Calendar 2004

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Morning Topics
Afternoon Topics
Lecture
Workshop
Lecture
Workshop
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1		 Mon (6/14) Program Overview - Introduction to Bioinformatics, description of program (JM, NWP, SS) Campus Orientation - Campus tour, students get campus ID cards and computer accounts. Write email to instructors. Form a user group. Molecular Life Science Review - Central Dogma, amino acid similarities, protein structure (JM) or Programming Review - Introduction to PHythos - data types and simple I/O (NWP) Molecular life Science: Group amino acids into families. programming. Write a program looking up the Hydrophobicity of an amino acid
Tues (6/15) 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 (6/16) Phython II - Control Structures (NWP) Write a sliding window program to compute %GC Database Searching - Evolutionary basis of sequence alignment. scoring matrices (JM) Create your own scoring matrix and use Dotter to reanalyze p53 sequenses
Thur (6/17) Alignment - Global an local alignment, Needleman-Wunsch algorithm (JM) Manually align two sequences using Needleman-Wunsch alg. and score using fixed scores Phython III - File I/O, functions, list comprehensions (NWP) Write a program to compute the PAM/BLOSUM score of two amino acids
Fri (6/18) Professional Development (WJ, SS) Resume Writing Research site visit
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2		 Mon (6/21) Sequence databases - Primary and secondary, GenBank formats (JM) Find examples of primary and secondary databases, Find records in EMBL and GenBank Statistics - Basic probability, counting techniques, Bayes; Theorem (SH) Statistics Workshop
Tue (6/22) Statistics - Markov chains (SH) Statistics Workshop Statistics - Hidden Markov chains (SH) Statistics Workshop
Wed (6/23) Local and Global alignment algorithms - longest common subsequence algorithm (LCS), dynamic programming (NWP) Implement LCS algorithm - scoring Rationale for searching sequence databases - FASTA and BLAST (JM) Use BLAT to determine sequence similarities. E-value alterations
Thur (6/24) Extensions to Global and Local Alignment - Affine Gap Penalties, ends-free alignment (NWP) Implement LCS algorithm - traceback Sequence alignment project (NWP) Groups start to work on project
Fri (6/25) Multiple sequence alignment - ClustalW, other multiple sequence alignment programs (JM) Align protein sequences from GenBank using ClustalW Research Seminar (Dr. Magnus Nordborg, USC) Group Discussion: Report on research/products of research site
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3		 Mon (6/28) Extensions to Global Alignment - local aslignment, affine gap penalties (NWP) Programming Workshop (NWP) 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
Tue (6/29) Ethics of the human genome (JF) Ethics workshop Phylogenetic Analysis - terminology, types of trees, character evolution, reconstruction (Dr. Torres) PAULP software workshop
Wed (6/30) Protein Structure - difference between secondary and tertiary structure, deep view SIMS (JM) DeepView Tutorial
http://www.usm.maine.edu/
~rhodes/SPVTut/text/
SPdbVTut.html		 Proteomics - Two-D gel electrophoresis, Mass spectrometry tech (JM) Analysis of two dimensional gel data at EMBL site
Thur (7/1) Programming Workshop (NWP) Signal transduction pathways (JM) Workshop on Signaling pathway analysis
Fri (7/2) First year students demonstration of sequence alignment project Beach Party

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 Mon (7/5) Holiday
Tue (7/6) Microarrays - cluster Analysis (SS) Workshop on Cluster analysis Work At Research Site
Wed (7/7) Microarrays - cluster Analysis (SS) Workshop on Cluster analysis Work At Research Site
Thur (7/8) Microarrays - cluster Analysis (SS) Workshop on Cluster analysis Work At Research Site
Fri (7/9) Protein structure modeling - tertiary structure modeling. Deep View (JM) Use of Deep view to model protein structures. Structure comparisons First year students present written assignments Student evaluation of didactic faculty instruction
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Mon-Thur (7/12-7/15) Work at research site
Fri (7/16) Work at research site Research Seminar (Dr. Sivanesan Dakshanamurthy, Georgetown) Group Discussion: Report on research activities
Mon-Thur (7/19-7/22) Work at research site
Formative surveys of students and research mentors
Fri (7/23) Work at research site Seminar on how to apply to graduate school, programs in Bioinformatics, and scholarships (SS, WJ) University visits to Cal Tech, USC, or UCLA
Mon-Fri (7/26-7/30) Work at research site
Wed (7/28) Work at research site Second year students present programming project
Mon-Thur (8/2-8/5) Work at research site
Fri (8/6) Work at research site Research seminar (Dr. Paul Martin harrison, Yale University) Group Discussion: Report on research activities
Mon-Thur (8/9-8/12) Work at research site
Fri (8/13) Work at research site Research seminar (Dr. Eric Mjolness, UCI) Group Discussion: Discussion of industry vs academia research experiences
Mon-Wed (8/16-8/18) Work at research site
Student exit interviews and summative surveys of students and research mentors
Thur (8/19) Student research presentations Work at research site
Fri (8/20) Student research presentations
Student, research mentors, didactic faculty complete quantitative rubrics of presentations 		Luncheon and research seminar (Dr. Janet Sinsheimer, UCLA)
Focus group for research mentors
 

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

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