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Course Schedule
2nd Regional Training
Course on Bioinformatics Applied to Tropical Diseases
In Southeast Asia
September 29 - October 10, 2003
Faculty of Science, Mahidol University, Bangkok, Thailand
| Venue |
||
08.30-09.00 |
Welcome remarks: Dean, Faculty of Science,
Mahidol University Audio visual presentation: Mahidol University |
P114 |
09.00-10.00 |
Lecture: Introduction to Bioinformatics Chuong Huynh |
|
10.00-10.20 |
Coffee/Tea Break |
P115 |
10.20-12.00 |
Lecture: Basic Linux I and II Alan Durham |
P114 |
12.00-13.00 |
Lunch |
P115 |
13.00-14.00 |
Lecture: PERL Scripting Language I Alan Durham |
P114 |
14.00-14.30 |
Participant introduction |
CBAG |
| 14.30-14.45 |
Coffee/Tea Break |
|
| 14.45-18.30 | Workshop: Linux installation and Network concepts Alan Durham, Hidayat Trimarsanto, Worapol Ratanachuen, Suang Udomvaraphunt |
|
19.00-20.00 |
Welcome
reception |
|
Day
2: Tuesday 30 September 2003 |
Venue |
|
09.00-10.00 |
Lecture: NCBI Resources I Chuong Huynh |
P114 |
10.00-10.20 |
Coffee/Tea Break
|
P115 |
10.20-12.00 |
Lecture: NCBI resources II and Assign Self Exercise Chuong Huynh |
P114 |
12.00-13.00 |
Lunch
|
P115 |
13.00-14.40 |
Workshop: Algorithms and Programs Alan Durham |
CBAG |
| 14.40-15.00 | Coffee/Tea Break |
|
15.00-18.30 |
Workshop: Basic Linux Commands
Alan Durham |
|
| 18.30-19.00 | Workshop: Getting familiar with software used in the
workshop Alan Durham, Hidayat Trimarsanto |
CBAG |
19.00-20.00 |
Dinner
|
P115 |
| 20.00-22.00 | Self Study - Reading Assignment | CBAG |
| Day
3 : Wednesday 1 October 2003 |
Venue |
|
09.00-10.30 |
Lecture: Database Fundamentals Alan Durham |
P114 |
10.30-10.50 |
Coffee/Tea Break
|
P115 |
10.50-12.00 |
Lecture: Fundamentals of Sequence Formats and Analysis Chuong Huynh |
P114 |
12.00-13.00 |
Lunch
|
P115 |
13.00-14.00 |
Workshop: Software installationI Chuong Huynh, Hidayat Trimarsant, Suang Udomvaraphunt |
CBAG
|
14.00-15.30 |
Workshop:BLAST Install and Basics
Chuong Huynh, Worapol Ratanachuen, Mila Juricek, Hidayat Trimarsanto, Worachart Sirawaraporn |
|
15.30-15.45 |
Coffee/Tea Break |
|
| 15.45-18.30 | Workshop: PERL Scripting Language II |
|
19.00-20.00 |
Dinner
|
P115 |
20.00-22.00 |
Self study/library time/Reading Assigment | CBAG |
| Day
4: Thursday 2 October 2003 |
Venue |
|
09.00-10.00 |
Lecture: Bioinformatics, genomics, and
functional approaches toward a better understanding of malaria pathogenesis Brian M. Cooke |
P114 |
10.00-10.20 |
Coffee/Tea Break
|
P115 |
10.20-12.00 |
Lecture: EMBOSS and JEMBOSS software package I Mila Juricek |
P114 |
12.00-13.00 |
Lunch
|
P115 |
13.00-13.20 |
Workshop: Overview of TDR Pathogens and Vector Genomes Chuong Huynh |
CBAG |
| 13.20-14.30 | Workshop: BLAST Basics (continue) Chuong Huynh, Hidayat Trimarsanto |
|
14.30-14.40 |
Break
|
|
14.40-17.00 |
Workshop: PERL Scripting Language III Alan Durham, Hidayat Trimarsanto |
|
17.00-17.20 |
Coffee/Tea Break |
|
| 17.20-18.30 | Workshop: PERL Scripting Language III Practice and
Questions Alan Durham, Hidayat Trimarsanto |
|
| 18.59-19.00 | Do 1-minute Survey | |
19.00-20.00 |
Dinner
|
P115 |
20.00-22.00 |
Self study/library time | CBAG |
Day
5: Friday 3 October 2003 |
Venue |
|
09.00-10.00 |
Lecture: EMBOSS and JEMBOSS software packages
II Mila Juricek |
P114 |
10.00-10.20 |
Coffee/Tea Break
|
P115 |
10.20-12.00 |
Workshop: PERL Scripting Language IV Alan Durham |
CBAG |
12.00-13.00 |
Lunch
|
|
13.00-14.00 |
Workshop: EMBOSS Installation and Setup Mila Juricek, Hidayat Trimarsanto |
CBAG
|
14.00-14.10 |
Break
|
|
| 14.10-15.45 | Workshop: Hands-on EMBOSS and JEMBOSS I (including
sequence conversion with SeqRet) Mila Juricek, Hidayat Trimarsanto |
|
15.45-16.00 |
Coffee/Tea Break |
|
16.00-18.30 |
Workshop: Hands-on EMBOSS and JEMBOSS
II Mila Juricek, Hidayat Trimarsanto |
|
| 18.59-19.00 | Do 1-minute Survey | |
19.00-20.00 |
Dinner
|
P115 |
20.00-22.00 |
Self study/Discussion | CBAG |
Day
6: Saturday 4 October 2003 |
Venue |
|
09.00-10.00 |
Lecture: General guidelines for writing
a good grant proposal Worachart Sirawaraporn |
P114 |
10.00-10.20 |
Coffee/Tea Break
|
P115 |
10.20-12.00 |
Lecture: Funding resources and TDR South-South Initiative Worachart Sirawaraporn |
P114 |
| 12.00-12.01 | Do 1-minute Survey | CBAG |
| 12.01-12.30 | Introduce Group Project-Bioinformatics Group Focus Questions | |
12.30-13.30 |
Lunch
|
P115 |
Free time |
||
Day 7
: Sunday 5 October 2003 Holiday (Excursion: Acient City, Samut Prakan) [more] |
Second Week :
Day
8 : Monday 6 October 2003 |
Venue |
|
09.00-10.00 |
Lecture: Principle of Pairwise Sequence
Alignment Stuart Brown |
P114 |
10.00-10.20 |
Coffee/Tea Break
|
P115 |
10.20-12.00 |
Lecture: Principle of Multiple Sequence Alignment Stuart Brown |
P114 |
12.00-13.00 |
Lunch
|
P115 |
13.00-15.00 |
Workshop: Pairwise Alignment Stuart Brown, Hidayat Trimarsanto, Worachart Sirawaraporn, Mila Juricek |
CBAG
|
15.00-15.20 |
Coffee/Tea Break
|
|
15.20-16.30 |
Workshop: Hands-on Multiple Sequence Alignment using
CLUSTAL W Stuart Brown, Chuong Huynh, Worapol Ratanachuen, Mila Juricek, Hidayat Trimarsanto, Worachart Sirawaraporn |
CBAG |
| 16.30-17.00 | Review: Sequence Alignment Hidayat Trimarsanto |
|
| 17.00-18.30 | Workshop: Hands-on Multiple Sequence Alignment using
CLUSTAL W Stuart Brown, Chuong Huynh, Worapol Ratanachuen, Mila Juricek, Hidayat Trimarsanto, Worachart Sirawaraporn |
|
| 18.30-19.00 | Workshop: Go over today's workshop exercises on alignment Stuart Brown |
|
| 18.59-19.00 | Do 1-munute Survey | |
19.00-20.00 |
Dinner
|
P115 |
20.00-22.00 |
Self study/library time or Review | CBAG |
Day
9 : Tuesday 7 October 2003 |
Venue |
|
09.00-10.30 |
Lecture: Principle of phylogenesis: construction
and analysis Stuart Brown |
P114 |
10.30-10.50 |
Coffee/Tea Break
|
P115 |
10.50-11.15 |
Lecture: Phylogenomics: functional prediction of uncharacterized
genes by evolutionary analysis Stuart Brown |
P114 |
| 11.15-12.00 | Lecture: Protein Patterns Stuart Brown |
|
12.00-13.00 |
Lunch
|
P115 |
13.00-15.00 |
Workshop: Phylogenetic construction and analysis I Stuart Brown, Chuong Huynh, Hidayat Trimarsanto, Mila Juricek |
CBAG
|
15.00-15.20 |
Coffee/Tea Break
|
|
| 15.20-16.20 | Review: Sequence Alignment Workshop: Free time to work on grup project |
|
16.20-18.20 |
Workshop: Phylogenetic construction and analysis (continue) Stuart Brown, Chuong Huynh, Hidayat Trimarsanto, Mila Juricek |
|
| 18.20-18.59 | Workshop: Go over today's workshop exercises on pylogenetic Stuart Brown |
|
| 18.59-19.00 | Do 1-minute Survey | |
19.00-20.00 |
Dinner
|
P115 |
20.00-22.00 |
Group project, self study/library time | CBAG |
Day
10 : Wednesday 8 October 2003 |
Venue |
|
09.00-10.00 |
Lecture: Gene Prediction Chuong Huynh |
P114 |
10.00-10.20 |
Coffee/Tea Break
|
P115 |
10.20-10.45 |
Lecture: Gene Prediction (continue) | P114 |
10.45-12.00 |
Lecture: Gene analysis using EMBOSS Mila Juricek |
|
12.00-13.00 |
Lunch
|
P115 |
13.00-15.30 |
Workshop: Emboss (continue) Mila Juricek, Stuart Brown, Hidayat Trimarsanto |
CBAG |
15.30-15.50 |
Coffee/Tea Break
|
|
15.50-17.30 |
Workshop: Emboss (continue) | |
17.30-18.20 |
Review: Interpretating BLAST Output Stuart Brown |
|
18.20-18.59 |
Group project | |
18.59-19.00 |
Do 1-minute Survey | |
19.00-20.00 |
Dinner
|
P115 |
20.00-22.00 |
Self study and library time | CBAG |
Day
11 : Thursday 9 October 2003 |
Venue |
|
09.00-10.00 |
Lecture: Homology modeling : principles,
tools and techniques Dr. Hongwei Huang (Accelrys) |
P114 |
10.00-10.20 |
Coffee/Tea Break
|
P115 |
10.20-12.00 |
Lecture: Inhibitor design based on protein structure Dr. Hongwei Huang (Accelrys) |
P114 |
12.00-13.00 |
Lunch
|
P115 |
13.00-14.00 |
Secondary Structure Prediction Stuart Brown |
CBAG
|
| 14.00-14.30 | Workshop Lecture: Human and Pathogen Seqwuence Variation
(and SNP) Stuart Brown |
|
14.30-14.50 |
Coffee/Tea Break
|
|
14.50-15.30 |
Workshop Lecture: Transcript-based Resources at NCBI Chuong Huynh |
|
15.30-16.30 |
Workshop Lecture: Gene Annotation Techniques (Demo
: Artemis) Hidayat Trimarsanto |
|
| 16.30-17.00 | Workshop Demo: Whole Genome Vistualization Hidayat Trimarsanto |
|
| 17.00-18.59 | Group Project | |
| 18.59-19.00 | Do 1-minute Survey | |
19.00-20.00 |
Dinner
|
P115 |
20.00-22.00 |
Group project | CBAG |
Day
12 : Friday 10 October 2003 |
Venue |
|
09.00-10.00 |
Lecture: An Introduction
to CodeLink Bioarray Platform for Gene Expression Henry Tan (Amersham BioScience) |
P114 |
10.00-10.20 |
Coffee/Tea Break
|
P115 |
10.20-11.45 |
Lecture: The next step in proteomics - adding function
to identification Henry Tan (Amersham BioScience) |
P114 |
11.45-12.00 |
Overview of Course CD Content Chuong Huynh |
|
12.00-13.00 |
Lunch
|
P115 |
13.00-15.30 |
Workshop: Answer Group Project Questions | CBAG
|
15.30-16.00 |
Course Evaluation --> then Coffee/Tea Break |
|
16.00-16.30 |
Certificate | |
16.30-19.00 |
Farewell Party | P114 |
| Day
13 : * Saturday 11 October 2003 Departure * |
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