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Overview

Written by Richard Bruskiewich
Friday, 06 June 2008 08:27
Welcome to the Crop Research Informatics Laboratory, one of the alliance projects of IRRI, Philippines and CIMMYT, Mexico.
Last Updated ( Monday, 22 September 2008 13:58 )

Bioinformatics Workshop

Written by Nelzo Ereful

Wednesday, 11 October 2006 22:13

The first Bioinformatics Workshop for Crop Researchers will be held on 24-28 March 2008 at the Burma Room, Training Center. This training is tightly meshed with the Bioinformatics online course, located at http://mcclintock.generationcp.org, as its major source of materials.

	Schedule of the Bioinformatics Workshop

Part 1 Bioinformatics
	Start	End	Duration	Activity/ Topic	Facilitator
24-Mar-08	8:30	9:00	0:30	Registration	Jemi/ Jeff
	9:00	9:30	0:30	Opening Remarks/ Introduction to Bioinformatics	Richard Bruskiewich
	9:30	10:00	0:30	Introduction to biological databases	Nelzo Ereful
	10:00	10:15	0:15	Break
	10:15	10:45	0:30	Continuation…
	10:45	11:15	0:30	Sequence characterization – Sequence formats, ORFFinding, Upstream/ promoter region, and gene prediction	Nelzo Ereful
	11:15	11:30	0:15	Sample exercise	Nelzo Ereful

	1:30	2:45	1:15	Local resources	Mau/Jun
				Introduction to Unix
				Introduction to HPC/ Overview of the OS options for Bioinformatics
	2:45	3:00	0:15	Break
	3:00	4:00	1:00	Running programs in Unix (BLAST, BLAT, WU-BLAST, Repeat Masker, etc.)	Mau/Jun

25-Mar	8:30	9:45	1:15	Sequence analysis (Pairwise and MSA)	Jemi Aquino
	9:45	10:00	0:15	Break
	10:00	11:00	1:00	Continuation
	11:00	11:45	0:45	Sequence characterization 2	Nelzo Ereful

	1:30	3:00	1:30	Protein sequence analysis	Samart Wanchana
	3:00	3:15	0:15	Break
	3:15	4:30	1:15	Introduction to Phylogenetic analysis	Ken McNally

26-Mar	8:30	9:45	1:15	Introduction to phylogenomic analysis	Samart Wanchana
	9:45	10:00	0:15	Break
	10:00	11:30	1:30	GreenPhylDB, a phylogenomic database for plant comparative genomics	Matthieu Conte

	1:30	2:45	1:30	Genome browsers (Gbrowse)	Jun
	2:45	3:00	0:15	Break
	3:00	3:30	0:30	Cont of Genome browsers	Jun
Part 2. Genetic analysis
	3:30	4:30	1:00	Gene tagging of agronomic traits with intro to Qgene	Michael Thomson

27-Mar	8:30	9:45	1:15	Introduction to Primer Design using Primer3	Jeff D
	9:45	10:00	0:15	Break
	10:00	11:30	1:30	Designing primers specific for SNP detection, gene family amplification (degenerate) and primers for cloning a gene	Ken McNally

	1:30	2:30	1:00	Computational approaches on QTL analysis	Arvind Kumar
	2:30	3:00	0:30	MapManager	Suzette Madamba
	3:00	3:15	0:15	Break
	3:15	4:30	1:15	Cont (MapManager)

28-Mar
	8:30	9:30	1:00	Intro to R	Thomas Metz
	9:30	10:00	0:30	Quantitative analysis using R	Beng Bartolome
	10:00	10:15	0:15	Break
	10:15	10:45	0:30	Cont (Quantitative analysis using R)	Beng Bartolome
	10:45	11:45	1:00	QTL Cartographer	Jerome Bernier

	1:30	2:45	1:15	Candidate gene analysis	Jun Ulat
	3:00	3:15	0:15	Break
	3:15	3:45	0:45	Closing Ceremonies/ Awarding of Certificates	Richard/ Achu

Last Updated ( Monday, 24 November 2008 13:19 )