1. Southern California Bioinformatics Summer Institute
Wendie Johnston, Jamil Momand,
Sandra Sharp, Nancy Warter-Perez

2. SoCalBSI Mission
To identify and educate college students for successful careers in bioinformatics
Student Requirements:
Junior year undergraduate through 2nd year of graduate school
Majoring in Computer-related field or Molecular Life Science field
3.0 GPA minimum
Desires a career in Bioinformatics field

3. Goals of SoCalBSI
1) Familiarize computer science and molecular life science students with bioinformatics software programs
2) Introduce programming skills that will enable students to independently write programs 
3) Explore the social, moral and ethical issues associated with the human genome sequence  
4) Offer career counseling and expose to career opportunities
5) Provide research experiences with professional bioinformaticists
6) Create opportunities for interactions with bioinformaticists
7) Foster long-lasting professional relationships

4. Molecular
Life Science
Central Dogma
Molecular Basis of Disease
DNA Primary Sequence
Protein Primary, Secondary, Tertiary Structure
Molecular Evolution
Signal Transduction
Computer Science
Structured Programming
Data Structures
Algorithms
Complexity Analysis
Software Engineering
Core Bioinformatics
Literature Searching
NCBI Model
Scoring Matrices
Dynamic Programming
Global vs. Local Sequence Alignment
Multiple Sequence Alignment
Phylogenetic Trees
Molecular Life Science Databases
Protein Modeling
Microarrays
Proteomics
Statistics
Probability Theory
Hidden Markov Chain
Bayes’ Theory
Expect Value
Rule of Counting
Ethics
Privacy
Security
Human Genome

5. Achievement of Program Goals
S. Sharp-coPI
Research Training
N. Warter-Perez-coPI
Didactic Training
W. Johnston-coPI
Professional Development
Jackie Leung
Post-Summer Followup Graduate School Opportunities
B. Krilowitz
Project Evaluation
-Special Topics instructors
-J. Faust
-E. Torres
-S. Heubach
Program Coordinator
Coordination of
Research Mentors
BioDiscovery
Caltech
City of Hope
Protein Pathways
UCLA
USC
ViaLogy
-Student Recruitment
-WebPage Development
-Speaker Travel
-Budget
-Scheduling
-Student Housing
-Field Trips
-Research Seminar Speakers
-T. Chen -M. Pelligrini
-B. Hoff -D. Robbins
-G. Larson -S. Tavare
-E. Mjolsness -B. Wold
-M. Nordborg -T. Yeates

6. Who are you? 8 Males, 6 Females
7 graduate students and 7 undergraduates
11 from CA, 1 from MA, 1 from TX, 1 from NM
Majors in Biochemistry, Biology, Biostatistics, Computer Science, Cybernetics, Engineering, Mathematics

7. Open hours Computer Workstations open from 8 am-8 pm
SoCalBSI office PS noon M-Th, F 8-4.
Eating on campus
Campus Escort

9. Welcome to SoCalBSI June 16, 2003 Review of course prerequisites
Course objectives
Become proficient at using existing bioinformatics software
Understand the statistics behind bioinformatics
Write an algorithm that answers a specific bioinformatics problem
Become acquainted with some ethical issues surrounding the science of the human genome project

10. Rationale for offering SoCalBSI Program
Give participants a chance to understand how popular bioinformatics algorithms operate (Clustal W, BLAST, BLIMPs).
Give the students the opportunity to create software that uses concepts from Bioinformatics history
Give the students an insight into bioinformatics so they can make an intelligent determination of how to achieve education and career goals.

11. Learning Goals of Didactic Portion of the Program
Introduce software and databases currently used by bioinformaticists
Introduce the organization of the data. How data is gathered and how it is annotated.
Introduce statistics of data analysis.
Introduce the concept of dynamic programming
Give the students an opportunity to create an algorithm that analyzes sequence data
Encourage the student to research a bioinformatics company and report on its products.

12. Course logistics
Course Website (
Power point presentation
In-class Workshop
References
Writing assignment

13. Definition of Bioinformatics
Many definitions at the moment:
Use of computers to catalog and organize biological information into meaningful entities.
Conceptualization of biology in terms of molecules and the application of “informatics” techniques (from disciplines such as applied math, computer science and statistics) to understand and organize the information associated with these molecules

14. Bioinformatics is Multidisciplinary
Genomics
Computer
Science
Drug Design
Math
Molecular
Life Sciences
Phylogenetics
The name Bioinformatics suggests that it is multidisciplinary. Fields on the right, in black, represent established fields found on most college campuses. These fields all contribute strongly to the way in which molecular life sciences is taught and is practiced. On the left are more specialized fields that also contribute to Bioinformatics-genomics is the study of whole genomes of organisms. Drug design is heavily influenced by three dimensional structure analysis of potential protein targets and influenced by DNA array analyses. Phylogenetics, an old discipline is now able to proceed much more rapidly given the sequence information becoming available and new software packages designed to categorize the sequence information. Structural biology is also affected by the vast amount of 3-d structure info being deposited in the PDB. There is a strong union between CS, Math, Statistics and Molecular Biology.
Statistics
Structural
Biology

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

16. How is Bioinformatics Used?
Bioinformatics is often 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”.

17. Useful textbooks on the subject
Bioinformatics: A Practical Guide to
the Analysis of Genes and Proteins,
Second Edition by Andreas D.
Baxevanis (Editor), B. F. Francis
Ouellette
ISBN:
GenBank database
Sequence alignment programs

18. Useful textbooks on the subject (2)
Computational Molecular Biology
by Pavel A. Pevzner
ISBN:
Discussion of dynamic
programming
Needleman-Wuncsh method
Smith-Waterman method
Recursive functions

19. Useful textbooks on the subject (3)
Discovering Genomics, Proteomics
& Bioinformatics
by Campbell and Heyer
ISBN:
Genome sequence acquisition
and analysis.
Basic and applied research with
DNA microarrays.
Proteomics.
Modeling whole-genome circuits.
Transition from genetics to
genomics: medical case studies.

20. Basis of molecular biology
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

21. How can one use bioinformatics to link diseases to genes?
Old days: functional cloning of genes
Careful description of disease
Establish link between disease and metabolic defect
Isolate protein
Isolate cDNA
Determine if DNA is mutated in human
Disease
Function
Gene
Map

22. How can one use bioinformatics to link diseases to genes?
New days: positional cloning of genes
Find genetic markers associated with disease
Sequence DNA in close proximity to the markers
Compare DNA from afflicted individuals to DNA of normal individuals (database)
Find abnormality
Predict gene function from sequence information
Disease
Map
Gene
Function

23. What is the approach used to sequence genomes?
Divide and conquer
Split the genome into fragments
Clone into vectors that can accept large fragments: yeast artificial chromosomes (YAC Library)
Landmarks within the genome can be obtained using Sequence Tagged Sites (STS)
Sequences of YAC clones are matched with each other.
Sequences that overlap form contigs.

24. History of the Human Genome Project
1953
1972
1977
1980
1982
1984
1985
1986
1987
Watson,
Crick
DNA
structure
Berg,
1st recombinant
DNA
Maxam,
Gilbert,
Sanger
sequence
DNA
Botstein,
Davis,
Skolnick
White
propose to
map human
genome with
RFLPs
Wada
proposes to
build automated sequencing
robots
MRC
publishes
first large
genome
Epstein-Barr
virus (170 kb)
Sinsheimer hosts meeting to discuss HGP at UCSanta
Cruz;
Kary Mullis develops PCR
DOE begins genome studies with $5.3 million
Gilbert announces plans to start company to sequence and copyright DNA; Burke, Olson, Carle develop YACs; Donis-Keller publish first map (403 markers)

25. History of the Human Genome Project (continued)
1988
1989
1990
1991
1992
1993
1995
1996
Hood
produces
first automated sequencer;
Dupont devolops fluorescent dideoxy-
nucleotides
NIH supports the HGP;
Watson heads the project and allocates part of the budget to study social and ethical issues
Hood,
Olson, Botstein Cantor propose using
STS’s to map the human genome
Proposal
to sequence
20 Mb in model organism by 2005;
Lipman, Myers publish the BLAST algorithm
Venter announces strategy to sequence ESTs. He plans to patent
partial cDNAs;
Uberbacher develops GRAIL, a gene finding program
Simon develops BACs; US and French teams publish first physical maps of chromosomes; first genetic maps of mouse and human genome published
Collins is named director of NCHGR; revise plan to complete seq of human genome by 2005
Venter publishes first sequence of free-living organism:
H. influenzae (1.8 Mb);
Brown publishes on DNA arrays
Yeast genome is sequenced (S. cerevisiae)

26. History of the Human Genome Project (continued)
1997
1998
1999
2000
2001
2003
Blattner, Plunket complete E. coli sequence; a capillary sequencing machine is introduced.
SNP project is initiated; rice genome project is started; Venter creates new company called Celera and proposes to sequence HG within 3 years; C. elegans genome completed
NIH proposes to sequence mouse genome in 3 years; first sequence of chromosome 22 is announced
Celera and others publish Drosphila sequence (180 Mb); human chromosome 21 is completely sequenced; proposal to sequence puffer fish; Arabadopsis sequence is completed
Celera publishes human sequence in Science; the HGP consortium publishes the human sequence in Nature
Completed genomes:
112 Microbial
18 Eukaryotes
1275 Viruses

27. 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.

28. Useful Websites that give information on Bioinformatics courses
- Syllabus