Calendar 2006

 

 
Morning Topics
Afternoon Topics
Lecture
Workshop
Lecture
Workshop
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1		 Mon (6/19) Program Overview - Introduction to Bioinformatics, description of program (JM, NWP, SS) Q&A session with 2nd year students

Campus Orientation, campus tour, students pick up driving permits.

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

Moleculr life science review, central dogma, amino acid similarities, protein structure (JM) and Programming review, intro to Python, data types and simple I/O (NWP) Molecular life science: sickle cell anemia. Programming: write a program to lookup the hydrophobicity of an amino acid.
Tues (6/20) Literature Databases - Information organization and retrieval, NCBI Entrez (JM) PubMed/MedLine - Create Cubby profile, perform search for breast cancer gene information Sequence Comparisons - Sliding window programs, dot plots, dotter program (JM) Sliding window concept and dotter program Create hydrophobicity plot. Use Dotter program to compare two sequences
Wed (6/21) Phython II - Control Structures (NWP) Write a sliding window program to compute %GC Python III - file I/O, functions, list comprehensions (NWP) Write a program to compute the PAM/BLOSUM score of two amino acids
Thur (6/22) Database searching - evolutionary basis of sequence alignment scoring matrices (JM) Create your own scoring matrix and use Dotter to reanalyze p53 sequences Sequence databases- Primary and secondary GenBank formats (SS) Find examples of primary and secondary databases, find records in EMBL and GenBank (1st years only)
Fri (6/23) Professional Development (WJ, SS) Resume Writing Research site visit
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2		 Mon (6/26) Statistics- Basic progability, counting techniques, Bayes' theorem (SH) Statistics workshop Statistics - Markov chains (SH) Statistics Workshop
Tue (6/27) Statistics - Hidden Markov chains (SH) Statistics Workshop Overview of local and global alignment and rationale for searching databases - FASTA and BLAST (JM) Use BLAST to determine sequence similarities. E-value alterations
Wed (6/28) Dynamic programming - Longest Common Subsequence Algorithm (LCS) (NWP) Implement LCS algorithm - scoring

Python IV - scopes, modules, doc strings, debuggin (NWP)

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

Implement LCS algorithm- traceback
Thur (6/29) Pairwise Global and Local Alignment - affine gap penalties, ends-free alignment (NWP) Groups start to work on sequence alignment project Space efficient algorithms (NWP) Sequence alignment project
Fri (6/30) Multiple sequence alignment - clustalW other multiple sequence alignment programs (JM) Align protein sequences form GenBank using ClustalW Research Seminar
Dr. Anton Nekrutenko 		Group Discussion: Report on research/products of research site (WJ, SS) until 5pm.
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3		 Mon (7/3) Protein Structure Prediction - secondary structure prediction and secondary structure databases (JM) Use PSIPRED to predict secondary structure of p53 protein. Determine accuracy of PSIPRED using PDB record Ethics of the human genome (JF) Ethics Workshop
Tue (7/4) Holiday
Wed (7/5) Protein Structure - difference between secondary and tertiary structure, deep view SIMS (JM) DeepView Tutorial
http://www.usm.maine.edu/
~rhodes/SPVTut/text/
SPdbVTut.html		 Signal transduction pathways (JM) Workshop on Signaling pathway analysis
Thur (7/6) Microarrays - principles of expression microarray (SS) Introduction to GeneSpring data analysis Microarrays - principles of major clustering algorithms (SS) use GenSpring for cluster analysis and recognizing and dealing with variability in accquired data
Fri (7/7) Microarrays - Sources of uncertainty and error in microarray analysis (SS) Use Excel to Process primary data and minimize error Sequence alignment project programming workshop (NWP). 2nd yr students will mentor first year students until 5pm

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4

 Mon (7/10)

1st yr students demonstration of sequence alignment project

Students and faculty assess presentation. 2nd yr students help evaluate

Beach Pary
Tue (7/11) Work at Research Site
Wed (7/12) Work at Research Site
Thur (7/13) Work at Research Site
Fri (7/14) Work At Research Site Student evaluation of didactic faculty instruction and student post-didactic instruction self-assessment of requisite bioinformatics skills/knowledge (1st yr students only)

Troup discussion: report on research activities; 2nd yr students present previous yr's research

Writing assignment 1st draft due (1st yr students only until 5pm)

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Mon-Thur (7/17-7/20) Work at research site
Fri (7/21) Work at research site Writing assignment critique workshop Group discussion: report on research activities until 5pm
Mon-Thur (7/24-7/27) Work at research site
Work ethic surveys of students and research mentors
Fri (7/28) Work at research site Research Seminar:
Dr. Nuno Bandeira 		Group discussion: report on research activities: 2nd yr students present programming projects until 5pm.
Mon-Thur (7/31-8/3) Work at research site
Fri (8/4) Work at research site Research Seminar
MathWorks: Robert Henson 		Group Discussion: Report on research activities until 5pm
Mon-Thur (8/7-8/10) Work at research site
Fri (8/11) Work at research site How to apply to graduate school, programs in bioinformatics and scholarships (SS, WJ, Dr. Susan Kane) Group Discussion: Report on research activities. Former SoCalBSI Participant Guest Frances Tong until 5pm
Mon-Thur (8/14-8/17) Work at research site
Fri (8/18) Work at research site Research Seminar:
Dr. Chuanbo Xu 		Group Discussion: Discussion of industry vs academia research experiences until 5pm
Mon-Tues (8/21-8/22) Work at research site
8/21: Final assessment of core of students' bioinformatics skills and knowledge (BK)
Wed (8/23) Student research presentations
Students, research mentors, didactic faculty complete quantitative rubrices of presentations 		Work at research site
Student exit interviews
Thur (8/23) Student research presentations
Student, research mentors, didactic faculty complete quantitative rubrics of presentations 		Luncheon and research seminar (Dr. Russell Doolittle)
Focus group assessment of SoCalBSI program by research mentors (BK)
 

Presenter Key:
JM (Jamil Momand), NWP (Nancy Warter Perez), SS (Sandra Sharp), WJ (Wendie Johnston), SH (Silvia Heubach), JF (Jennifer Faust) , BK (Beverly Krilowicz)

Color key:
Lectures, workshops and research activities in black.
Special tours and program activities in green.
Seminars in blue.
Assessment activities in red.