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  Events - February 2014


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

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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.


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:

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
Red Clover Genome to Help Restore Sustainable Farming
The Genome Analysis Centre (TGAC) in collaboration with IBERS, has sequenced and assembled the DNA of red clover to help breeders improve the beneficial traits of this important forage crop.
Turning up the Tap on Microbes Leads to Better Protein Patenting
Mining millions of proteins could become faster and easier with a new technique that may also transform the enzyme-catalyst industry, according to University of California, Davis, researchers.
Tardigrade's Are DNA Master Thieves
Tardigrades, nearly microscopic animals that can survive the harshest of environments, including outer space, hold the record for the animal that has the most foreign DNA.
GMO Food Animals Should be Judged by Product, Not Process
In a world with a burgeoning demand for meat, milk and eggs, regulatory policies around the use of biotechnologies in agriculture need to be based on the safety and attributes of those foods rather than on the methods used to produce them, says a UC Davis animal scientist.
Cancer-Fighting Tomato Component Traced
The metabolic pathway associated with lycopene, the bioactive red pigment found in tomatoes, has been traced by researchers at the University of Illinois.
TGAC Announces Milestone in Wheat Research
A more complete and accurate wheat genome assembly is being made available to researchers, by The Genome Analysis Centre (TGAC) on 12 November 2015.
Shedding Light on the Origin of the Date Palm
Researchers also find ‘genetic mutation’ that is responsible for dates’ color.
New Way to Find DNA Damage
University of Utah chemists devised a new way to detect chemical damage to DNA that sometimes leads to genetic mutations responsible for many diseases, including various cancers and neurological disorders.
Speeding Up Potato Breeding
A joint project is investigating the potential of drones for speeding up the development of new potato varieties.
Gene Editing Could Enable Pig-To-Human Organ Transplant
The largest number of simultaneous gene edits ever accomplished in the genome could help bridge the gap between organ transplant scarcity and the countless patients who need them.
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