STFC/NERC Bioinformatics & Environmental 'Omics Network

Lead Research Organisation: University of St Andrews
Department Name: Biology

Abstract

The widespread impact of the genomics revolution has reached into every aspect of biology. As a result of new technologies for molecular investigation, the composition of the genome and the various organisational layers that exist between the genome and organismic response to the environment are now better described. These organisational layers, known as 'omics (e.g., genomics, transcriptomics, proteomics, metabolomics, etc), are now accessible for investigation in their entirety. This scope of investigation has not only opened unparalleled opportunities for a more complete understanding of how organisms or communities interact with the environment but also created an informatics challenge unprecedented in environmental biology. With technical advances in instrumentation, the sheer volume of data generated by 'omics investigation is orders of magnitude higher that has been the norm in environmental biology, creating new challenges for data storage, data analysis, and indeed optimisation of data structures generally. At the same time, important new opportunities for innovation in addressing critical problems can arise from the effective blending of bioinformatics and environmental 'omics.
To leverage the full potential of these developments to deliver its strategy, 'Next Generation Science for Planet Earth', the NERC has established a virtual Environmental 'Omics Synthesis Centre to facilitate the coalescence and emergence of novel scientific approaches to environmental 'omics. EOS is tasked with enabling the emergence of novel scientific synthesis within the NERC community that might benefit from environmental 'omics as well as contribute to its development. STFC has a well-established infrastructure for addressing complex data on the scale that is likely to be generated through future investigations in environmental 'omics. Therefore there is substantial potential for synergism between the emerging need for enhanced scale of bioinformatics approaches to environmental 'omics as indentified by the NERC and the existing facilities base in the STFC, to the benefit of both.
The present STFC Global Networks call provides a timely opportunity for the development of strong connections between STFC and NERC interests in environmental sciences. Indeed, the bioinformatics challenge presented by environmental 'omics was specifically highlighted at the second STFC Environment Futures Workshop (http://www.stfc.ac.uk/resources/pdf/FuturesEnv2Report.pdf). The NERC EOS is just now being established, so that network building with STFC scientists at this stage will ensure that the extensive resource base of the STFC will be an integral part of bioinformatics and environmental 'omics as collaboration between these fields is developed over the next five years.
We plan to conduct two workshops per year, addressing in each case targeted research areas where there is anticipated potential for synergy between STFC and NERC. At the outset, indicative workshop themes for exploring joint STFC and NERC development of the potential of bioinformatics and environmental 'omics include:
a) Novel data structures, novel algorithms and ontologies. The bioinformatics challenges raised by environmental 'omics are widely recognised, but both the detailed nature of these challenges and effective approaches for addressing them require further development.
b) Linking environmental 'omics to other large scale data structures and models, for example those involving climate and other major environmental cycles.
c) The interplay between environmental biological processes and human health, for example environmental toxicology and environmental pollution as a source of health-threatening antimicrobial resistance.
d) Modelling complex biological interactions underlying basic ecosystem services and their resilience to environmental change.

Planned Impact

As the STFC/NERC Bioinformatics & Environmental 'Omics Network tackles significant environmental issues by identifying ways to harness the combined power of bioinformatics and environmental 'omics, beneficiaries will include industry and government - and, indeed, in the broadest sense, the environment. Because the Network will from its very start bring together researchers with individuals from the private sector and government to explore future possibilities for solutions to pressing themes, the UK will have a head start in development of related innovation and understanding. As just one example, a workshop on the interplay between environmental biological processes and human health will explore the potential for collaboration on issues such as health-threatening antimicrobial resistance that are of interest to pharmaceutical and other companies, as well as to agencies committed to environmental regulation or public health. Each of the Network workshops is expected to spark follow-on research collaborations that will lead to novel findings relevant to such themes as: development of novel data structures; novel algorithms and ontologies; the interplay between environmental biological processes and human health; climate and other major environmental cycles; complex biological interactions underlying basic ecosystem services and their resilience to environmental change. Innovation within each of these themes can lead to both academic and non-academic impacts.

Publications

10 25 50
 
Description We completed six networking workshops addressing: 'Workflow approaches to investigation of biological complexity', STFC RAL, 15-16 October 2013; 'Omics Miniaturisation - Taking 'omics into the field: from handheld devices to autonomous monitoring stations', CEH, Wallingford, 8-9 May 2014; 'Developing Cloud computing to support data intensive biology', University of Warwick, 4-5 June 2015; 'Remote sensing technology to support sustainability and conservation', Royal Botanic Garden Edinburgh, 18-19 February 2016; 'Developing Integrated Multi-level models of the Environment', University of Liverpool, 8-9 March 2016; 'Archaeogenomics', University of Warwick, 28-29 April 2016.
Exploitation Route The miniaturisation workshop was used as a basis for an engineering grant proposal to develop instrumentation. The cloud-based computing workshop is aligned with NERC Big Data capital funding to develop cloud-based computational methods for omics bioinformatics and the workshop will lead up to more broad demonstration of this capability. The remote sensing workshop aligned with multiple successful follow-on proposals to STFC and the British Council.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software)

 
Description Our findings have led to three successful funding applications: STFC Global Challenges grant (phylogenetic computation Barker, Winn, Meagher), remote sensing (two STFC Global Futures grants), a British Council Newton Researcher Links to support a multinational workshop in Brazil on remote sensing, and a STFC GCRF project on remote sensing in dry tropical forests that is currently in progress. There has been considerable recent follow-on activity in the area of remote sensing and biodiversity. This is reported in detail in our submission for ST/P003281/1.
First Year Of Impact 2015
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Culture, Heritage, Museums and Collections
Impact Types Cultural,Societal,Economic

 
Description British Council Research Links award - "Remote Sensing for Biodiversity and Ecosystem Services Inventory", co-investigator Dr Jean Ometto, INPE, Brazil
Amount £48,500 (GBP)
Funding ID 2017-RLWK9-359477089 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2018 
End 08/2018
 
Description Global Challenges Programme
Amount £43,341 (GBP)
Organisation Science and Technologies Facilities Council (STFC) 
Sector Public
Country United Kingdom
Start 06/2014 
End 06/2015
 
Description Global Futures Programme
Amount £49,299 (GBP)
Organisation Science and Technologies Facilities Council (STFC) 
Sector Public
Country United Kingdom
Start 12/2015 
End 11/2016
 
Description Global Futures Programme
Amount £61,580 (GBP)
Funding ID ST/P003281/1 and ST/P003265/1, joint submission 
Organisation Science and Technologies Facilities Council (STFC) 
Sector Public
Country United Kingdom
Start 03/2017 
End 12/2017
 
Description NERC Field Spectroscropy
Amount £70,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2017 
End 01/2018
 
Title TreeLeast - workflow software for conservation assessment 
Description This software was developed from a follow-on award to Dr Malin Rivers (Botanic Gardens Conservation International) and Dr Alex Hardisty (University of Cardiff) , "Workflow development for conservation assessments for the Global Tree Assessment". 
Type Of Technology Software 
Year Produced 2017 
Impact This software is facilitating a comprehensive global assessment of conservation IUCN status for on the order of 60,000 tree species. 
 
Description 13 November 2017 presentation to CNPq, Brasilia, Brazil 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Supporters
Results and Impact Presentation on "STFC/NERC Bioinformatics & Environmental 'Omics Synthesis: Adventures in meta-science - from cloud computing to remote sensing" to programme officers and others at CNPq. This was an engagement meeting to assist CNPq in the development of a future funding call.
Year(s) Of Engagement Activity 2017
 
Description 7-9 March 2018, presentation to CNPq wokshop on "CENTRO DE SÍNTESE EM BIODIVERSIDADE E SERVIÇOS ECOSSISTÊMICOS" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Presentation on "Perspectives on communication strategy and stakeholder dialogue". This talk included findings from fieldwork that took place in October 2017. The talk was designed to inform development of an upcoming call for proposals from CNPq for a programme with potential for collaborative UK Newton Fund collaboration.
Year(s) Of Engagement Activity 2018
 
Description Archaeogenomics, University of Warwick, 28-29 April 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Archaeogenomics in Environmental Science was an STFC/NERC-supported workshop at the University of Warwick in April, 2016, bringing together specialists in ancient DNA based genomics and related fields to develop interdisciplinary goals and collaborative efforts. Thirteen institutions from the UK and abroad were represented by 29 participants spanning environmental 'omics and science-based archaeology

A key workshop goal was to discuss of methodological and subject areas for the development of overarching Highlight Topics ideas based on long-term archaeological and biomolecular 'omic data. Themes from the meetings emerged as i) resilience of biodiversity to human impact, ii) competing interests in food species evolution in a changing environment, iii) leveraging databases and multi-informatic resources, and iv) coping with catastrophic change. The overarching emergent key theme was the utility of the long-term biomolecular record to understand resilience and adaptation to a changing environment.

In summary, archaeogenomics is well-positioned to contextualize modern environmental and social challenges in light of long-term patterns in the biomolecular record.
Year(s) Of Engagement Activity 2016
 
Description Developing Cloud computing to support data intensive biology, University of Warwick, 4-5 June 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Cloud computing holds great promise for the future of Big Data analysis. This is particularly true for data intensive areas such as environmental omics, where large datasets are likely to reside in centralised storage facilities, such as Jasmin, EBI, or ELIXIR. Cloud-based computing allows users to analyse such data on HPC systems by creating 'instance-based' computer images that can be ported directly to the computer system where such data resides. Thus, users can access big data and analyse it using the full power of remote HPC facilities while at the same time using a familiar interface with customised software. Thus, cloud-based computing has the potential to combine accessible and customised interfaces with the full computational power and storage capacity of state-of-the-art HPC systems.

This workshop will explore the current state of cloud-based computing facility and what steps are needed to bring the full power of cloud-based computing to the wider scientific community, including environmental omics.
Year(s) Of Engagement Activity 2015
URL http://environmentalomics.org/cloud-computing/
 
Description Developing integrated multi-level models of the environment, Univerrsity of Liverpool, 8-9 March 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact This workshop was sponsored by our project and was organised by a member of our network, Prof Francisco Falciani and a NERC EOS Fellow, Dr Phllip Antczak.
Year(s) Of Engagement Activity 2016
 
Description Omics Miniaturisation - Taking 'omics into the field: from handheld devices to autonomous monitoring stations, CEH, Wallingford, 8-9 May 2014 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The objective of this workshop is to identify the key environmental questions that could be leveraged given field based 'omics devices, identify those current developments that may underpin such devices and identify the major engineering challenges that need to be overcome to ensure these devices are realised. Our intent is to generate potential road-maps that may deliver this technology into the hands of appropriate research community.
Year(s) Of Engagement Activity 2014
URL http://environmentalomics.org/omics-miniaturisation/
 
Description Remote sensing technology to support sustainability and conservation, Royal Botanic Garden Edinburgh, 18-19 February 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Remote sensing technologies have advanced to a potential position of prominence in investigation of biological properties of ecosystems at a large, even global, scale. In order to promote the integration of the technological potential of remote sensing, this workshop is being convened to explore current and potential applications of remote sensing to environment biology, with an emphasis on sustainability and conservation biology. Our intent is to facilitate the matching of existing technologies to large-scale biological investigation and also to highlight scientific and technical challenges for future innovation.
Year(s) Of Engagement Activity 2016
URL http://environmentalomics.org.gridhosted.co.uk/stfcnerc-futures-network-home/
 
Description Using remote sensing in the study of Amazonian Ecosystems, 2nd TPI Network Workshop, Porto Velho, RO, Brazil, 23-24 February 2016 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This workshop was co-sponsored by the STFC/NERC Bioinformatics and Environmental 'Omics. It was a satellite session following the RBGE workshop the preceding week and was intended to serve as knowledge exchange with a wider network. The workshop drew together research interests ranging from biology to geography to archaeology. The workshop included a field component that included media coverage in the form of a television documentary team.
Year(s) Of Engagement Activity 2016
URL http://tpinet.org/activities/2nd-tpi-network-workshop/
 
Description Workflow approaches to investigation of biological complexity, STFC RAL, 15-16 October 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Many scientific challenges in environmental 'omics entail diverse data inputs from multiple sources as well as across multiple levels of biological organisation. Thus, research in environmental 'omics requires novel approaches that are inherently equipped to deal with data diversity and complexity.
The scientific workflow approach provides the potential to address the biological complexity inherent to environmental omics. A scientific workflow is a series of linked components, such as data computation, manipulation and analysis, used in scientific problem-solving. Scientific workflows help to visualise the flow of data through (potentially) complex computations in a user-friendly way.
Biological systems can manifest complexity in many ways. For example, integration of genomic information across multiple species in a particular ecosystem, now feasible due to advances in genome sequencing technology, can be coupled with information about functional domains within genomes -- and their context dependent properties within specific organisms -- to match genomic information to larger scale processes of adaptation and ecosystem function. One of the challenges of integration across multiple levels is that information available at each level is dynamic and also subject to changing biological interpretation, such as changing understanding of genome function or changing taxonomic classification that refines knowledge of the evolutionary history of the system. Viewing this complexity through a workflow approach allows not only identification and interpretation of higher-order emergent properties of complex systems, but also the ability to integrate models that take into account changing information..
In this first workshop of the STFC/NERC Bioinformatics & Environmental 'Omics Network, we will be exploring the nature of workflow approaches and how they can be applied to specific scientific challenges in the realm of 'omics. Future workshops will address more targeted scientific themes, building on methodological approaches considered in this inaugural workshop.
Year(s) Of Engagement Activity 2013
URL http://environmentalomics.org/workflows/