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Overview PDF Print E-mail
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 PDF Print E-mail
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-088:309:000:30Registration

Jemi/ Jeff

9:009:300:30Opening Remarks/ Introduction to Bioinformatics

Richard Bruskiewich

9:3010:000:30Introduction to biological databases

Nelzo Ereful

10:0010:150:15Break 
10:1510:450:30Continuation… 
10:4511:150:30Sequence characterization – Sequence formats, ORFFinding, Upstream/ promoter region, and gene prediction

Nelzo Ereful

11:1511:300:15Sample exercise

Nelzo Ereful

     
1:302:451:15Local resources

Mau/Jun

   Introduction to Unix
   Introduction to HPC/ Overview of the OS options for Bioinformatics
2:453:000:15Break 
3:004:001:00Running programs in Unix (BLAST, BLAT, WU-BLAST, Repeat Masker, etc.)

Mau/Jun

      
25-Mar8:309:451:15Sequence analysis (Pairwise and MSA)

Jemi Aquino

9:4510:000:15Break 
10:0011:001:00Continuation 
11:0011:450:45Sequence characterization 2

Nelzo Ereful

     
1:303:001:30Protein sequence analysis

Samart Wanchana

3:003:150:15Break 
3:154:301:15Introduction to Phylogenetic analysis

Ken McNally

      
26-Mar8:309:451:15Introduction to phylogenomic analysis

Samart Wanchana

9:4510:000:15Break  
10:0011:301:30GreenPhylDB, a phylogenomic database for plant comparative genomics

Matthieu Conte

     
1:302:451:30Genome browsers (Gbrowse)

Jun

2:453:000:15Break 
3:003:300:30Cont of Genome browsers

Jun

 

Part 2. Genetic analysis

 
  3:304:301:00Gene tagging of agronomic traits with intro to Qgene

Michael Thomson

 
 
 27-Mar8:309:451:15Introduction to Primer Design using Primer3

Jeff D

 
 9:4510:000:15Break  
 10:0011:301:30Designing primers specific for SNP detection, gene family amplification (degenerate) and primers for cloning a gene

Ken McNally

 
       
 1:302:301:00Computational approaches on QTL analysis

Arvind Kumar

 
 2:303:000:30MapManager

Suzette Madamba

 
 3:003:150:15Break  
 3:154:301:15Cont (MapManager)  
        
 28-Mar      
 8:309:301:00Intro to R

Thomas Metz

 
 9:3010:000:30Quantitative analysis using R

Beng Bartolome

 
 10:0010:150:15Break  
 10:1510:450:30Cont (Quantitative analysis using R)

Beng Bartolome

 
 10:4511:451:00QTL Cartographer

Jerome Bernier

 
       
 1:302:451:15Candidate gene analysis

Jun Ulat

 
 3:003:150:15Break  
 3:153:450:45

Closing Ceremonies/ Awarding of Certificates

Richard/ Achu 

 
    

 

 

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