1. Course Summary June 2, 2005 Programming Workshop Overview of course (presentation) Protein modeling, part 2 Instructor evaluations

2. Course Summary Course Learning Objectives (from course syllabus): Retrieve gene sequence information from GenBank Use BLAST program to conduct gene similarity searches Predict protein functional motifs with BLIMPs Write algorithms that will perform a simple search of gene sequences stored in a database Understand the statistics used in scoring aligned sequences in common programs. Display and compare 3-D structures of proteins

3. List of software programs you should be familiar with PubMed Dotter Needleman-Wunsch global alignment Smith-Waterman local alignment BLAST PSI-BLAST FASTA Chou-Fasman Kyte-Doolittle (hydrophobicity) GOR BLIMP PSIPRED DeepView (Swiss PDB viewer)

4. List of databases that we studied Online Mendelian Inheritance of Man MedLine GenBank SWISSPROT Protein Information Resource ProSite BLOCKS Protein Data Bank (PDB)

5. Concepts in bioinformatics ENTREZ-Suite of connected programs that allow for analysis of genes and proteins Modular nature of proteins Sliding window Alignment methods (Local vs. Global) Dynamic programming Statistics (E-value, Counting principle)

6. Concepts in bioinformatics II Primary and secondary databases Similarity vs. identical amino acids Scoring matrices (PAM, BLOSUM, PSSM) Neural networks Protein structure prediction Create software program that aligns sequences based on scoring matrices

7. Future of bioinformatics Traditionally divided into two camps-users and developers CSULA students should have an advantage over the typical applicant to graduate school or industry position Online Journal of Bioinformatics Bio InformBio Inform-a newsletter for bioinformaticists

8. Extra Questions for Evaluation Extra questions to add to the evaluation (Place on Prof. Momand’s evaluation form) Question 12: This course will help you further your career. Question 14: The programming component increased your understanding of the field of bioinformatics. Question 15: The course workload, compared to other 4 unit science classes, was (a) too heavy, (b) too light, (c) just right. Aside from specific comments on Prof. Momand please use part D of the evaluation form to comment on each of the following topics: 1) What prerequisite courses would help you increase your performance in this course? 2) What components of the bioinformatics field would you like to see expanded into a second, more advanced, course?