Calendar 2005

 

 
Morning Topics
Afternoon Topics
Lecture
Workshop
Lecture
Workshop
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1		 Mon (6/13) Program Overview - Introduction to Bioinformatics, description of program (JM, NWP, SS) Campus Orientation, campus tour, students pick up driving permits. 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: writea program to lookup the hydrophobicity of an amino acid.
Tues (6/14) 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 (6/15) 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 (6/16) Database searching - evolutionary basis of sequence alignment scoring matrices (JM) Create your own scoring matrix and use Dotter to reanalyze p53 sequences Alignment - Global and local alignment, Needleman-Wunsch algorithm (JM) Manually align two sequence using Needleman-Wunsch alg and score using fixed scores
Fri (6/17) Professional Development (WJ, SS) Resume Writing Research site visit
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2		 Mon (6/20) Statistics - hidden Markov chains (SH) Statistics workshop Statistics - Markov chains (SH) Statistics Workshop
Tue (6/21) Statistics- Basic probability, counting techniques, Bayes' Theorem (SH) Statistics Workshop Sequence databases- primary and secondary, GenBank formats (JM) Find examples of primary and secondary databases, find records in EMBL and GenBank
Wed (6/22) Rationale for searching sequence databases- FASTA and BLAST (JM) Use BLAST to determine sequence similarities. E-value alterations Local and Global alignment algorithms - longest common subsequence algorithm (LCS), dynamic programming (NWP) Implement LCS algorithm- scoring
Thur (6/23) Extensions to Global and Local Alignment - Affine Gap Penalties, ends-free alignment (NWP) Implement LCS algorithm - traceback Python IV - scopes, modules, doc strings, debuggin (NWP) Groups start to work on sequence alignment project
Fri (6/24) Extensions to global alignment- local alignment, affine gap penalties (NWP) Programming workshop (NWP) (Genome-wide Electronic Northerns) Dr. Jim Holloway Group Discussion: Report on research/products of research site
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3		 Mon (6/27) Multiple sequence alignment- ClustalW, other multiple sequence alignment programs (JM) Align protein sequences from GenBank using ClustalW 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 (6/28) Ethics of the human genome (JF) Ethics workshop Phylogenetic Analysis - terminology, types of trees, character evolution, reconstruction (Dr. Torres) PAULP software workshop
Wed (6/29) 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 (6/30) Programming Workshop (NWP) Signal transduction pathways (JM) Workshop on Signaling pathway analysis
Fri (7/1) First year students demonstration of sequence alignment project. Students and faculty assess presentations Beach Party

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 Mon (7/4) Holiday
Tue (7/5) Microarrays - cluster Analysis (SS) Workshop on Cluster analysis Work At Research Site
Wed (7/6) Microarrays - cluster Analysis (SS) Workshop on Cluster analysis Work At Research Site
Thur (7/7) Microarrays - cluster Analysis (SS) Workshop on Cluster analysis Work At Research Site
Fri (7/8) First year students present written assignments Student evaluation of didactic faculty instruction Work at Research Site
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Mon-Thur (7/11-7/14) Work at research site
Fri (7/15) Work at research site (Analysis of Human single Nucleotide Polymorphison (SNP) and Haplotype Block Structure) Dr. Tim Chen Group Discussion: Report on research activities
Mon-Thur (7/18-7/21) Work at research site
Formative surveys of students and research mentors
Fri (7/22) Work at research site Free Afternoon
Mon-Fri (7/25-7/28) Work at research site
Fri (7/29) 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
Mon-Thur (8/1-8/4) Work at research site
Fri (8/5) Work at research site (Modeling the growing plant stem) Dr. Bruce Shapiro Group Discussion: Report on research activities
Mon-Thur (8/8-8/11) Work at research site
Fri (8/12) Work at research site (Pathway analysis of expression and RNAi data) Dr. Matteo Pellegrini Group Discussion: Discussion of industry vs academia research experiences
Mon-Tues (8/15-8/16) Work at research site
Wed (8/17) Student research presentations Work at research site
Thurs (8/18) Student research presentations
Student, research mentors, didactic faculty complete quantitative rubrics of presentations 		Luncheon and research seminar (Dr. Eric Davidson)
Focus group for research mentors
Fri (8/19) Student exit interviews and summative surveys of students and research mentors Free Afternoon
 

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.