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  Events - February 2014


Agricultural-Omics

17 Feb 2014 - 21 Feb 2014 - EMBL-EBI,Hinxton, Cambridge, UK



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Overview

This course will provide an overview of data resources, tools and analysis pipelines for 'omics datasets within the agricultural sciences. It will be delivered using a mixture of lectures, practical computer sessions and discussions based on agricultural case studies and public domain data. Additionally there will be opportunity to review the key opportunities and challenges within this field.

Audience

This course is aimed at researchers working within the agricultural sciences who have some previous experience of bioinformatics. Some of the tools to be introduced on the course will require the use of Unix commands and the R statistics package.  We strongly recommend that you familiarise yourself with these. Free tutorials are available from:

http://www.ee.surrey.ac.uk/Teaching/Unix/

http://www.r-tutor.com/r-introduction

Syllabus, Tools and Resources

During this course you will learn about…

  • Genomics : Velvet, Soap, BWA, SAMtools, BCFtools, VCFtools, Ensembl Genomes, PhyBase, PlantsDB, Plaza
  • Transcriptomics: Fastx, Allpaths-LG, Velvet, Bowtie, R, Bioconductor
  • Metagenomics: The Metagenomics Portal, RDP classifier, MEGAN, CARMA
  • Proteomics: PRIDE, OMSSA, PX submission tool
  • Metabolomics: MetaboLights

Learning Objectives

After this course you should be able to…

  • Discuss a variety of workflow approaches to omics technologies
  • Browse and access a range of agricultural omics data available in public repositories
  • Use tools to aid with the analysis of agricultural omics data
  • Appreciate some advantages and limitations of some omics methods and analyses
  • Assess the significance of specific analyses in the context of wider omics workflow


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