NERC-MDIBL Environmental Genomics 2015

A NERC funded short course to guide genomics research applied to environmental sciences


Date: 22-27 March 2015

Location: The University of Birmingham, UK

Number of places: Between 25 and 50

Open to: Participation is open to everyone.
Priority is given to NERC-funded PhD students and early-career postdocs. Confirmation for attendance will be announced March 2, 2015.

Cost: FREE

Course leaders: John Colbourne, Joseph Shaw, Mark Viant, Xin Zhou

Research Organisations involved: University of Birmingham (UK), BGI China National GeneBank (Shenzhen, China), Mount Desert Island Biological Laboratory (USA)

This training opportunity in Environmental Genomics is the second European/UK instalment of a successful annual course originating from Mount Desert Island Biological Laboratory. It trains PhD students and early career postdoctoral scientists to investigate how gene function is influenced by environmental conditions while accounting for variation that exists within and among natural populations. The course is built on the paradigm that this multidisciplinary research field encompassing ecology, evolution, toxicology, biostatistics and informatics will most effectively grow by training early career environmental scientists to properly design comprehensive, large-scale, Next Generation Sequencing (NGS) experiments enabled by drastically increased sample-throughput and lower costs. Most importantly, the challenges of manipulating and analysing population-level genomics (big) data must be addressed.

The course provides a significant introduction and much hands-on training experience so that participants can initiate their own environmental genomics study and network with others in the field to launch Environmental Scientist careers in academia and industry.

Participants are taught using open-source analysis tools and existing OMICS data:

Course Presentations

  • Library construction methods and QC
  • Introduction to automation systems
  • Introduction to the sequence data workflow
  • Software solutions for the sequence and metabolomics data workflows & their applications for environmental research
  • Review of sequencing technology, its strengths and weaknesses
  • RNA-Seq alignment to individualize transcriptomes
  • Statistical considerations for analysing genome-scale data

Bioinformatics Training

  • Introduction to R
  • Visualization of sequence and metabolomics data for quality assurance
  • Visualization of complex data
  • Navigating the command line
  • Data analysis workshop using R to analyse Tuxedo output
  • Gene set enrichment analysis
  • Exploring genome sequence variation
  • Help desk to explore participants research questions

Synthesis Sessions

  • Models in search of ecology vs ecology in search of models
  • What can I extract from the sequence data for my investigations
  • Integrating omics data
  • How do I obtain funding for my Environmental Genomics project

Evening Lecture Series

There will be four evening lectures designed to highlight environmental omic applications that draw on the expertise of our guest faculty.

Daphnia is used for training because of its growing use as a model system for environmental genomics and for improving environmental health protection, yet the skills learned during the course will be applicable to all study systems with mature genomics resources.

Open to: Participation is open to everyone.
Priority is given to NERC-funded PhD students and early-career postdocs.
Please note those participants from NERC funded positions are eligible for travel and accommodation bursaries (maximum award £350). Participants will be informed after the closing date if they have been awarded this bursary and will be reimbursed after the course.