1. 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

2. 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.

3. 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.

4. Course logistics Course Website (http://www.calstatela.edu/faculty/jmomand /Bioinformaticscourse.html)http://www.calstatela.edu/faculty/jmomand /Bioinformaticscourse.html Syllabus Power point presentations Homework assignments In-class Workshop References

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

6. Bioinformatics is Multidisciplinary Computer Science Math Statistics Structural Biology Phylogenetics Drug Design Genomics Molecular Life Sciences

7. Unknown Function How much of the genome is defined?

8. 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

9. Useful textbooks on the subject Beginning Python: From Novice to Professional, Apress 2005 ISBN: 159059519X

10. Basis of molecular life sciences Hierarchy of relationships (some exceptions): Genome Gene 1Gene 3Gene 2Gene X Protein 1Protein 2Protein 3Protein X Function 1Function 2Function 3Function X

11. 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.Celera Both groups have published the sequence of the human genome.

12. 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/