eGenomics: Genomes and the environment

5-6 September 2005


General information

 

This workshop is designed to investigate the emerging scientific interface between genomic and environmental research. It will examine if and how projects and facilities funded by the NERC might take a lead in enabling researchers to ask new questions that depend upon the availability and efficient integration of genomic and environmental data. This workshop will aim to bring together several relevant parties within NERC for a session of talks and open discussion. Participants would ideally include:

There are many new initiatives represented by this list of potential participants. This community needs to work together closely to promote data sharing and interdisciplinary activities if we hope to enable NERC and NERC allied researchers to harness the full potential of the data and facilities we have. This workshop will provide a forum for many of these people to meet face-to-face for the first time thus facilitating initial interactions and encouraging future communication and co-operation. The proposed agenda includes a series of ‘lightening’ talks where a number of individuals will give a brief overview of the activities and developments within their area. This will familiarize the group with the wide range of activities ongoing in NERC. There will also be a few longer talks concentrating on current research activities. These talks will help define in more detail some of the challenges and opportunities ahead. There will also be extended periods dedicated to open discussion. This time would be used for us to further articulate our needs as a community, identify bottlenecks to scientific advancement in this area, debate ways to overcome them, and establish how we might work together better. The final session of the workshop will be dedicated to developing a roadmap that will help us to achieve both our practical goals of further harmonization within NERC (especially within the area of meta-data capture) and our longer-term goals of developing appropriate and user-friendly solutions in this rapidly growing area of science.

This workshop is being organised by Dawn Fields of the Centre for Ecology and Hydrology, Oxford, and Bela Tiwari of the Environmental Genomics Data Centre.

Aim of the workshop

The aims of this workshop are to:

  1. define more clearly the science questions that are driving the need for access to genomic and environmental data in NERC and in the wider community;
  2. develop a list questions that could be addressed if we had better access to interdisciplinary data;
  3. discuss how we should best store such interdisciplinary data in the future to maximize potential for use and ensure accessibility;
  4. review current ways that NERC research data is made available to the wider community and further explore the scientific possibilities associated with this data;
  5. determine how projects like the PG&P Marine Metagenomics Consortium can seamlessly access and exploit genomic and oceanographic data;
  6. identify new linkages and potential partnerships between groups that might lead to future grant applications / projects / publications
  7. develop a better awareness of how e-science technologies and concepts might provide solutions for data exchange, storage, accessibility, dissemination, and analysis;
  8. develop a specific understanding of how the NERC Data GRID could help us achieve the above goals;
  9. explore the idea of a “Virtual NERC community” (AccessGrid nodes etc).

Programme

Monday 5th September

10:00

Registration and coffee

10:30

Welcome, background and goals of workshop [ppt] (Dawn Field and Bela Tiwari, Oxford Centre for Ecology and Hydrology)

Session I: Finding and characterizing genes and genomes in the environment: Metagenomics
Session Chair: Andy Johnston

10:45

Plenary Speaker: Genomes and metagenome of saturated brines [ppt] (Francisco Rodriguez-Valera, Universidad Miguel Hernández)

11:30

Marine microbial metagenomics - the need to integrate environmental and genomic databases [ppt] (Ian Joint, Plymouth Marine Laboratory)

10:50

Grid-based, high throughput, metabolic reconstruction of metagenomic datasets (Michael Barton, University of Newcastle)

12:10

So, what’s so wrong with Petri Dishes then? (Andy Johnston, University of East Anglia)

12.30

Wrap up Questions

12:40

Putting a Green Thumb on the Genomics Hand – Canadian Research Efforts in Environmental Genomics (Terry McIntyre, Environment Canada)

13:00

Lunch

Session II Molecular Basis of Phenotypes of Environmental and Ecological Relevance
Session Chair: Tamas Dalmay

14:00

ESTs and ecogenomics: addressing the neglected taxon sequence deficit (Mark Blaxter, University of Edinburgh)

14:20

What can metabolomics contribute to environmental research? (Mark Viant, University of Birmingham)

14:40

Role of microRNAs in phenotypic plasticity to environmental changes (Tamas Dalmay, University of East Anglia)

15:00

Ecogenomics of Marine Synechococcus (Martin Ostrowski, University of Warwick)

15:20

Transcriptional profiling and SNP analysis of the Pacific oyster, Crassostrea gigas: Resistance and susceptibility to summer mortality. (Anna Goostray, Plymouth Marine Laboratory)

15:40

Coffee

Session III: Data Standards
Session Chair: Jason Snape

16:15

"Env": a new standard for environmental genomics (Joe Wood, Environmental Genomics Data)

16:30

Towards a new genomic standard that captures ecological and environmental information (Dawn Field, Oxford Centre for Ecology and Hydrology)

16:45

The scientific and regulatory drivers for ’omic’ data standards: What wider community benefits can be derived? (Jason Snape, Astrazeneca)

17:00

Fitting discipline-based metadata standards into the wider world (Bryan Lawrence, British Atmospheric Data Centre)

17:15

close



Tuesday 6th September

Session III: Data Management
Session Chair: Bela Tiwari

9:00

The Ecological Data Grid project (Neil Bennett, CCLRC Daresbury Laboratory)

9:20

EnvBase: A knowledgebase for environmental genomics (Tim Booth, The Environmental Genomics Data Centre)

9:40

Genomic data at the British Oceanographic Data Centre (Gwen Moncoiffe, British Oceanographic Data Centre)

10:00

Soil Biodiversity Programme: Data Management (Lynne Irvine, Lancaster Centre for Ecology and Hydrology)

10:20

Wrap up Questions and open discussion on "Data Capture, Exchange, and Analysis: Harmonization of Efforts"

11:00

Coffee

Session IV: E-Science and GRID Solutions
Session Chair: Anil Wipat

11:30

AccessGRID node technology (Nic Bertrand, Oxford Centre for Ecology and Hydrology)

11:50

NIEeS and eScience (Stuart Ballard, NIEeS)

12:10

Open Discussion on "Issues and challenges"

13:00

Lunch

14:00

Open Discussion "A Roadmap for the future"

15:00

formal close of workshop and coffee

Location

The workshop will take place in the Centre for Mathematical Sciences, Cambridge. Details of the location, including travel plans, can be obtained here.

Overnight accommodation will be provided in Churchill College Cambridge (accommodation and breakfast). The workshop dinner on the evening of 5th September will also be held in Churchill College.

Centre for Mathematical Sciences, main entrance.

Churchill College from the junction with the main road. The entrance is on the right hand side of this photograph.

Registration

There is no registration charge for this workshop. Accommodation in Churchill College and meals (including the conference dinner) for UK academic participants will be provided with no charge. Registration is essential and must be done using our on-line form. This should be done using our on-line form.

The NIEeS will refund reasonable travel expenses.

In the event of any difficulty in booking, including not receiving an email confirmation within 24 hours, please email the NIEeS office.

Contact and further information

For information about registration, and all other types of queries, please contact the NIEeS office in the first instance.

Last update:Thu, Apr 21, 2005