[Bio-Linux] Fwd: daphnia-genomics Environmental Genomics Course: Birmingham March 23-27

[Tim Booth]

Dear All,

Apologies if you receive this multiple times, but I hope this will be of
interest to some people on this list.  For any queries please respond
directly to John rather than to me or to the mailing list.

Cheers,

TIM

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From: John Colbourne <j.k.colbourne at bham.ac.uk>
> 
Subject: daphnia-genomics Environmental Genomics Course: Birmingham
March 23-27
> 
Date: 8 February 2015 06:49:32 GMT
> 
To: "daphnia-genomics at lists.bham.ac.uk"
<daphnia-genomics at lists.bham.ac.uk>
> 
> 
NERC-MDIBL Environmental Genomics Course, 2015
> 
Online Registration Site: www.birmingham.ac.uk/EnGen
> 
Dates: March 23-27, 2015
> 
Location: 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 to attend will be announced March 2, 2015.
> 
Course Leaders: John Colbourne, Joseph Shaw, Mark Viant, Xin Zhou
> 
Research Organizations Involved: University of Birmingham (UK), BGI
China National GeneBank (Shenzhen, China), Mount Desert Island
Biological Laboratory (USA)
> 
> 
Description
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 the 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, 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 intensive training in seminar and laboratory
formats, especially around expression profiling by RNA-Seq. Topics
covered include bioinformatics using sequence analysis workflows and R
statistical analysis tools, plus experimental design for environmental
genomics research. For the laboratory, participants will be introduced
to automated sample preparation as well as preparing their own
RNA-sequencing libraries.
The course provides a significant introduction and some 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.
> 
Course Content
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 their growing use as model
systems 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.
> 
> 
School of Biosciences, The University of Birmingham
Birmingham, B15 2TT, United Kingdom
> 
Mount Desert Island Biological Laboratory
Old Bar Harbor Rd., Salisbury Cove, ME 04672