2003 Southern California Bioinformatics Summer Institute
Calendar 2003
Description of Calendar.
Morning Topics |
Afternoon Topics |
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Lecture |
Workshop |
Lecture |
Workshop |
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| w e e k 1 |
Mon (6/16) | 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 - data types, control constructs I/O (NWP) | Molecular life Science: Group amino acids into families. programming. Write a C++ program to map an amino acid to a PAM index. |
| Tues (6/17) | 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 (6/18) | Data Structures and Debuggin - Arrays, String Class - member functions and operators (NWP) | Write a sliding window program to compute hydrophobicity | Database Searching - Evolutionary basis of sequence alignment. scoring matrices (JM) | Create your own scoring matrix and use Dotter to reanalyze p53 sequenses | |
| Thur (6/19) | Alignment - Global an local alignment, Needleman-Wunsch algorithm (JM) | Manually align two sequences using Needleman-Wunsch alg. and score using fixed scores | Algorithm development - Demonstrate how to develop the Needleman-Wunsch algorithm (NWP) | Given a globally aligned sequence, compute the score using fixed match/mismatch score and affine gap penalties | |
| Fri (6/20) | Professional Development (WJ, SS) | Resume Writing | Research site visite | ||
| w e e k 2 |
Mon (6/23) | Sequence databases - Primary and secondary, GenBank formats (JM) | Find examples of primary and secondary databases, Find records in EMBL and GenBank | Statistics - Equally likely outcomes, counting techniques, Bayes' Theorem (SH) | Statistics Workshop |
| Tue (6/24) | Statistics - Markov chains and Hidden Markov chains, Expect value (SH) | Statistics Workshop | Software engineering fundamentals - Projects, functions and File I/O (NWP) | Write a program to compute the PAM/BLOSUM score of two amino acids | |
| Wed (6/25) | Rationale for searching sequences databases - FASTA and BLAST (JM) | Use BLAST to determine sequence similarities. E-value alterations | Longest Common Substring Algorithm (LCS) - Dynamic Programming (NWP) | Implement LCS algorithm - scoring | |
| Thur (6/26) | Smith-Waterman Algorithm - Extensions to LCS, affline gap penalties (NWP) | Implement LCS algorithm - traceback | Multiple Sequence Alignment - ClustalW, other multiple sequences alignment programs (JM) | Align protein sequences from GenBank using ClustalW | |
| Fri (6/27) | 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 | Research Seminar (Dr. Matteo Pellegrini) | Group Discussion: Report on research/products of research site | |
| w e e k 3 |
Mon (6/30) | Protein Structure - Differences between secondary and tertiary structure. Deep View SIMS (JM) | Deep View Tutorial | Protein Structure Modeling - Tertiary structure modeling. Deep View (JM) | Use of Deep View to model protein structures. Structure comparisons |
| Tue (7/1) | Proteomics - Two-D gel electrophoresis, Mass spectrometry tech (JM) | Analysis of two dimensional gel data at EMBL site | Programming Workshop (NWP) | ||
| Wed (7/2) | Ethics of the Human Genome (JF) | Ethics Workshop | Phylogenetic Analysis - terminology, types of trees, character evolution, reconstruction (Dr. Torres) | PAULP software workshop | |
| Thur (7/3) | Microarrays - Cluster Analysis (SS) | Workshop on Cluster Analysis | Signal transduction pathways (JM) | Workshop on Signaling pathway analysis | |
| Fri (7/4) | Holiday | ||||
| w e e k s 4 to 10 |
Mon (7/7) | Course summary (JM, NWP) Student evaluation of didactic faculty instruction | Demonstration of local alignment project | Visit Bioinformatics Company | Beach Party |
| Tue-Thur (7/8-7/10) | Work at research site | ||||
| Fri (7/11) | Work at research site | First students present written assignments | |||
| Mon-Thur (7/21-7/24) | Work at research site | ||||
| Fri (7/18) | Work at research site | Research Seminar (Dr. Todd Yeates) | Group Discussion: Report on research activities | ||
| Mon-Thur (7/21-7/24) | Work at research site | ||||
| Fri (7/25) | Work at research site | Seminar on how to apply to graduate school, programs in Bioinformatics, and scholarships (SS, WJ) | University visits to CalTech, USC, or UCLA | ||
| Mon-Thur (7/28-7/31) | Work at research site | ||||
| Fri (8/1) | Work at research site | Second year students present programming project | |||
| Mon-Thur (8/4-8/7) | Work at research site | ||||
| Fri (8/8) | Work at research site | Research seminar (Dr. David J. Robbins) | Group Discussion: Report on research activities | ||
| Mon-Thur (8/11-8/14) | Work at research site | ||||
| Fri (8/15) | Work at research site | Research seminar (Dr. Hoff) | Group Discussion: Discussion of industry vs academia research experiences | ||
| Mon (8/18) | Dr. Eric Davidson luncheon (1PM-3PM) | ||||
| Mon-Thur (8/18-8/21) | Work at research site Sudent exit inverviews and summative surveys of students and research mentors |
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| Fri (8/22) | Student research presentations Student, research mentors, didactic faculty complete quantitative rubrics of presentations |
Luncheon and research seminar (Dr. Wold) Focus group for research mentors |
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Presenter Key: Color key: |
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