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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


Further information
Scientific News
New Tech Enables Epigenomic Analysis with a Mere 100 Cells
A new technology that will dramatically enhance investigations of epigenomes, the machinery that turns on and off genes and a very prominent field of study in diseases such as stem cell differentiation, inflammation and cancer has been developed by researchers at Virginia Tech.
TOPLESS Plants Provide Clues to Human Molecular Interactions
Scientists at Van Andel Research Institute have revealed an important molecular mechanism in plants that has significant similarities to certain signaling mechanisms in humans, which are closely linked to early embryonic development and to diseases such as cancer.
Toxin from Salmonid Fish has Potential to Treat Cancer
Researchers from the University of Freiburg decode molecular mechanism of fish pathogen.
Study Finds Non-Genetic Cancer Mechanism
Cancer can be caused solely by protein imbalances within cells, a study of ovarian cancer has found.
Long-sought Discovery Fills in Missing Details of Cell 'Switchboard'
A biomedical breakthrough reveals never-before-seen details of the human body’s cellular switchboard that regulates sensory and hormonal responses.
Rice Disease-Resistance Discovery Closes the Loop for Scientific Integrity
Researchers reveal how disease resistant rice detects and responds to bacterial infections.
The Mystery of the Instant Noodle Chromosomes
Researchers from the Lomonosov Moscow State University evaluated the benefits of placing the DNA on the principle of spaghetti.
New Mussel-Inspired Surgical Protein Glue
Korean scientists have developed a light-activated, mussel protein-based bioadhesive that works on the same principles as mussels attaching to underwater surfaces and insects maintaining structural balance and flexibility.
Vital Protein in Healthy Fertilization Process Identified
Researchers at the National Institutes of Health have discovered a protein that plays a vital role in healthy egg-sperm union in mice.
Teeth Reveal Lifetime Exposures to Metals, Toxins
Researchers have identified dental biomarkers to reveal links between early iron exposure and late life brain diseases.
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