Course Schedule

International Training Course on Functional Genomics
Applied to Insect Vectors of Human Diseases

January 17-28, 2005

Center for Vectors and Vector-Borne Diseases (CVVD) and
Center for Bioinformatics and Applied Genomics (CBAG)

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 : January 31, 2005

Day 1 : Monday 17 January, 2005		Venue
08.30-09.00	Welcome remarks: Dean, Faculty of Science, Mahidol University	P114
09.00-09.30	Lecture: Overview on Functional Genomics: Current Approaches and Future Developments Worachart Sirawaraporn	P114
09.30-10.15	Coffee/Tea Break	P115
10.15-10.45	Lecture: TDR Research Programmes on Functional Genomics of Vectors and Pathogens Yeya Toure	P114
10.45-12.00	Faculty Tour (library, CBAG and CVVD)
12.00-13.00	Lunch	Canteen
13.00-14.00	Lecture: Genetic Modification of Insects of Medical Importance: Past, Present and Future Marcelo Jacobs-Lorena	P114
14.00-14.30	Participant Introduction	CBAG
14.30-15.30	Lecture: NCBI Resources and Tools (I) Chuong Huynh
15.30-16.00	Coffee/Tea Break
16.00-17.00	Lecture: NCBI Resources and Tools (II) Chuong Huynh
17.00-18.30	Workshop: Networking Concepts and Software Installation Chuong Huynh , Worachart Sirawaraporn, Worapol Ratanachuen
19.00-20.30	Welcome reception	P114

Day 2 : Tuesday 18 January, 2005		Venue
09.00-10.00	Lecture: Insect Genomics I: From Drosophila to Anopheles Kitsos Louis	P114
10.00-10.30	Coffee/Tea Break	P115
10.30-11.30	Lecture: Insect Genomics II: General Overview of Vector Databases and Future Applications Kitsos Louis	P114
11.30-12.00	Q & A	P114
12.00-13.00	Lunch	Canteen
13.00-15.00	Workshop: NCBI Resources - Excercise Chuong Huynh, Worachart Sirawaraporn, Worapol Ratanachuen	CBAG
15.00-15.30	Coffee/Tea Break
15.30-16.30	Lecture/Workshop: Overview on Anobase Kitsos Louis
16.30-19.00	Lecture/Workshop: Anobase Hands-on and Excercises Kitsos Louis, Chuong Huynh
19.00-21.00	Dinner Time	Hotel

Day 3 : Wednesday 19 January, 2005		Venue
09.00-10.00	Lecture: Molecular Approaches to the study of Plasmodium-Mosquito Interactions Marcelo Jacobs-Lorena	P114
10.00-10.30	Coffee/Tea Break	P115
10.30-11.30	Lecture: Anopheles Gene Plot and AnoBase Jules Milgram	P114
11.30-12.00	Q & A	P114
12.00-13.00	Lunch	Canteen
13.00-14.00	Lecture: Ensemble: Anopheles Genome Browser Kitsos Louis	CBAG
14.00-15.00	Lecture: Microarrays Methodology and Analysis George Dimopoulos
15.00-15.30	Coffee/Tea Break
15.30-17.30	Lecture/Workshop: Hands-On PlasmoDB and Excercises Jules Milgram, Chuong Huynh , Worachart Sirawaraporn, Worapol Ratanachuen
17.30-19.00	Lecture/Workshop: Applications of Microarray in Vector Biology Research George Dimopoulos
19.00-21.00	Dinner Time	Hotel

Day 4 : Thursday 20 January, 2005		Venue
09.00-10.00	Lecture: Whole Genome Sequencing and Assembly Brandan Loftus	P114
10.00-10.30	Coffee/Tea Break	P115
10.30-11.30	Lecture: Aedes aegypti Genome Annotation Brendan Loftus	P114
11.30-12.00	Q & A	P114
12.00-13.00	Lunch	Canteen
13.00-14.00	Lecture: The Transcriptome of Aedes aegypti Brendan Loftus	P114
14.00-15.00	Lecture: Molecular Biology and Proteomics of the Mosquito Peritrophic Matrix Marcelo Jacobs-Lorena	P114
15.00-15.30	Coffee/Tea Break	CBAG
15.30-17.00	Lecture/Workshop: Protein and Nucleic Acid Databases Chuong Huynh, Jules Milgram, Worachart Sirawaraporn, Worapol Ratanachuen
17.00-19.00	Lecture/Workshop: Microarrays Methodologies George Dimopoulos
19.00-20.00	Dinner Time	Hotel

Day 5 : Friday 21 January, 2005

Venue

09.00-10.00

Lecture: Molecular approaches to improve control of vector-borne diseases
     Kitsos Louis

P114

10.00-10.30
Coffee/Tea Break

P115

10.30-11.30
Lecture: Fundamental of Mass Spectrometry: Instrumentation and application mechanisms
     Jiangyong Li

P114

11.30-12.00 Q & A

12.00-13.00
Lunch

Canteen

13.00-14.00
Lecture: Large Scale Proteomics and Sample Preparation
     Jiangyong Li

P114

14.00-15.00
Lecture: PERL Scripting (I)
     Jules Milgram

CBAG

15.00-15.30
Coffee/Tea Break

15.30-16.30
Lecture: PERL Scripting (II)
     Jules Milgram

16.30-17.30 Course Evaluation (First week)

18.00-19.00
Review: PERL Scripting I, II
     Jules Milgram

19.00-21.00
Dinner Time

Hotel

Day 6 : Saturday 22 January, 2005
(Excursion: To be Announced)

Day 7: Sunday 23 January, 2005
(Free Day)

Day 8: Monday 24 January, 2005

Venue

09.00-10.00
Lecture: Mass Spectrometry to study protein post-translational modifications
     Jiangyong Li
P114

10.00-10.30
Lecture: Sequence Alignment and Algorithms
     Chuong Huynh

10.30-11.00
Coffee/Tea Break

11.00-12.00
Lecture: PERL Scripting (III)
     Jules Milgram

CBAG

12.00-13.00
Lunch

Canteen

13.00-14.00 Lecture: PERL Scripting (III)
     Jules Milgram
CBAG

14.00-15.00
Lecture: Sequence Alignment and Algorithms
     Chuong Huynh, Jules Milgram, Worachart Sirawaraporn, Worapol Ratanachuen

15.00-15.30
Coffee/Tea Break

15.30-18.00
Lecture/Workshop: BLAST & FASTA (cont’n)
     Chuong Huynh, Jules Milgram, Worachart Sirawaraporn, Worapol Ratanachuen

18.00-19.00
Review: Sequence Alignment and Sequence Search Tools
     Chuong Huynh

19.00-21.00
Dinner Time

Hotel

Day 9: Tuesday 25 January, 2005

Venue

09.00-10.00

Lecture: PERL Scripting (IV)
     Jules Milgram

P114

10.00-10.30
Coffee/Tea Break

P115

10.30-11.30
Lecture: Multiple Sequence Alignment
     Chuong Huynh

P114

11.30-12.00 Q & A

12.00-13.00
Lunch

Canteen

13.00-14.00
Lecture: PERL Scripting (V)
     Jules Milgram

CBAG

14.00-15.00 Workshop: Multiple Seq Alignment
     Chuong Huynh, Jules Milgram, Worachart Sirawaraporn, Worapol Ratanachuen

15.00-15.30
Coffee/Tea Break

15.30-16.30
Lecture: Introduction to MySQL (I)
     Jules Milgram

16.30-17.30
Lecture: Introduction to MySQL (II)
     Jules Milgram

17.30-19.00
Self Study

19.00-21.00
Dinner Time

Hotel

Day 10: Wednesday 26 January, 2005

Venue

09.00-10.00

Lecture: Introduction to EMBOSS (I)
     Jules Milgram

P114

10.00-10.30
Coffee/Tea Break

P115

10.30-11.00
Lecture: Introduction to EMBOSS (II)
     Jules Milgram

P114

11.30-12.00 Q & A

12.00-13.00
Lunch

Canteen

13.00-15.00
Workshop: MySQL (part2: continued)
     Jules Milgram

CBAG

15.00-15.30
Coffee/Tea Break

15.30-17.00
Lecture/Workshop: EMBOSS installation and Exploring the software
     Jules Milgram, Chuong Huynh, Worachart Sirawaraporn, Worapol Ratanachuen

17.00-19.00
Workshop: Exercises: Analysis of sequences using EMBOSS
     Jules Milgram, Chuong Huynh, Worachart Sirawaraporn, Worapol Ratanachuen

19.00-21.00
Dinner Time

Hotel

Day 11: Thursday 27January, 2005

Venue

09.00-10.00

Lecture: Molecular Phylogeny
     Jules Milgram

P114

10.00-10.30
Coffee/Tea Break

P115

10.30-11.30
Lecture: Principle of Protein Structure and Protein Structure Databases
     Chuong Huynh

P114

11.30-12.00 Q & A

12.00-13.00
Lunch

Canteen

13.00-15.00
Workshop: Phylogeny practical
     Jules Milgram, Chuong Huynh, Worachart Sirawaraporn, Worapol Ratanachuen

CBAG

15.00-15.30
Coffee/Tea Break

15.30-16.30
Recorded Lecture: Exploring 3D Molecular Structures Using NCBI Tools - A Field Guide
      Eric Sayer

16.30-19.00
Workshop: NCBI Structure
     Chuong Huynh, Jules Milgram , Worachart Sirawaraporn, Worapol Ratanachuen

19.00-21.00
Dinner Time

Hotel

Day 12: Friday 28 January, 2005

Venue

09.00-10.00

Lecture: Oligonucleotide Probes: Design and Applications in Molecular Biology Research
     Worachart Sirawaraporn

P114

10.00-10.30
Coffee/Tea Break

P115

10.30-12.00
Lecture: Writing a Grant Proposal
     Worachart Sirawaraporn

P114

12.00-13.00
Lunch

Canteen

13.00-14.30
Lecture: Funding Resources and TDR South-South Network
     Worachart Sirawaraporn

P114

14.30-15.00
Coffee/Tea Break

CBAG

15.00-15.30 Overview of course CD content

15.30-16.00 Course Evaluation (second week)

16.00-18.00
Certificate and Farewell Party

P114

Day 13: Saturday 29 January, 2005
Hotel Check-Out and Departure