UK Multi-Scale Biology Network

Lead Research Organisation: University of Nottingham
Department Name: Sch of Mathematical Sciences

Abstract

Life, from single cells such as bacteria, to populations of plants and animals is complex and multi-layered. Processes acting at one scale can have profound effects on a system at larger and smaller scales. For example, single bacterial cells, whose size is a fraction of the width of a human hair, can form colonies whose behaviour is massively influenced by their collective interaction. Molecular and physical events at the tip of growing plant roots or shoots can have profound effects on the whole plant, and therefore on food production. Diseases that manifest themselves at the scale of whole organs (e.g. lungs, hearts, livers) often arise due to microscopic changes at the level of the individual cells that make up those organs.

Multi-scale biology seeks to improve our understanding of these multi-layered biological systems by developing new approaches that combine biological sciences with other disciplines such as mathematics, physics, computer science and engineering. This means gathering data at multiple relevant scales (e.g. single cell and whole tissue scale; individual plants/animals and farm or ecosystem scale) and developing tools for reasoning about and modelling such systems whilst taking into account how changes at one scale may impact the system at other scales.

Multi-scale biology presents many new challenges to the relevant disciplines, and many opportunities to exploit capabilities developed in different contexts. For example, weather forecasting and climate modeling rely on sophisticated computer models and techniques of data analysis which could be adapted for use in the biological context. Experience in those fields demonstrates how important is the availability of large amount of quantitative data defined over space, time, and across scales, and suggests that a major shift is required in the biosciences to make routine the generation of similarly detailed data. On the other hand, many advances have been made in the analysis and computer modelling of multiscale biological systems, but many of the models are hard to re-use or combine with other tools in novel ways. Thus a community effort is required to share best practice, to encourage the development and adoption of standards for sharing data and models, to identify opportunities in the field, and to bring together teams of scientists to address grand challenges in the biosciences, such as global food security, sustainability, healthcare, and the reduction and replacement of animals in research. The proposed network will run community building events (where many scientists from different disciplines give short "pitches" about their work and how it can contribute to multi-scale biology), hackathons and study groups (where teams work together over a week in an intensive way to develop computational tools or models), and a summer school (providing training in multi-scale biology). Furthermore, the network will host a website to facilitate community interactions and resource sharing, and support exchange visits between research groups to help launch new collaborations.

Technical Summary

'Predictive biology' is expected to underpin developments across the BBSRC remit, with impacts on global food security, sustainability, synthetic biology and healthcare. Predictive biology needs to integrate data gathered at multiple spatial (e.g. molecules, cells, organs) and temporal (e.g. catalytic, metabolic, developmental) scales, in order to produce an integrated understanding of how multi-scale biological systems function.

Currently, most research related to Multi-Scale Biology (MSB) builds on individual developments of experimental, mathematical and computational methods, and there is great potential to coordinate data and model generation, sharing and re-use. Furthermore, MSB will drive technological developments such as improvements in spatial and temporal resolution, simultaneous measurement of complementary data, and in extracting information from data. Experiences from other predictive sciences (e.g. weather and climate modelling) demonstrates the importance of large amounts of quantitative data defined over space, time, and across scales. MSB could learn a lot from these other research domains. Thus, in order to strengthen links within the UK MSB community, and to build bridges with other relevant communities, we will establish a UK Multi-Scale Biology Network.
The network will organise a number of activities:
* A springboard meeting that starts to identify biological systems ripe for MSB approaches, open problems that should be addressed to facilitate exploration of these biological systems, and expertise in other domains that can contribute to multi-scale biology.
* A web site for community building and resource sharing.
* Hackathons and study groups that catalyse the development of exemplar in MSB.
* Hot topic workshops.
* A Summer school exposing life scientists to techniques in MSB.
* An international conference for knowledge sharing and developing international collaborations within MSB.
* Collaborative exchanges between groups

Planned Impact

Multi-scale biology is an emerging research area, currently time intensive and often involving ab initio development of tools that could instead be adapted and reused. Methodological and technological developments can be exploited not only to improve the quality and usability of multi-scale approaches, but also to accelerate their further development. The Network will therefore seek to achieve its impact in large part through encouraging the widespread uptake of multi-scale approaches: it will do this by a variety of approaches to communication and training, by identifying mechanisms by which to improve the ease of use, reproducibility, adaptability and breadth of applicability of the associated tools and by providing exemplars of successful research projects.

Academic beneficiaries:
Engaging with a wide variety of academic communities (including computer scientists, engineers, mathematicians, physicists and social scientists, as well as bioscientists) is a central goal of the Network and all of its activities will be heavily promoted through its website, by the compilation of extensive mailing lists and through the relevant learned societies. The proposed Study Groups, hackathons and Summer schools represent tried and tested pathways to academic impact, providing convincing proof-of-concept studies and generating new collaborations, research proposals, publications, models and tools. The hot-topic workshops will familiarise participants with the state of the art in specific methodologies, while the collaborative visits will facilitate the putting together of the cross-disciplinary teams that will be crucial to success in multi-scale biology. The springboard meeting and international conference will seek to promote the approach to as broad a range of researchers as possible, as well as showcasing the network.

Commercial beneficiaries:
The Network will also heavily promote its activities to the relevant industrial sectors (including biotechnology, food and pharmaceutical), seeking (for example) Study-Group problem presenters from industry and presenting success stories of the application of the approach. The above mechanisms for engaging with academic beneficiaries thus apply equally to commercial ones and industrial participants have contributed actively to the development of the Network.

Engagement with the broader public:
Both the novelty and the long-term significance of the field will make it of interest and appeal to a wide range of other communities, including the media, undergraduates, school teachers and pupils, as well as the general public. Hence while the main efforts of the Network will be directed at promoting the approach to the disparate research communities required for its success and sustainability, the website and press releases will also target the general public, seeking to raise awareness of the power of multi-scale approaches and of their relevance to many key priorities, including global food security, sustainability, lifelong health and antimicrobial resistance.
Funding bodies and policy makers:
The portfolio of effective applications of multi-scale approaches put in place by the Network can also be expected to have an influence on UK research priorities and, taking a long-term view of likely developments in the field, opportunities to promote its activities in this way will also be sought.

International impact:
Network members are well-connected with relevant researchers overseas and will draw on their expertise and on engagement with leading-edge research elsewhere in informing the development of the Network. The Network will in consequence also play an important role in building multinational collaborations, in influencing European research policy and in contributing to the development of internationally recognised multi-scale model and data exchange formats.

Publications


10 25 50
 
Description For year 1 of this award we met the objectives of the Multiscale Biology Network:
• A springboard meeting - held in Nottingham, 1 June 2015, with 55 participants
• Establish a web site for Multi-Scale Biology - launched in May 2015. The associated mailing list now has 121 members.
• A hackathon - scheduled for 20-22 April 2016
• A one-day workshop - held in Sheffield, 1 December 2015, with 59 participants.
• 1st call for proposals to support collaborative visits, designed to pump-prime new collaborations. 1st closing date was 31 Jan 2016, 2nd will be 30 April 2016.

The activities have helped to foster a community working around biological systems whose behaviour crucially relies upon interactions between spatial scales, for example how the growth of tissues in our bodies depends on the mechanics of the tiny individual cells that make up those tissues; or how the growth of individual plants affects our ability to feed a growing population.
Exploitation Route By enhancing the dialogue between specialists working on multiscale biology in different application areas, we expect to see improvements in our understanding of a wide range of important biological systems.
Sectors Agriculture, Food and Drink,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
URL http://multiscalebiology.org.uk
 
Description MSBnet collaboration between Bindi Brook and Gerry Meininger 
Organisation University of Missouri
Country United States of America 
Sector Academic/University 
PI Contribution I coordinate the UK network which has an explicit aim to encourage new collaborations between scientists working on multiscale biology. I coordinate the call for proposals, evaluation of proposals by the MSBnet steering group, and announcements, etc.
Collaborator Contribution Relating airway micro-structure to tissue function: Bindi Brook (Mathematical Sciences, University of Nottingham) for exchange with the lab of Prof Gerald Meininger (Department of Medical Pharmacology and Physiology, University of Missouri-Columbia)
Impact Disciplines involved : mathematics, computational science, medicine, biology. No outputs yet.
Start Year 2017
 
Description MSBnet collaboration between Bindi Brook and Gerry Meininger 
Organisation University of Nottingham
Department School of Life Sciences
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution I coordinate the UK network which has an explicit aim to encourage new collaborations between scientists working on multiscale biology. I coordinate the call for proposals, evaluation of proposals by the MSBnet steering group, and announcements, etc.
Collaborator Contribution Relating airway micro-structure to tissue function: Bindi Brook (Mathematical Sciences, University of Nottingham) for exchange with the lab of Prof Gerald Meininger (Department of Medical Pharmacology and Physiology, University of Missouri-Columbia)
Impact Disciplines involved : mathematics, computational science, medicine, biology. No outputs yet.
Start Year 2017
 
Description MSBnet collaboration between Dr Daniele Tartarini and Dr James Grogan 
Organisation University of Oxford
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution I coordinate the UK network which has an explicit aim to encourage new collaborations between scientists working on multiscale biology. I coordinate the call for proposals, evaluation of proposals by the MSBnet steering group, and announcements, etc.
Collaborator Contribution Investigating Surrogate Modelling Approaches for Tumour Growth: exchange between Dr Daniele Tartarini, (Insigneo Institute for in silico medicine, University of Sheffield) and Dr James A. Grogan (Wolfson Centre for Mathematical Biology, University of Oxford)
Impact Disciplines involved : mathematics, computational science, medicine, biology. No outputs yet.
Start Year 2017
 
Description MSBnet collaboration between Dr Daniele Tartarini and Dr James Grogan 
Organisation University of Sheffield
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution I coordinate the UK network which has an explicit aim to encourage new collaborations between scientists working on multiscale biology. I coordinate the call for proposals, evaluation of proposals by the MSBnet steering group, and announcements, etc.
Collaborator Contribution Investigating Surrogate Modelling Approaches for Tumour Growth: exchange between Dr Daniele Tartarini, (Insigneo Institute for in silico medicine, University of Sheffield) and Dr James A. Grogan (Wolfson Centre for Mathematical Biology, University of Oxford)
Impact Disciplines involved : mathematics, computational science, medicine, biology. No outputs yet.
Start Year 2017
 
Description MSBnet collaboration between Francis Woodhouse and Ruth Baker 
Organisation University of Cambridge
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution I coordinate the UK network which has an explicit aim to encourage new collaborations between scientists working on multiscale biology. I coordinate the call for proposals, evaluation of proposals by the MSBnet steering group, and announcements, etc.
Collaborator Contribution Transport in networked environments: Francis Woodhouse (Department of Applied Mathematics and Theoretical Physics, University of Cambridge) and Ruth Baker (Mathematical Institute, University of Oxford)
Impact Disciplines involved : mathematics, computational science, biology. No outputs yet.
Start Year 2017
 
Description MSBnet collaboration between Francis Woodhouse and Ruth Baker 
Organisation University of Oxford
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution I coordinate the UK network which has an explicit aim to encourage new collaborations between scientists working on multiscale biology. I coordinate the call for proposals, evaluation of proposals by the MSBnet steering group, and announcements, etc.
Collaborator Contribution Transport in networked environments: Francis Woodhouse (Department of Applied Mathematics and Theoretical Physics, University of Cambridge) and Ruth Baker (Mathematical Institute, University of Oxford)
Impact Disciplines involved : mathematics, computational science, biology. No outputs yet.
Start Year 2017
 
Description MSBnet collaboration between Miguel Bernabeu and Helen Byrne 
Organisation University of Edinburgh
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution I coordinate the UK network which has an explicit aim to encourage new collaborations between scientists working on multiscale biology. I coordinate the call for proposals, evaluation of proposals by the MSBnet steering group, and announcements, etc.
Collaborator Contribution "Towards a mechanistic understanding of haematocrit changes in tumour vasculature", for exchange visits between Edinburgh and Prof Helen Byrne (University of Oxford).
Impact Disciplines involved : mathematics, computational science, biology. No outputs yet.
Start Year 2016
 
Description MSBnet collaboration between Miguel Bernabeu and Helen Byrne 
Organisation University of Oxford
Department Department of International Development
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution I coordinate the UK network which has an explicit aim to encourage new collaborations between scientists working on multiscale biology. I coordinate the call for proposals, evaluation of proposals by the MSBnet steering group, and announcements, etc.
Collaborator Contribution "Towards a mechanistic understanding of haematocrit changes in tumour vasculature", for exchange visits between Edinburgh and Prof Helen Byrne (University of Oxford).
Impact Disciplines involved : mathematics, computational science, biology. No outputs yet.
Start Year 2016
 
Description Hacking the Boundaries 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Participants from 5 institutions met in Edinburgh for a hack event, aimed at the developers of multi-scale models and of the corresponding software tools. Several such tools have been developed, each driven by different biological application areas. This event aimed to pinpoint challenges facing each group and to scope the potential for learning/re-purposing of tools.
Year(s) Of Engagement Activity 2016
URL http://www.multiscalebiology.org.uk/events/event/hacking-the-boundaries-edinburgh/
 
Description MSBnet Springboard meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact We kicked off the UK Multiscale Biology Network with a Springboard meeting in Nottingham in June 2015. There were 55 registered participants, including many that were new to the Network. A report from on a community blog can be found here: http://blog.garnetcommunity.org.uk/multi-scale-biology-meeting/
Year(s) Of Engagement Activity 2015
URL http://www.multiscalebiology.org.uk/springboard-meeting-report/
 
Description Multiscale Biology Study Group 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact The Multiscale Biology Study Group took place in the School of Mathematics at the University of Birmingham from 12th-15th December 2016, funded by the Multiscale Biology Network and POEMS (Predictive Modelling for Healthcare Technology through Maths), organised by Sara Jabbari, Rosemary Dyson and Dave Smith. The study group brought together around 50 mathematicians and computer scientists from the UK and abroad to work intensively on problems from biology and healthcare research.

The topics studied were: identifying and preventing pre-eclampsia in pregnancy, imaging and analysing plant root growth, immune cell cancer, efficient methods for reconnecting blood vessels in plastic surgery and understanding the structure and permeability of blood vessels. At the beginning of the week, key concepts were introduced and discussed by the biology and healthcare professionals leading each problem, after which attendees split into five groups and began working on the projects. Throughout the week, innovative solutions were developed in all areas; drawing on fluid dynamics, stochastic and mechanistic modelling and image analysis to deepen understanding of the problems faced.

Mid-week presentations for each project were given, updated attendees and gave an opportunity to provide insight into other work. These presentations were predominantly given by postgraduate students who were enthusiastic in their participation. At the end of the week each group gave a final presentation of their work. After each presentation, project organisers were asked two questions: was the problem answered adequately, and what is the scope for future work. All project leaders noted fast progress and an excellent ability for attendees to share ideas and support throughout the week. After a successful week for each group, joint projects are expected to follow, with high hopes for future publications and grant proposals.
Year(s) Of Engagement Activity 2016
URL http://www.multiscalebiology.org.uk/meeting-report-msbnet-poems-multiscale-biology-study-group-2016/
 
Description Sheffield Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact The second one-day workshop of the UK Multiscale Biology Network took place in Sheffield on 1 December 2015. There were 59 registered participants, but in the end 74 people turned up.

The day included three keynote talks, a series of TED-style talks, two discussion sessions, a talk from the Medical Research Council (MRC) exploring funding opportunities in Multiscale Biology and a number of posters. The TED-style talks were a particular highlight, with some attendees commenting that they learnt as much from some of these 8 minute talks as they usually do from a much longer presentation.

Further details of the programme and attendees can be found at the event page here: http://www.multiscalebiology.org.uk/events/event/sheffield-workshop/
Year(s) Of Engagement Activity 2015
URL http://www.multiscalebiology.org.uk/events/event/sheffield-workshop/
 
Description The Tissue Issue: BRIDGING SCALES IN MODELS OF CELL TO TISSUE BEHAVIOUR 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The Society for Experimental Biology (SEB) Cell Symposium 'Bridging scales in models of cell to tissue behaviour: recent progress and future challenges' took place at Lady Margaret Hall, University of Oxford from the 12th to 15th September 2016. Attended by 48 researchers from the UK and further afield, this meeting received financial support from the SEB, the MSB network and the EPSRC programme grant '2020 Science'.
Year(s) Of Engagement Activity 2016
URL http://www.multiscalebiology.org.uk/meeting-report-bridging-scales-in-models-of-cell-to-tissue-behav...