2008 Southern California Bioinformatics Summer Institute

Program Overview - Introduction to Bioinformatics, description of program (JM, NWP, SS)
2nd Year Students Q&A

Location: E&T C256

Campus Orientation, campus tour, students pick up driving permits (RC)

Student pre-didactic instruction self-assessment of requisite bioinformatics skills/knowledge

Molecular life science review, central dogma, amino acid similarities, protein structure (SS).
Location: E&T C256

Programming review, intro to Python, data types and simple I/O (NWP)
Location: E&T A331

Molecular life science: sickle cell anemia.
2nd Year TA

Programming: write a program to look up the hydrophobicity of an amino acid.
2nd Year TA

Literature Databases - Information organization and retrieval, NCBI entries (SS)

Location: E&T C256

PubMed/MedLine - Create Cubby profile, perform search for breast cancer gene information.

Introduce Writing Assignment

Python II - Control Structures (NWP)

Location: E&T C256

Database Searching - evolutionary basis of sequence alignment scoring matrices (JM)

Location: E&T C256

Professional Development (SS, WJ)

Bring Resume
(2nd Year)

Professional Development (SS, WJ)

(2nd Year)

Mixer with research Mentors. Learn about research opportunities.
(2nd Year)

Location: PS 607

Mixer with research Mentors. Learn about research opportunities.
(2nd Year)

Location: PS 607

Sequence Databases - Primary and Secondary GenBank formats (SS)

Find examples of primary and secondary databases, find records in EMBL and GenBank.

Finalize Writing Assignments

Statistics - Basic probability, counting techniques, Bayes' theorem (SH)
Location: E&T C256

Fellow Ranking of Research Mentors Due by Email to RC by 9:00 AM

Statistics Workshop

Statistics - hidden Markov Chains

Location: E&T C256

Statistics Workshop

Dynamic programming - longest common subsequence algorithm: LCS (NWP)

Location: E&T C256

Python IV - Scopes, modules, doc strings, debugging (NWP)

Local and Global Alignment algorithms - LCS, dynamic programming (NWP)

Pairwise global and local alignment - affine gap penalties, ends-free alignment (NWP)

Location: E&T C256

Multiple sequence alignment - ClustalW other multiple sequence alignment programs (JM)

Location: E&T C256

Protein structure prediction - Secondary structure prediction and secondary structure databases (JM)

Location E&T: C256

Use PSIPRED to predict secondary structure of P53 protein. Determine accuracy of PSIPRED using PDB record.

Ethics of the human genome (KV).

Location: PS 612

Protein structure - difference between secondary and tertiary structure, deep view SIMS (JM)

Location: E&T C256

DeepView Tutorial:
www.usm.maine.edu/
~rhodes/SPVTut/text/
SPdbVTut.html

Microarrays - Principles of Expression Microarray (SS)
Location: E&T C256

2nd Year TA

Introduction to GeneSpring data analysis

2nd Year TA

Microarrays - Principles of major clustering algorithms (SS)

2nd Year TA

Use GeneSpring for cluster analysis and recognizing and dealing with variability in acquired data.

2nd Year TA

Sequence alignment project programming workshop (NWP)

2nd Year TA

Sequence alignment project programming workshop (NWP)

2nd Year TA

Beach Party Hosted by Nancy Warter-Perez

Beach Party Hosted by Nancy Warter-Perez

Holiday - Independence Day

Demonstration of Sequence Alignment Project. (2nd yr students should attend)

Students and faculty assess presentation.

Assessment Presentation (BK)

Student Evaluation and Assessment Available Online.

Student evaluation of didactic faculty instruction and student post-didactic instruction self-assessment of requisite bioinformatics skills/knowledge due.

Research Site

Research Site

Research Site

Research Site

Research Site

Research Seminar
Dr. Janet Sinsheimer
Lunch: PS # 607
Seminar: PS # 306

Lunch provided

Research Site

Writing assignment due. Email writing assignment to SS and WJ by 9:00 AM

Research Site

Research Site

Research Site

Research Site

Research Site

Research Site

Writing assignment critique workshop.

Location: E&T C256

Group discussion: Report on research activities until 5:00 PM (SS, WJ, JM)

Friday Night
Social/Dinner at Sandy Sharp's House

Research Site

Work ethic surveys of students and research mentors

Research Site

Research Site

Research Site

Research Site

Research Site

Research Site

Research Seminar
Dr. Steve Mayo
Lunch: PS # 607
Seminar: PS # 306

Lunch provided

Research Site

Final Writing Assignment Due. Email writing assignment to SS and WJ by 9:00 AM

Research Site

Research Site

Research Site

Research Site

Research Site

Research Site

Research Seminar
Dr. Eleazar Eskin
Lunch: PS # 607
Seminar: PS # 306

Research Site

Research Site

Research Site

Research Site

Research Site

Research Site

Research Site

Group Discussion Report on research activities. Start 1:00 PM (SS)

Location: PS 223 (1:00 pm)

Group discussion: Report on research activities until 5:00 PM (SS)

Friday Night
Social/Dinner at Jamil Momand's House

Research Site

Research Site

Research Site

Research Site

Research Site

Research Site

Research Site

How to apply to graduate school, programs in Bioinformatics and Scholarships (SS, WJ, SK)

Final presentations by Alana Canfield & David Schwarz

Location: PS # 607

Lunch provided

Students present final run-through of research presentation until 6:30 PM (SS, NWP, WJ)

Location: PS # 607 & 223 (two groups)

Dinner provided

Research Site

Mentors Evaluate Students (online)

Research Site

Research Site

Research Site

Research Site

Final Assessment of core students' bioinformatics skills and knowledge (BK)

Student exit interviews (BK) Location: BS 262. 7:00 AM - 1:00 PM (students will be given assigned times)

Research Site

Final Assessment of core students' bioinformatics skills and knowledge (BK)

Student exit interviews (BK) Location: BS 262. 7:00 AM - 1:00 PM (students will be given assigned times)

Research Site

Research Site

Student Research Presentation (8:45 AM - 12:00 PM)
Location: E&T C154

Student, research mentors, didactic faculty complete quantitative rubrics and presentations

Student Research Presentation (8:45 AM - 12:00 PM)
Location: E&T C154

Student, research mentors, didactic faculty complete quantitative rubrics and presentations

Focus Group Assessment of SoCalBSI program by research mentors: 12:00 PM -12:30 PM (BK)

Location: E&T A-223

Lunch: Engineering Building Outdoor Patio Area: 12:30 PM - 1:30 PM

Student Research Presentation (1:30 PM - 4:45 PM)
Location: E&T C154

Student, research mentors, didactic faculty complete quantitative rubrics and presentations

Check Out Day (On-Campus Housing Students)

Presenter Key:
JM (Jamil Momand), NWP (Nancy Warter Perez), SS (Sandra Sharp), WJ (Wendie Johnston), SH (Silvia Heubach), RJ (Richard Johnston), KV (Kayley Vernallis), BK (Beverly Krilowicz), SK (Susan Kane), RC (Ronnie Cheng)

Location Key:
PS (Physical Sciences Building), E&T (Engineering & Technology Building), BS
(Biological Sciences Building)
Campus Map: www.calstatela.edu/univ/maps/cslamap.htm

Color key:
BLACK - Lectures, Workshops and Research Activities
GREEN - Student Deliverables
BLUE - Research Seminars
RED - Assessment Activities
PURPLE - Social Events
ORANGE - Second Year Students Must Attend or Assist