Course Schedule 2004

Changes in the course schedule from the printed schedule will be indicated in red.

Shortcuts:
Week #1: Tue Wed Thu Fri Sat Sun Mon

1^st week

28^th September 2004, Tuesday

09:30-9:45	Welcome Remarks by Prof. V.S. Chauhan, Director – ICGEB and Course Organizers	V. S. Chauhan
9:45-10:00	Introduction by participants	All participants
10:00-10:15	Introduction to the course by course organizer	Dinesh Gupta
10:15-11:00	Overview of Bioinformatics	Chuong Huynh
11:00-11:15	Coffee break
11:15-12:00	Linux introduction	Chuong Huynh
12:00-13:00	Linux demo	Chuong Huynh, Dinesh Gupta
13:00-14:00	Lunch
14:00-15:00	Linux Commands - Lecture	Chuong Huynh, Dinesh Gupta
15:00-15:15	Coffee break
15:15-16:00	Visit to ICGEB	Shirshendu Mukherjee
16:00-18:00	Linux practice - Commands	Chuong Huynh, Dinesh Gupta
18:00-19:00	Linux practice - Installation	Gowtham
	Reading Assignment

29^th September 2004, Wednesday

09:00-11:00	Linux practice	Chuong Huynh
11:00-11:15	Coffee Break
11:15-12:15	Overview of TDR pathogen/vector genomes	Chuong Huynh
12:15-13:00	Genome sequencing, assembly, sequencing technology and strategies	Chuong Huynh
13:00-14:00	Lunch
14:00-1500	~~Genome assembly overview~~ NCBI Resources - I	Chuong Huynh
15:00-15:15	Coffee Break
15:15-17:15	NCBI resources – I - exercises	Chuong Huynh
17:15-18:00	Review and evaluations	Chuong Huynh
	Reading Assignment

30^th September 2004, Thursday

09:00-09:45	Sequence formats and conversion of formats	Dinesh Gupta
09:45-11:00	NCBI resources – II	Chuong Huynh
11:00-11:15	Coffee Break
11:15-13:00	NCBI resources II - exercises	Chuong Huynh
13:00-14:00	Lunch
14:00-15:00	~~NCBI resources exercise –I contd.~~ Fundamentals of Sequence Analysis	Chuong Huynh
15:00-15:15	Coffee Break
15:15-16:15	Gene Finding and Annotation Techniques Basics	Chuong Huynh
16:15-18:00	Review and evaluations	Chuong Huynh
	Reading Assignment

1^st October 2004, Friday

09:00-10:00	~~NCBI resources exercices – II~~ NCBI Genome Workbench	Chuong Huynh
10:00-11:00	Structural genomics	R. Natesh
11:00-11:15	Coffee Break
11:15-12:00	Basics of Sequence alignments, scoring matrices: Global and local alignments	Raghava
12:00-13:00	BLAST	Raghava
13:00-14:00	Lunch
14:00-15:00	Local BLAST installation and interpretation of BLAST runs	Raghava
15:00– 15:15	Coffee break
15:15 - 16:15	Proteomic Tools	Amit Sharma
16:15– 17:15	Protein structure predictions	Raghava
17:15- 18:00	~~Prediction of Sub-cellular localization of proteins~~ Protein Functional Annotation	Raghava
	Reading Assignment

2^nd October 2004 , Saturday

09:00-10:00	PERL – I Lecture (will open in new window)	Andrew Lynn
10:00-11:00	PERL – II Practical (will open in new window)	Andrew Lynn
11:00-11:15	Coffee Break
11:15-12:00	EMBOSS - I	Dinesh Gupta
12:00-13:00	EMBOSS - II - Practical	Dinesh Gupta
13:00-14:00	Lunch
	Reading Assignment

3^rd October 2004 Sunday

ALL Day

Reading Assignment

2^nd Week

4^th October 2004, Monday

09:00-10:00	Multiple sequence alignments	Cathal Seoighe
10:00-11:00	Multiple sequence alignments: workshop	Cathal Seoighe
11:00-11:15	Coffee Break
11:15-12:15	Bioedit - DEMO	Cathal Seoighe
12:15-13:00	Descriptive introduction to phylogenetics	Cathal Seoighe
13:00-14:00	Lunch
14:00-15:00	EMBOSS installation and exercises	Dinesh
15:00-15:15	Coffee Break
15:15-16:00	Genetic distances	Cathal Seoighe
16:00-18:00	Genetic distances: workshop	Cathal Seoighe

5^th October 2004, Tuesday
(BELOW LINKS WILL NOT WORK, its in 2nd CourseCD)

09:00-10:00	~~Overview of Gene Finding and Annotation techniques~~ Brief Oral Only Research Presentation	~~Chuong Huynh~~ All Course Participants
10:00-11:00	Promoter prediction in genomes using Artificial Neural Networks	Krishna Chari
11:00-11:15	Coffee Break
11:15-12:15	Phylogenetics Methods I	Cathal Seoighe
12:15-13:00	Phylogenetics Methods I: workshop	Cathal Seoighe
13:00-14:00	Lunch
14:00-15:00	Phylogenetic methods I: workshop	Cathal Seoighe
15:00-15:15	Coffee Break
15:15-16:15	Phylogenetic Methods II	Cathal Seoighe
16:15-18:00	Phylogenetics Methods II: workshop	Cathal Seoighe
	Group Project Assigned

6^th October 2004, Wednesday

09:00-10:30	Protein sequence databases	Urmila Kulkarni-Kale
10:30-10:45	Coffee Break
10:45-11:45	Inferring selection pressure and adaptive evolution	Cathal Seoighe
11:45-13:00	codeml workshop	Cathal Seoighe
13:00-14:00	Lunch
14:00-15:00	codeml workshop (continued)
15:00-15:15	Coffee Break
15:15- 17:00	Epitope Prediction Methods & synthetic peptide vaccine design: Japanese encephalitis virus case study [Combined with Protein Molecular Modeling]	Urmila Kulkarni-Kale
17:00-18:00	~~Comparative genomics: workshop~~ Comparative Genomics - Lecture	Cathal Seoighe
~~16:15-17:30~~	~~Protein Molecular modeling~~	~~Urmila Kulkarni-Kale~~
~~17:30-18:00~~	~~Review and catch-up~~	~~Cathal Seoighe~~
	Reading Assignment

7^th October 2004, Thursday

08:45-09:00	Group Pictures -- on lawns directly to the right as you walk toward the guest house	Instructors and Participants
09:00-10:00	~~EMBL resources~~ Protein Sequence Database - Workshop	Urmila Kulkarni-Kale
10:00-11:00	Artemis as genome viewing and annotation tool - Lecture and	Arnab Pain
11:00-11:15	Coffee Break
11:15-12:15	Artemis - Live Demo	Arnab Pain
12:15- 13:00	Practical (Module 1: Artemis Prokaryotic)	~~Urmila Kulkarni-Kalez~~ Arnab Pain
13:00-14:00	Lunch
14:00-15:00	~~Primer designing~~ Genome alignment using MUMmer and BLAST2	~~Worachart Sirawaraporn~~ Urmila Kulkarni-Kale
15:00-15:15	Coffee Break
15:15-16:15	~~Grant writing~~ Genome Alignment - Practical	~~Worachart Sirawaraporn~~ Urmila Kulkarni-Kale
16:15-17:30	ractical (Module 1: Artemis Prokaryotic) (continued) ~~Gene prediction and exercises~~	Arnab Pain
17:30-18:30	Gene Prediction - Lecture	Arnab Pain
~~18:00- 19:00~~	~~Role of Bioinformatics in vaccine and drug development.~~	~~Urmila Kulkarni-Kale~~

	Distance Learning
	Primer designing	Worachart Sirawaraporn
	Grant writing	Worachart Sirawaraporn
	Epitope Prediction Methods - Workshop	Urmila Kulkarni-Kale

8^th October 2004, Friday

09:00- 10:00	Comparative Genomics using ACT - Lecture	~~Worachart Sirawaraporn~~ Arnab Pain
10:00-11:00	~~Artemis: Annotation~~ Practical: Module 2: Artemis Eukaryotic	Arnab Pain
11:00-11:15	Coffee Break
11:15-13:00	~~Artemis: Annotation~~ Practical: Module 3: Artemis Advanced	Arnab Pain
13:00-14:00	Lunch
14:00-15:00	~~Whole genome annotation~~ Practical: Module 4: Gene Prediction Exercises	Arnab Pain
15:00-15:15	Coffee break
15:15-16:00	~~Annotation using web based tools~~ Practical: Module 5: Small Scale Annotation	Arnab Pain
16:00-16:30	Comparative Genomics using ACT - Live Demo	Arnab Pain
16:30-18:00	~~Annotation using web based tools exercises~~ Practical: Module 6: Comparative Genomics	Arnab Pain

9^th October 2004, Saturday

09:00- 10:00	~~Comparative genomics using ACT~~ Practical: Module 6: Comparative Genomics (continued)	Arnab Pain
10:00-11:00	ACT: live demo Practical: Module 7: Generating ACT comparison files using BLAST	Arnab Pain
11:00-11:15	Coffee Break
11:15-12:15	Artemis/ACT Exercises - Catchup	Arnab Pain
12:15-13:00	Cheminformatics in postgenomic era	Prasad Bharatam
13:00-14:00	Lunch

<== DATA Freeze for Course CD

10^th October 2004 Sunday

11^th October 2004 , Monday

09:00	Group Project Due
09:00-10:00	Information theory and DNA binding sites	Krishna Chari
10:00-11:00	Group presentations	All participants Proctor: Arnab Pain
11:00-11:15	Coffee break
11:15-12:00	Group presentations	All participants
12:00-13:00	Lecture Hunt for suitable gene for stress tolerance (the usage of DNA chips)	Ashwini Parekh
13:00-14:00	Lunch
14:00-15:00	Lecture: On Some Aspects of Structure Based Drug Design	Chandan Raychaudhury
15:00-16:00	Lecture: Drug Designing for Infectious Diseases	V. Kothekar

<== Monday's lectures will be available via FTP download

List of faculty:

Chuong Huynh, National Centre for Biotechnology Information (NCBI), United States of America

Cathal Seoighe, South African National Bioinformatics Institute (SANBI), South Africa

Arnab Pain, The Wellcome Trust Sanger Institute, United Kingdom

Dinesh Gupta, International Centre for Genetic Engineering and Biotechnology (ICGEB), India

Worachart Siraworaporn, Mahidol University, Thailand

Urmila Kulkarni-Kale, University of Pune, India

Amit Sharma, International Centre for Genetic Engineering and Biotechnology (ICGEB), India

Andrew Lynn, Jawaharlal Nehru University (JNU), India

Ashwini Parekh, Jawaharlal Nehru University (JNU), India

Krishna Chari, Jawaharlal Nehru University (JNU), India

Prasad V. Bharatam, National Institute of Pharmaceutical Education and Research (NIPER), India

R. Natesh

1st week

2nd Week

1^st week

2^nd Week