:: Center For Bioinformatics and Applied Genomics ::

Course Schedule

5^th Regional Training Course on Bioinformatics Applied to Tropical Diseases In Southeast Asia
September 18-29, 2006
Faculty of Science, Mahidol University, Bangkok, Thailand

Week 1: Mon Tue Wed Thu Fri Sat Sun
Week 2: Mon Tue Wed Thu Fri Sat

Last Update : September 28, 2006

First week

Day 1 : Monday 18 September 2006		Venue
08.00-08.30	Registration (Participants and Observers)	B301
08.30-09.00	Welcome remarks: Dean, Faculty of Science, Mahidol University
09.00-09.30	Course overview Worachart Sirawaraporn
09.30-10.30	Lecture: Introduction to Bioinformatics Chuong Huynh
10.30-11.00	Coffee/Tea Break
11.00-12.00	Faculty Tour: visiting Department of Biochemistry, Faculty Main Library, and Center for Bioinformatics and Applied Genomics (CBAG)
12.00-13.00	Lunch	CBAG
13.00-13.30	Participant Introduction
13.00-15.00	Lecture: NCBI Resources (I, II) Chuong Huynh
15.00-15.30	Coffee/Tea Break
15.30-17.00	Workshop: Cygwin and Software Installation Chuong Huynh, Dinesh Gupta, Urmila Kulkarni-Kale, Worachart Sirawaraporn
17.00-18.30	Workshop: NCBI Resources - Exercise Chuong Huynh, Dinesh Gupta, Urmila Kulkarni-Kale, Worachart Sirawaraporn
19.00-20.30	Welcome reception (sponsored by GE Healthcare BioSciences (Thailand) Co.Ltd.)	Samsen Villa Restaurant

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Day 2: Tuesday 19 September 2006		Venue
09.00-10.00	Lecture : PERL Scripting (I) Arthur Jules Milgram	B301
10.00-10.30	Coffee/Tea Break
10.30-11.30	Lecture: Nucleic Acid Databases Urmila Kulkarni-Kale
11.30-12.00	Q & A
12.00-13.00	Lunch	CBAG
13.00-15.00	Lecture / Workshop: Fundamental of Sequence Analysis Chuong Huynh
15.00-15.30	Coffee/Tea Break
15.30-18.00	Workshop: Cygwin Commands Chuong Huynh, Arthur Jules Milgram
18.00-19.00	Reading Assignment, Q&A
19.30-21.00	Dinner	Hotel

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Day 3 : Wednesday 20 September 2006		Venue
09.00-10.00	Lecture: PERL Scripting (II) Arthur Jules Milgram	B301
10.00-10.30	Coffee/Tea Break
10.30-11.30	Lecture: Pairwise Sequence Alignment and Algorithms Urmila Kulkarni-Kale
11.30-12.00	Q & A
12.00-13.00	Lunch	CBAG
13.00-15.00	Lecture/Workshop: BLAST & FASTA search Urmila Kulkarni-Kale , Chuong Huynh, Arthur Jules Milgram, Dinesh Gupta, Worachart Sirawaraporn
15.00-15.30	Coffee/Tea Break
15.30-17.00	Lecture/Workshop: Local BLAST installation and analysis Chuong Huynh, Arthur Jules Milgram, Dinesh Gupta, Worachart Sirawaraporn
17.00-18.00	Workshop: Databases, Sequence Search Tools and Interpretation of the Results Urmila Kulkarni-Kale , Chuong Huynh, Arthur Jules Milgram, Dinesh Gupta, Worachart Sirawaraporn
18.00-19.00	Group Assignment for Group Project Chuong Huynh, Urmila Kulkarni-Kale, Dinesh Gupta, Worachart Sirawaraporn
19.30-21.00	Dinner	Hotel

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Day 4: Thursday 21 September 2006		Venue
09.00-10.00	Lecture: PERL Scripting (III) Arthur Jules Milgram	B301
10.00-10.30	Coffee/Tea Break
10.30-11.30	Lecture: Multiple Sequence Alignment Urmila Kulkarni-Kale
11.30-12.00	Q & A
12.00-13.00	Lunch	CBAG
13.00-14.00	Lecture/ Workshop: Scoring matrices Urmila Kulkarni-Kale
14.00-15.00	Workshop: Multiple Sequence Alignments Urmila Kulkarni-Kale
15.00-15.30	Coffee/Tea Break
15.30-17.00	Review: PERL Scripting I-III Arthur Jules Milgram
17.00-19.00	Work on Group Project, Self study and Q&A
19.30-21.00	Dinner	Hotel

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Day 5: Friday 22 September 2006		Venue
09.00-10.00	Lecture: PERL Scripting (IV) Arthur Jules Milgram	B301
10.00-10.30	Coffee/Tea Break
10.30-11.30	Lecture: Protein and Protein Structure Databases Dinesh Gupta
11.30-12.00	Q & A
12.00-13.00	Lunch	CBAG
13.00-14.00	Lecture/Workshop: Introduction to Special Genome Databases: PlasmoDB and Ensembl Arthur Jules Milgram
14.00-15.00	Workshop: Exploring PlasmoDB and Ensembl Arthur Jules Milgram, Dinesh Gupta, Chuong Huynh, Worachart Sirawaraporn
15.00-15.30	Coffee/Tea Break
15.30-16.00	Course evaluation for the first week
16.00-19.00	Work on Group Project Self study and Q&A
19.30-21.00	Dinner	Hotel

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Day 6: Saturday 23 September 2006
Self study

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Day 7: Sunday 24 September 2006
Free day

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Second Week :

Day 8: Monday 25 September 2006		Venue
09.00-10.00	Lecture: PERL Scripting (V) Arthur Jules Milgram	B301
10.00-10.30	Coffee/Tea Break
10.30-11.30	Lecture: Molecular Phylogeny Urmila Kulkarni-Kale
11.30-12.00	Q & A
12.00-13.00	Lunch	CBAG
13.00-15.00	Workshop: Phylogenetic Analysis and Interpretation Urmila Kulkarni-Kale
15.00-15.30	Coffee/Tea Break
15.30-17.00	Workshop: Construction of phylogenetic trees and analysis Urmila Kulkarni-Kale, Dinesh Gupta, Chuong Huynh, Worachart Sirawaraporn
17.00-18.30	Review: PERL Scripting (IV, V) Arthur Jules Milgram
18.30-19.00	Work on Group Project Self study and Q&A
19.30-21.00	Dinner	Hotel

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Day 9: Tuesday 26 September 2006		Venue
09.00-10.00	Lecture: Introduction to EMBOSS Dinesh Gupta	B301
10.00-10.30	Coffee/Tea Break
10.30-11.30	Lecture: Comparative genomics and Genome Alignment Urmila Kulkarni-Kale
11.30-12.00	Q & A
12.00-13.00	Lunch	CBAG
13.00-15.00	Lecture / Workshop: EMBOSS installation and exploring the software Dinesh Gupta, Chuong Huynh, Urmila Kulkarni-Kale, Worachart Sirawaraporn
15.00-15.30	Coffee/Tea Break
15.30-17.00	Lecture/Workshop: Overview and Update on TDR pathogens and Vector Genomes Chuong Huynh
17.00-19.00	Work on Group Project Self study and Q&A
19.30-21.00	Dinner	Hotel

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Day 10 : Wednesday 27 September 2006		Venue
09.00-10.00	Lecture: Comparative genomics and Genome Alignment (I) Urmila Kulkarni-Kale	B301
10.00-10.30	Coffee/Tea Break
10.30-11.30	Lecture: Epitope Prediction Methods & synthetic peptide vaccine design: Japanese encephalitis virus case study Urmila Kulkarni-Kale
11.30-12.00	Q & A
12.00-13.00	Lunch	CBAG
13.00-15.00	Workshop: Comparative genomics and Genome Alignment & epitope prediction Urmila Kulkarni-Kale
15.00-15.30	Coffee/Tea Break
15.30-19.00	Work on Group Project
19.30-21.00	Dinner	Hotel

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Day 11 : Thursday 28 September 2006		Venue
09.00-10.30	Lecture: Principle of Protein Structure, Protein Structure Databases and secondary structure prediction Dinesh Gupta	B301
10.30-11.00	Coffee/Tea Break
11.00-12.00	Lecture: Molecular modeling: principle and Inhibitor Design Dinesh Gupta
12.00-13.00	Lunch	CBAG
13.00-15.00	Workshop Lecture: Molecular Modeling Tools Dinesh Gupta, Urmila Kulkarni-Kale, Worapol Ratanachuen, Worachart Sirawaraporn
15.00-15.30	Coffee/Tea Break
15.30-19.00	Work on Group Project
19.30-21.00	Dinner	Hotel

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Day 12 : Friday 29 September 2006		Venue
09.00-10.00	Group Presentation All participants and facilitators	B301
10.00-10.30	Coffee/Tea Break
10.30-12.00	Group Presentation (Cont)
12.00-13.00	Lunch	CBAG
13.00-14.00	Lecture: Primer design and applications in Molecular Biology Research Worachart Sirawaraporn
14.00-15.30	Lecture: Grant Writing and Funding Resources Worachart Sirawaraporn
15.30-16.00	Course Evaluation
16.00-16.30	Certificate
16.30-18.00	Farewell Party	Ros-Sa-Bieng Restaurant

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Day 13 : Saturday 30 September 2006
Departure * Check out time is NOON *