24th October 2005, Monday

09:00-9:30

Registration etc.

 

09:30-9:45

Welcome Remarks by The Director ICGEB and Dinesh Gupta

V. S. Chauhan and Dinesh Gupta

9:45-10:00

Introduction by participants

All participants

10:10-11:00

The bioinformatics experiment

Jessica Kissinger

11:00-11:15

Coffee break

 

11:15-12:00

Linux introduction

Dinesh Gupta

12:00-13:00

Linux practice

Dinesh Gupta

13:00-14:00

Lunch

 

14:00-15:00

Visit to ICGEB

Shirshendu Mukherjee

15:00-15:15

Coffee break

 

15:15-17:00

BLAST

Jessica Kissinger

17:00-18:00

Local BLAST and interpretation of results

All participants, JK, Dinesh Gupta

25th October, Tuesday

09:00-10:00

Introduction to Bioinformatics databases: Nucleic Acid Databases

Dinesh Gupta

11:00-11:15

Coffee Break

 

11:15-12:15

Pairwise sequence alignments

Urmila

12:15-13:00

Multiple sequence alignments

Urmila

13:00-14:00

Lunch

 

14:00-1500

Sequence alignment: demo and assignments

Urmila

15:00-15:15

Coffee Break

 

15:15-17:15

Epitope prediction

Urmila

17:15-18:00

Review

Dinesh/Urmila

26th September 2004, Wednesday

09:00-10:00

Genome alignment using MUMmer and BLAST2

Urmila

10:00-11:00

Comparative genomics of viruses

Urmila

11:00-11:15

Coffee Break

 

11:15-12:15

Algorithms

Alan Durham

12:15-13:00

Sequence Assembly

Jessica Kissinger

14:00-15:00

Sequence Assembly Phred/Phrap

Jessica Kissinger

15:00-15:15

Sequence Assembly Phred/Phrap Demo

Jessica Kissinger

15:15-16:15

Free Computer time

All Participants

16:15-18:00

PERL
(For all Perl Lectures)

Alan Durham

27th October 2004, Thursday

09:00-10:00

Phylogeny reconstruction concepts and methods

Jessica Kissinger

11:00-11:15

Coffee Break

 

11:15-13:00

Phylogeny demo and practice

JK and all participants

13:00-14:00

Lunch

 

14:00-15:00

PERL

Alan Durham

15:00 15:15

Coffee break

 

15:15 - 16:15

PERL

Alan Durham

28th October 2005, Friday

09:00-10:00

PERL I Lecture

Alan Durham

10:00-11:00

PERL II Practical

Alan Durham

11:00-11:15

Coffee Break

 

11:15-13:00

Parasite databases, how to find what you need

Jessica Kissinger

13:00-14:00

Lunch

 

14:00-15:00

EMBOSS - I

Dinesh

15:00-15:15

Coffee break

 

15:15-18:00

EMBOSS II practice

Dinesh, all participants

29th October 2005 Saturday

09:00-10:00
Databases

Alan Durham

10:00-11:00
PERL

Alan Durham

11:00-11:15

Coffee Break

 

11:15 13:00

PERL

Alan Durham

13:15 14:00

Lunch

 

30th October, 2005

Sunday, free time

2nd Week

31st October 2005, Monday

10:00-11:00

Artemis as genome viewing and annotation tool - Lecture

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)

Arnab Pain

13:00-14:00

Lunch

 

14:00-15:00

Cygwin: install linux in your windows PC (Software)

Dinesh

15:00-15:15

Coffee Break

 

15:15-16:15

PERL

Alan Durham

16:15-17:30

Practical (Module 1: Artemis Prokaryotic) (continued)

Arnab Pain

17:30-18:30

Gene Prediction - Lecture

Arnab Pain

 

 

 

 

 

1st November, Tuesday (half day)

9:00-11:00

Review and practice

Arnab Pain, Dinesh

11:00-11:15

Coffee break

 

11:00-13:00

Self study

All participants

2nd November, 2005, Wednesday

09:00- 10:00

Comparative Genomics using ACT - Lecture

Arnab Pain

10:00-11:00

Practical: Module 2: Artemis Eukaryotic

Arnab Pain

11:00-11:15

Coffee Break

 

11:15-13:00

Practical: Module 3: Artemis Advanced

Arnab Pain

13:00-14:00

Lunch

 

14:00-15:00

Practical: Module 4: Gene Prediction Exercises

Arnab Pain

15:00-15:15

Coffee break

 

15:15-16:00

Practical: Module 5: Small Scale Annotation

Arnab Pain

16:00-16:30

Comparative Genomics using ACT Live Demo

Arnab Pain

16:30-18:00

Practical: Module 6: Comparative Genomics

Arnab Pain

3rd November, 2005, Thursday

09:00- 10:00

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

 

11:15-12:00

Artemis/ACT Exercises - Catchup

Arnab Pain

12:00-13:00

Protein Structure Prediction: Homology Modelling and Methods for Fold Recognition

Debasis Mohanty

13:00-14:00

Lunch

 

14:00-15:00

Understanding biosynthesis of complex metabolites using computational biology
Part I and Part II

Debasis Mohanty

15:00-15:15

Coffee break

 

15:15-16:00

Proteomic Tools

Amit Sharma

4th November, 2005, Friday

09:00- 10:00

PERL for bioinformatics  in a nutshell

Alan Durham

10:00-11:00

Computational analysis of DNA binding sites

K. Chari

11:00-11:15

Coffee Break

 

11:15-12:15

Metabolomics and Drug target identification from pathogenic organisms

Andrew Lynn

12:15-13:00

Grant writing

Worachart Sirawaroporn

13:00-14:00

Lunch

 

14:00-15:00

Rational Drug Design: an introduction

Andrew Lynn

15:00-15:15

Coffee break

 

15:15-16:30

Lecture by Sanjay Jain

Sanjay Jain

16:30-17:30

Primer Designing

Worachart