Protein 3

Protein X

Function 1

Function 2

Function 3

Function X

Public funding vs. Private
funding

Public
-
Taxpayers’ money, international
effort.

Private
-
Companies that invest money hope
to provide access to their information on a
fee basis.
Celera

also allows some free
information to small research groups.

Both groups have published the sequence of
the human genome.

Useful Websites that give information on
Bioinformatics courses

http://www.calstatela.edu/faculty/jmomand/Bioinformaticscourse.html

http://cmgm.stanford.edu/biochem118/bioinformatics.html

http://www.sdsc.edu/~gribskov/bimm140/bimm140_lectures.html

http://www.nslij
-
genetics.org/bioinfotraining/