Powerpoint for Bioinformatics course at CSULA

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Transcript Powerpoint for Bioinformatics course at CSULA

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
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.
1.
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
Genomics
Drug Design
Computer
Science
Molecular
Life Sciences
Phylogenetics
Structural
Biology
Math
Statistics
How much of the genome is defined?
Unknown Function
How is Bioinformatics Used?
Bioinformatics is used to help “focus”
the experiments of the benchtop scientist
Bioinformatics isn’t going to replace
lab work anytime soon
Experimental proof is still the
“Gold Standard”.
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 2
Gene 3
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/