Mathematics & Informatics for Environmental Omic Data Synthesis (Omics)

DNA spiral

The Mathematics & Informatics for Environmental Omic Data Synthesis (Omics) programme has a budget of £4 million. The programme directly relates to the delivery of the NERC Technologies science theme.

The programme aims to develop the fundamental knowledge needed to integrate large volumes of genomic, transcriptomic, proteomic and metabolomic data into wider environmental analyses to address new research questions. Another major aim of the programme is to promote the development of omic informatics as a professional niche within environmental research.

Through the programme the following activities are supported:

Second International Environmental Omics Synthesis conference

Closing date: 28 Jul
2014

9 Jul 2014

Registration is now open for the second International Environmental Omics Synthesis (iEOS) conference on omics applications, tools and resources focused on the environmental sciences.


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Experimental capability to probe the genetic composition of organisms and communities, and the expression of their functions through the proteins and metabolites they produce, has developed exponentially. The cost of sequencing technologies has fallen 10,000-fold over the past decade, and it is now possible to sequence a human in a week, compared to the first which took over a decade.

Similarly there have been major enhancements in proteomics and metabolomics delivered by improved separation technologies and mass spectrometer design. This explosion in capability has been driven by the bioscience and biomedical communities, but it creates unprecedented opportunities and changes fundamentally the way in which omics data may be obtained from, and related to, the environment.

The Omics programme will develop the fundamental knowledge needed to integrate large volumes of genomic, transcriptomic, proteomic and metabolomic data into wider environmental analyses to address new research questions.

A number of broad technological challenges now hinder the full potential of omics technologies in environmental science. For example:

  • How to make linkages between datasets and mesh together different types of omic information, as well as measurements on the whole organism and/or community level, given that in each case data is generated using different approaches.

  • How to integrate and draw meaningful connections between these omics data on species and communities with environmental conditions including the physical and chemical states of soils, oceans, freshwater and atmosphere.

  • How to manage, analyse and model such large-scale, complex datasets to address specific environmental questions posed. This latter challenge will require improved approaches for comparative, statistical, spatial and/or temporal analyses as well as novel workflow methodologies and solutions for data storage and curation.

Objectives

The Omics programme has a number of high-level strategic objectives which have been identified to meet the above challenges. These are:

  • To address new research questions, including areas of environmental science where the full potential for omics has not yet been harnessed.

  • To promote development of omic informatics as a professional niche within environmental research via discipline-hopping to/from mathematical and computational sciences and through wider community engagement and knowledge transfer from other research communities including biomedical, biological and physical sciences.

  • To realise the opportunities created by omics technologies and to ensure that their full potential is brought to bear on current and future science challenges, through strategic appointments of advanced research positions. These should take account of existing investments by NERC and, where appropriate, operate in partnership with others.

  • To provide underpinning knowledge in support of multiple science areas that cut across NERC's strategic science themes: biodiversity; climate systems; Earth system science; environment, pollution & human health; natural hazards; sustainable use of natural resources and technologies.

Timing

2012 - 2019

Can I apply for a grant?

No, not at this time.

Budget

This programme has a budget of £4 million.

Programme awards

Award details are shown in our online grants browser - Grants on the Web.

NERC Independent Research Fellowships in the priority area of Bioinformatics

View live details of the five Omics fellowships awarded - external link

View live details of the sixth Omics fellowships awarded - external link

The governance of the Omics programme encompasses a number of different bodies which undertake different roles.

Programme Executive Board

The Programme Executive Board (PEB) is responsible for providing the strategic direction for the programme, and is the ultimate decision making authority for the programme. The PEB is currently comprised of:

  • Dr Simon Kerley, NERC (Chair)
  • Dr Kevin Smith, STFC
  • Professor Thomas Meagher, University of St Andrews
  • Dr Jason Snape, AstraZeneca

Other individuals will be appointed to the PEB as the programme progresses.

Directorate

The Omics programme Directorate, based at the Centre for Ecology & Hydrology (CEH) and Cardiff University, is responsible for overseeing the proper management and coordination of the research and knowledge exchange activities undertaken, to ensure an integrated programme with maximum impact.

  • Co-Director: Professor Mark Bailey, CEH
  • Co-Director: Dr Peter Kille, Cardiff University
  • Programme Manager: Dr Tracey Timms-Wilson, CEH
  • Scientific Coordinator: Dr Mesude Bicak, CEH

Advisory & Implementation Group

The Advisory & Implementation Group (AIG) will provide independent strategic advice on the programme research direction to the Directorate and the PEB.

  • Dr Daniel Barker, University of St Andrews
  • Professor Terry Brown, University of Manchester
  • Dr Mario Caccamo, The Genome Analysis Centre (TGAC)
  • Dr Melody Clark, British Antarctic Survey (BAS)
  • Dr Guy Cochrane, EMBL European Bioinformatics Institute
  • Dr Francesco Falciani, University of Liverpool
  • Dr Claire Gachon, Scottish Association for Marine Science (SAMS)
  • Professor Thomas Meagher, University of St Andrews - Chair of AIG
  • Professor Jim Prosser, University of Aberdeen
  • Dr Christopher Quince, University of Glasgow
  • Dr Jason Snape, Astrazeneca
  • Professor Jane Thomas-Oates, The University of York
  • Professor Mark Viant, University of Birmingham
  • Ryan Liu Yuan, BGI Europe

Secretariat

The Secretariat based at NERC Swindon Office will liaise with the programme governing bodies to ensure efficient delivery of programme activities, coordinate grant funding activities and provide administrative support to the PEB.

  • Andy Lloyd, NERC

The NEOMICS[1] team have published a report to NERC that outlines potential options for the development and implementation of a strategy for omics.

Over the last ten years NERC has invested £28 million in omics research via the Environmental Genomics and Post-Genomics & Proteomics programmes. Following the end of this investment it is now appropriate to consider how to take NERC omics forward in the context of new technologies and rapidly increasing data volumes.

The development of this report has involved consultation with NERC and the wider science and stakeholder communities. Throughout the process, the NEOMICS team have worked closely with an advisory Expert Working Group chaired by Professor Thomas R Meagher (University of St Andrews).

The full report is available below but an executive summary with key conclusions and recommendations can be found in the shortened document.

NEOMICS report - summary (PDF, 690KB)

NEOMICS report (PDF, 1.7MB)

Annexes

Annex 1 (PDF, 292KB)

Annex 2 (PDF, 561KB)

Annex 3a (PDF, 191KB)

Annex 3b (PDF, 858KB)

Annex 3c (PDF, 251KB)

Annex 4 (PDF, 27KB)

Annex 5 (PDF, 35KB)

Annex 6 (PDF, 1.4MB)

Annex 7 (PDF, 23KB)

If you have any queries or comments please contact:

Andy Lloyd
Science programme officer
01793 442629


  1. Following an open invitation to tender, funding was awarded to NEOMICS, led by the Centre for Ecology & Hydrology (CEH) and the Cardiff School of Biosciences, to develop a NERC omics strategy.

    Members of the NEOMICS Team:

    • Dr Dawn Field (CEH) - Joint project leader
    • Dr Peter Kille (Cardiff University) - Joint project leader
    • Professor Mark Bailey (CEH)
    • Professor Mark Blaxter (Edinburgh University)
    • Dr Mark Viant (University of Birmingham)
    • Dr Norman Morrison (University of Manchester)
    • Dr Sarah Turner (CEH)

    Omics EWG Terms of Reference (PDF, 27KB)

The following documents and links are related to or give more information about this programme.

EOS: The NERC Environmental 'Omics Synthesis Centre - external link