BioImagingUK BIS Capital Infrastructure Submission: Biological and Medical Imaging

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Revision as of 08:49, 21 June 2014

This is an ongoing collaborative process to submit a response to the BIS consultation from the Light and Electron Microscopy community as decided at the June 11th BioImagingUK Meeting, at LRI London.

uestions:

Q4. What balance should we strike between meeting capital requirements at the individual research project and institution level, relative to the need for large-scale investments at national and international levels? (1000 words maximum)

Our world class research environment is underpinned by funding for the capital requirements of individual research projects and institutions. To complement this, strategic decision making at the national and international level is often required to coordinate investments in the national interest. This consultation seeks views on how to balance these complementary needs.

BioImagingUK (http://bioimaginguk.org) was founded in 2009 to address this exact question. BioImagingUK was formed as a grass roots consortium of the scientific community that depend on and develop imaging technologies for life sciences and medical research. Its goal is to define priorities for delivering imaging infrastructure across all levels of the scientific landscape in the United Kingdom. BioImagingUK aims to:

• drive the development of new imaging technologies
• ensure that there is shared access to and specialized expertise available for these technologies
• build the career models for the critical technical personnel that help to develop and run these technologies
• ensure the development of new training programmes to support and enable these technologies and to develop the next generation of scientists who will use these technologies;
• articulate the funding requirements and priorities to enable all of these activities to be built, delivered and maintained.

Indeed through several years of collaboration and strategic prioritization we have established that there is no single definition for the correct distribution of resources across the various scientific entities in the UK—this will differ depending on the scientific domain and technology. Here’s a concrete, community-derived example:in 2012 with funding from the Wellcome Trust, BBSRC, MRC and EPSRC we held the first national meeting of UK biological and medical imaging scientists who came together for two days to define the priorities for the development and delivery of imaging infrastructure for life sciences and biomedical research. This community (perhaps surprisingly, as the implications for funding and delivery of imaging technology mean significant change from the current status quo) unanimously agreed on the principles of the delivery of infrastructure at the institutional, regional and national level. A detailed analysis of these priorities and conclusions were published in a publically-written meeting report (http://bioimaginguk.org/images/0/04/BioImagingUK_Meeting_Summary_v5.pdf). Groups of imaging scientists representing many different imaging domains and applications,from Electron Microscopy, Light Microscopy, Pre-Clinical/Model System Imaging, Medical Imaging, Data and Software Tools, independently concluded that future investment in BioImaging infrastructure should be targeted at three different levels: National Facilities, Centres of Excellence and Department/Institute level facilities. The definitions, and most critically, the suggested technologies that should be delivered at each of these level was agreed by the community and published (http://www.bioimaginguk.org/images/e/ee/BioImagingUK_Technology_Priorities_v4.pdf). BioImagingUK aims to renew this list in early 2015.

How should the UK balance the commitments to these different entities? As noted in the consultation, there are always competing interests for funding, and never enough resources to fuel all the possible projects and direction developed in the dynamic, thriving environment of UK science. Moreover, there are several national and international projects that should also be supported, as they directly benefit and drive UK science. Of the illustrative scenarios presented in paragraph 40 of the consultation, Scenario 1 and 2 will probably deliver the most impact and best value, as they anticipate substantial investment in aging institutional capital infrastructure that must be renewed and/or replaced, while maintaining substantial contributions for Centres of Excellence, National Facilities and critical international projects that will benefit UK science.

Given inevitable competition for these funds, all research infrastructure must be maintained at an advanced, world-competitive level. In particular, National Facilities and Centres of Excellence are sites providing access to advanced, world-class technology critical for cutting edge scientific research. These sites should be identified, funded and reviewed using the established, proven, peer-review mechanisms that have built UK science. The BioImagingUK Strategy Meeting highlighted the need for periodic review of these resources where utility, impact and strategic importance are evaluated. No Facility or Centre should be a permanent institution and, as technology matures, diffuses or is superseded, Facilities and Centres would either evolve or be wound down in favour of new sites providing the next generation of imaging technology.

Finally, the BioImagingUK community has demonstrated an effective, community-based method for defining technologies that should be delivered via Centres of Excellence and National Facilities, namely the assembly of the community into open meetings, and open drafting of recommendations for funding priorities. There is no question that the established, powerful and productive peer review system used in UK science should be the final arbiter and source of funding, but open community recommendations, based on a broad sampling of the scientific priorities and goals of the community can serve as a powerful tool for applicants, reviewers, and funders. They may reveal consensus or even discord, but the rationale and community priorities will be known to all, and can contribute to strategic decisions.

Authors: Dave & Jason

Q5 How can we maximise collaboration, equipment sharing, and access to industry to ensure we make the most of this investment? (1000 words maximum)

In BioImagingUK this is the question that we have been trying to answer and address since 2009. In mid-2014 we have had significant success in this direction so we address this question not from the view of a wish list but indeed from the view of members of our Network with real experience in running a wide variety of different types of capabilities and facilities that provide access to the academic and industrial research sectors.

The first step towards achieving collaboration and sharing of technology and expertise is the development of an open community where capabilities are discussed, promoted, shared and prioritized. In BioImagingUK we use a series of open public meetings, an open Wiki (http://bioimaginguk.org) and an open mailing list to define our strategies and to discuss these priorities. While a relatively simple kind of activity we have shown that it can be enormously powerful. This approach produced the strategic prioritization described above, and indeed, this consultation response. Most recently this community has matured into the BioImagingUK Network funded by a combination of the BBSRC, MRC, EPSRC, and the Wellcome Trust. Only with this open community-minded approach can such a broad set of scientific domains, requirements and funding agencies be addressed.

We strongly endorse the concept that critical research infrastructures cannot be delivered physically to every research institution in the UK. There are not the resources nor the trained staff and the technical expertise available. Thus the creation of a tiered, distributed infrastructure where facilities and expertise build alongside world-class scientific excellence and made available to the community is the overriding theme that defines our approach.

These concepts exist not only within BioImagingUK but within Euro-BioImaging the European analogue to BioImagingUK. Euro-BioImaging seeks to deliver a pan-European imaging infrastructure that will support the scientific needs and aspirations of all EU scientists. As such there is natural collaboration and coincidence between the goals of BioImagingUK and Euro-BioImaging, and many of the concepts described below derive from Euro-BioImaging.

Two major themes for ensuring maximal collaboration:

1. Access to infrastructure must be fully funded, so all relevant expenses —running and staff costs, maintenance, travel etc. are accounted for. In other words, all costs incurred by the user in preparing for and executing the imaging experiment, and all costs incurred by the resource, including all costs associated with instrumentation, personnel, and lab resources must be covered. In general, the user cannot directly bear the full costs of using a resource, so models tht include funding for the user and the resource must be considered.

2. A resource must provide a “complete” solution, including advice on preparation of the sample, tissue or organism to be imaged, the imaging process itself, and perhaps most importantly tools for processing and analyzing the data, so that each user can potentially achieve a publishable result. As most imaging resources routinely collect many GB to TB of data, delivering maximal value from these resources demands that imaging infrastructure resources interface and collaborate with “big data” resources, for storage, sharing, analysis and visualization. This represents a major opportunity for synergy and collaboration between investments in “bug data” and investments in bioimaging.

Authors: Jason &...

Q6. What factors should we consider when determining the research capital requirement of the higher education estate? (1000 words maximum)

Higher Education Institutions (HEIs) are the engine of many of the current research discoveries. Despite the success and investment in many research institutes much of the research outputs in the UK come from research based at HEIs. Indeed a critical outcome of research based at HEIs is the unparalleled opportunity and access for training for the undergraduates who will be the STEM researchers of tomorrow. Using researchers as course lecturers and exposing undergraduate students to research in world competitive labs, using the best technology available is a strong driver for making STEM university training exciting and likely to be followed in a longer career. By linking the proximity of world-class research with HEIs there is an enormous capability and benefit for training and future discovery.

By no means does this statement require that all major research investments be placed at HEIs. Again the BioImagingUK community has repeatedly concluded that an environment of multiple different types of institutions can be used to provide the underlying research infrastructure.

Q7. Should - subject to state aids and other considerations - science and research capital be extended to Research and Technology Organisations and Independent Research Organisations when there are wider benefits for doing so? (1000 words maximum)

Seeking clarification...

Q8. What should be the UK's priorities for large scale capital investments in the national interest, including where appropriate collaborating in international projects? (1000 words maximum)

The impressive strength and breadth of the UK research base means that we are presented with a huge range of potential investment opportunities. Demand inevitably outstrips funding. Therefore, there is a constant need to prioritise, and this consultation seeks your views to inform our approach. These strategic judgements require us to look first at what international competitors are investing in, and identifying where it is in the UK national interest to collaborate in international infrastructure projects. This may involve significant contributions to projects around the world or hosting them in the UK. We are seeking views on which of the important projects laid out in this consultation (pages 54-58) should be the highest priority. We are also welcoming suggestions of new potential high priority projects not identified here.

BioImagingUK sees two major opportunities for investment that align quite closely with the identified priorities in the Capital Equipment Consultation.

1. The development of a distributed infrastructure for biological and medical imaging where critical technologies are placed either at institutions, centres for excellence or national facilities, depending on their overall expense, requirements for technical expertise and most importantly the scale to which the wider UK community needs access to these technologies. Our concepts of this wider ecology have been articulated repeatedly by members of the community and indeed with many of the members of both our Research Council and non-governmental charity-based funders. A major priority should be placed on capabilities for super-resolution as these technologies become more common but also several emerging technologies for high throughput imaging where a larger number of samples can be rapidly imaged rapidly to attain quantitative, systems-level analysis of organism and humans. as well as newer technologies that enable high resolution imaging not only of single cells but of tissues or whole animals. Combining high throughout automation with whole tissue or animal imaging can provide new models for understanding human development and disease.
   
   As part of the Euro-BioImaging’s First Open Call for Nodes (http://www.eurobioimaging.eu/sites/default/files/Euro-BioImaging%201st%20Open%20Call%20for%20Nodes%20-%20Summary%20290713.pdf), eight UK imaging facilities submitted expressions of interest (“EoIs”) for consideration and evaluation by Euro-BioImaging’s Independent Review Board. Each of these EoIs presented the technology, business model, and proposed several projects that required access to the proposed Node’s technology and expertise. The proposed technologies covered a range of super-resolution modalities, high throughput imaging and image processing and analysis. Seven of the eight proposals were recommended for funding and construction with the eighth requiring minor corrections—a very strong performance. These EoIs provided concrete examples of the diverse, world-class imaging technologies that are available in the UK and, critically, the demand for access to these technologies by the scientific community. The Euro-BioImaging EoIs have been submitted by BioImagingUK to BBSRC on their request as “Model Nodes”, examples of imaging technologies and expertise that are needed by the community and can be delivered, if funded appropriately.
2. Another major priority for BioImagingUK is the development of ’big data’ resources designed for imaging applications. Imaging by its very nature generates large datasets and indeed new modes of automation make it routine for imaging scientists to generate many GBs to TB of data in a single experiment. There are now several biological imaging systems in production in the UK, that routinely collect several TB each week. Developing tools for handling these critical datasets is an absolute necessity. Without these solutions these instruments will rapidly become white elephants as they collect datasets that are simply too large or complex to understand or to interpret.
   
   Several kinds of technology must be developed. Among these:

• • Data compression or reduction tools, to make the collected datasets more manageable while retaining sufficient resolution and sensitivity.
  • Analysis, processing and visualization tools
  • Data management platforms, for sharing, storing and processing larger image datasets.
  • Add more….

Moreover the development of centralized repositories where specific types of image data (‘reference images’) can be deposited and made publicly accessible is an important next step for the community. These datasets can be linked to other existing on-line repositories (e.g., public genomic resources) to linking of genomic with functional phenotypic data. Moreover these reference data will serve as benchmark datasets that will drive the development of new analytic and processing capabilities by algorithm developers and other data scientists.

In delivering these capabilities the UK must consider close and active participation with Euro-BioImaging and ELIXIR. Both of these EU scale projects anticipated the development of infrastructures, which map quite closely to the needs of the UK life and biomedical sciences. Given the scale of the infrastructures that must be built as well as the natural fact that these technologies are being developed and driven by an international community it makes eminent sense to link to these international communities to drive the development to imaging infrastructures. In particular there is now a unique opportunity to collaborate with Euro-BioImaging (http://www.eurobioimaging.eu/) and ELIXIR (http://www.elixir-europe.org/) to develop the “reference” image data repositories, with the publication of a joint MoU by these projects (http://www.eurobioimaging.eu/content-news/euro-bioimaging-elixir-image-data-strategy).

Author: Jason Paul and Kurt

Q9. What should the criteria for prioritising projects look like? (1000 words maximum)

Author: Anne, Lucy

Those engaged in the research process with a known track record for conducting high quality research would be best placed to develop the criteria for assessing the prioritisation of projects, in terms of feasibility, value for money, scientific excellent and contribution to the community. Currently scientific peer review is used to determine funding for responsive mode funding calls for research projects and this mechanism could continue for project prioritisation. The projects should be assessed on evidence based criteria, e.g. track record of producing excellent results in previous projects, knowledge in the subject area, appropriate support for the project in terms of intellectual and technical resources. A well thought through project plan with clear aims and developmental milestones There should be a benefit to UK society. Either economically (e.g. through industry), Technologically (increasing the intellectual capital), for Health / social well being. The project ideally would be in line with current community initiatives or would be of benefit to them, e.g. invention of a new technique which would increase efficiency, knowledge, sharing of resources It should show how it makes use of investments / resources which have been previously made and what the outcomes of the investment would be: e.g. training of staff in a particular technology, support of a resource which many researchers use, development of a technology, use of an existing technology in a new way to generate new information which is of benefit to health, industry etc).

Q10. Are there new potential high priority projects which are not identified in this document? (1000 word maximum)

Author: Anne, Jemima, Pippa, Lucy

Technological advances are rapidly creating better, faster and more sophisticated instruments which will need to be made available to the wider research community to maintain the reputation of UK research as one of the global forerunners. Development of these cutting edge instruments and techniques will need funder support so that we can maintain the strength, breadth and depth of UK science activities. Whilst driving the invention of new technology is critical, and making it available and accessible to the wider community is essential, continued support for the local capital infrastructure that underpins all major new advances is largely absent from this BIS document. Well-funded, accessible, local core facilities are key to the long term stability of UK science, and provide a strong foundation to support regional and national specialised labs. It is this model that will maintain our strong international reputation for high quality research and attract world class researchers to UK. This has been highlighted by the BioimagingUK community, to the extent that many would rank support of local facilities first, above mid-range and national infrastructure. In order to maximise the output of this investment in infrastructure it is essential that funds are made available to support these labs with motivated, dedicated, highly skilled staff and adequate instrument maintenance contracts. Along with cutting edge instrumentation, investment in a group of highly skilled experts who are able to learn, develop, implement and teach these new techniques will create confidence and ensure that the UK remains ahead of the curve for scientific and technical outputs. Core funding to provide stability for these crucially important posts will help retain staff and maximise investment in infrastructure because complex instrumentation is generally not used or maintained efficiently unless supported by dedicated staff. These posts are critical for the success of core facilities, and therefore for the success of UK research. Imaging technology in particular is a fast arena of development and it is crucial that the UK maintain their competitive advantage by continually replenishing and updating the technology available to the wider community, a challenge that increases as technology becomes more sophisticated and expensive. This has been previously recognised by the RCUK, as demonstrated by their exceptionally successful call for next generation imaging technologies, highlighted in their Framework for Capital Investment 2012 and by the proposal 4.6.

Q11. Should we maintain a proportion of unallocated capital funding to respond to emerging priorities in the second half of this decade? (1000 word maximum)

Authors, Ian Dobbie and Jason Swedlow.

It is often impossible to predict which directions or technologies will develop, and at what rate. The successful scientific research requires a landscape of both long term commitments to enable building significant research projects, programmes and institutes, but also a mechanism to rapidly redeploy some of its funding streams to take advantage of emerging fields.

Of particular interest in this regards are fields such as imaging, genomics, proteomics and computational approaches which are all advancing at a rapid pace and will enable significant new research to approaches in the next 5 years. It is significant that the UK is a leader in all these fields with a publication record second only the US, and world-leading research happening in all of these fields.

The recent MRC Next Generation Optical Microscopy call is a case in point. This call was initially posted as funded at a level of £18M, based on the extreme interest and strength of the applications the initiative was eventually funded at £25M, a significant increase in funding. This initiative has funded a number of developments in super-resolution imaging, eg Oxford NanO, Leeds?, NPL?, as well as providing funding for providing new instruments for general users (Edinburgh? Dundee? check examples).

Q12. Are the major international projects identified in the consultation the right priorities for this scale of investment at the international level? Are there other opportunities for UK involvement in major global collaborations? (1000 words maximum)

Authors: Jason