2007 Southern California Bioinformatics Summer Institute
Calendar 2007
Calendar updates are made throughout the program.
Last Update: 08/10/07
Morning Topics |
Afternoon Topics |
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Lecture |
Workshop |
Lecture |
Workshop |
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| w e e k 1 |
Mon (6/18) | Program Overview - Introduction to Bioinformatics, description of program (JM, NWP, SS) Q&A session with 2nd year students
Location: E&T C256 |
Campus Orientation, campus tour, students pick up driving permits. Student pre-didactic instruction self-assessment of requisite bioinformatics skills/knowledge |
Molecular life science review, central dogma, amino acid similarities, protein structure (SS) 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 (6/19) | Literature Databases - Information organization and retrieval, NCBI Entrez (SS)
Location: E&T C256 |
Introduce Writing Assignment 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 (6/20) | Python II - Control Structures (NWP)
Location: E&T C256 |
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 (6/21) | Database searching - evolutionary basis of sequence alignment scoring matrices (JM) Location: E&T C256 |
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 (6/22) | Professional Development (WJ, SS)
Location: PS 306 |
Finalize Writing Assignments | Research site visit | ||
| Sun (6/24) | Welcome Barbeque | ||||
| w e e k 2 |
Mon (6/25) | Statistics- Basic progability, counting techniques, Bayes' theorem (DC)
Location: E&T C256 |
Statistics workshop | Statistics - Markov chains (DC) | Statistics Workshop |
| Tue (6/26) | Statistics - Hidden Markov chains (DC)
Location: E&T C256 |
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 (6/27) | Dynamic programming - Longest Common Subsequence Algorithm (LCS) (NWP)
Location: E&T C256 |
Implement LCS algorithm - scoring | Python IV - scopes, modules, doc strings, debugging (NWP) Local and Global Alignment algorithms - LCS, dynamic programming (NWP) |
Implement LCS algorithm- traceback | |
| Thur (6/28) | Pairwise Global and Local Alignment - affine gap penalties, ends-free alignment (NWP)
Location: E&T C256 |
Groups start to work on sequence alignment project | Space efficient algorithms (NWP) | Sequence alignment project | |
| Fri (6/29) | Multiple sequence alignment - ClustalW other multiple sequence alignment programs (JM) Location: E&T C256 |
Align protein sequences form GenBank using ClustalW | Research Seminar Jeanette Papp, Ph.D See Speakers Page for more information.
Lunch: PS 250 |
Group Discussion: Report on research/products of research site (WJ, SS) until 5pm.
Friday Night Social/Dinner (Dr. Momand) |
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| w e e k 3 |
Mon (7/2) | 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 (JF) Location: PS 612 |
Ethics Workshop |
| Tue (7/3) | Protein Structure - difference between secondary and tertiary structure, deep view SIMS (JM)
Location: E&T C256 |
DeepView Tutorial http://www.usm.maine.edu/ ~rhodes/SPVTut/text/ SPdbVTut.html |
Signal transduction pathways (JM) | Workshop on Signaling pathway analysis | |
| Wed (7/4) | Holiday | ||||
| Thur (7/5) | Microarrays - principles of expression microarray (SS)
Location: E&T C256 |
Introduction to GeneSpring data analysis | Microarrays - principles of major clustering algorithms (SS) | use GeneSpring for cluster analysis and recognizing and dealing with variability in acquired data | |
| Fri (7/6) | Microarrays - Sources of uncertainty and error in microarray analysis (SS)
E&T C256 |
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 | ||
w 4 |
Mon (7/9) |
1st yr students demonstration of sequence alignment project Students and faculty assess presentation. 2nd yr students help evaluate Assessment Presentation (BK) Student Evaluation and Assessment Available Online (due 7/13) |
Beach Party ! | ||
| Tue (7/10) | Work at Research Site | ||||
| Wed (7/11) | Work at Research Site | ||||
| Thur (7/12) | Work at Research Site | ||||
| Fri (7/13) | 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) - Due Location: E&T C256 |
Group discussion: report on research activities; 2nd yr students present previous yr's research |
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| w e e k s 5 to 10 |
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| Mon (7/16) | Writing Assignment Due. E-mail writing assignment by 9:00 am (1st year students only). |
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| Mon-Thur (7/16-7/19) | Work at research site | ||||
| Fri (7/20) | Work at research site | Writing assignment critique workshop
Location: E&T C256 |
Group discussion: report on research activities until 5pm
Friday Night Social/Dinner (Dr. Sharp) |
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| Mon-Thur (7/23-7/26) | Work at research site Work ethic surveys of students and research mentors |
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| Fri (7/27) | Work at research site | Present Progress Reports. Location: PS 306 |
Group discussion: report on research activities: 2nd yr students present programming projects until 5pm. | ||
| Mon (7/30) | Final Draft Writing Assignment Due Email writing assignment by 9:00 am (1st year students only) |
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| Mon-Thur (7/30-8/2) | Work at research site | ||||
| Fri (8/3) | Work at research site | Research Seminar Dr. Soheil Shams See Speakers Page for more information Lunch: PS 250 |
Group Discussion: Report on research activities until 5pm | ||
| Mon-Thur (8/6-8/9) | Work at research site | ||||
| Fri (8/10) | Work at research site | Barbara Wold, Ph.D
Research Seminar See Speakers Page for more information. Lunch: PS 250 |
Group Discussion: Report on research activities.
Friday Night Social/Dinner (Dr. Johnston) |
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| Mon-Thur (8/13-8/16) | Work at research site | ||||
| Fri (8/17) | Work at research site | How to apply to graduate school, programs in Bioinformatics and Scholarships (SS, WJ, Dr. Susan Kane, and Cory Tobin: Former SoCalBSI Participant) Lunch: PS 306 |
Students present final run-through of tasks. Group Discussion: Discussion of industry vs academia research experiences until 6:30 pm. |
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| Mon-Tues (8/20-8/21) | Work at research site
Monday 8/20: Mentors evaluate students (online). |
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| Wed (8/22) | Work at research site Final assessment of core of students' bioinformatics skills and knowledge (BK) Student exit interviews (BK) - BS 262 12:00 P.M - 6:30 P.M (students will be given assigned times) |
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| Thur (8/23) | Student research presentations
(8:45 A.M - 12:00 P.M) Location:
Engineering & Technology Building Room # B-108 |
Focus group assessment of SoCalBSI program by research mentors:
12:00 P.M - 12:30 P.M (BK) Location: Engineering & Technology Building # A-223 |
Student research presentations (1:30 P.M -
4:45 P.M) Location: Engineering & Technology Building Room # B-108
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Presenter Key: Location Key: Color key: |
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