Biological Visualisation Network

Lead Research Organisation: Edinburgh Napier University
Department Name: School of Computing

Abstract

Biology is a visual science, from the way data is collected and analysed to how it is communicated to others. Traditionally pictures in scientific publications were hand-drawn; however they are now almost exclusively computer-generated. Biologists have been working with computer scientists and other experts in understanding graphical presentation techniques to automatically generate visualisations in biology. These range from graphical representations of molecules, representations of DNA sequences and genes, images of cells and organisms and metabolic pathways through to trees showing evolutionary processes.
Recently techniques have been developed that generate masses of data which can be used to analyse biological processes and functions, such as understanding how genes work and the effects they have on organisms. However this has presented a challenge in how to visually represent the data to allow biologists explore the data looking for patterns or trends that will help then understand the underlying biological processes. With the growing importance in visual techniques it is now the right time to spread the work about the benefits of biological visualisation.
To help more biologists discover and understand the new visualisation techniques and to engage other disciplines in helping to visually present this new data in a more effective manner we need to build a community resource for educating people. We will help introduce people with different expertise that can work together in coming up with new solutions and generally share their expertise and experience.
This proposal therefore plans to build a network of people interested in biological data visualisation. The network will develop a website to act as a resource for information on biological visualisation. We will also hold annual meetings for networking and educational purposes focussed around emerging trends in visualisation and challenges facing biology.

Technical Summary

Biology is a visually grounded scientific discipline-from the way data is collected and analysed to the manner in which the results are communicated to others. Traditionally pictures in scientific publications were hand-drawn; however they are now almost exclusively computer-generated. Many areas in biology have historically evolved "standard" ways of representing biological information including phylogenetics, molecular structures, metabolic pathways and cell structures, however this has presented challenges in developing techniques for automatically generating these familiar representations. In more recent areas such as genomics, novel computer visualisation techniques have emerged for representing sequences, alignments and gene expression information.

With the exponentially increasing amount of scientific data available all areas of biology now rely heavily on computational approaches for the analysis of data. Although computational techniques facilitate the management and analysis of this data, it is critical that scientists be able to participate intimately in the analysis steps using qualitative and quantitative abstractions of the underlying data, therefore visualisation is central to enabling scientists to make sense of their data and communicate it to others in a concise and meaningful way. However, presently, biologists' understanding of the range of visualisation techniques available, the most appropriate visual representation or encoding to use is limited to a small community.

This proposal aims to bring together the expertise across the country and provide a focus for engaging with the wider community to educate biologists in new technologies, inspire computer scientists and related disciplines in the challenges associated with visualising biological data and to encourage ongoing collaboration in the field of data visualisation.

Planned Impact

The Network in Biological Visualisation will have a major impact on biologists across the UK in terms of their knowledge of available visualisation tools for exploring their data, making them more efficient and effective in making biological discoveries. The network will also clarify outstanding problems facing biologists exploring and analysing their data, making it possible for scientists in other disciplines collaborating with the biologists to develop appropriate tools for visual biological data analysis. The network will open up possibilities for project proposals for future interdisciplinary funding.

Publications

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Farabella I (2015) : a Python library for assessment of three-dimensional electron microscopy density fits. in Journal of applied crystallography

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Graham M (2014) Vesper: Visualising species archives in Ecological Informatics

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O'Donoghue S (2018) Visualization of Biomedical Data in Annual Review of Biomedical Data Science

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Shaw PD (2014) Helium: visualization of large scale plant pedigrees. in BMC bioinformatics

 
Description This grant has funded a BBSRC network in Biological Visualisation. the Network has hosted 3 annual meetings and several smaller regional meetings. A website has been set up to host information regarding biological visualisation including presentations from the annual network meetings. The meetings have resulted in collaborations for funding in biological visualisation.
Exploitation Route The bivi website can be used to educate biologists in visualisation, for visualisation developers to learn about biology issues and for collaborations to be formed.
Sectors Agriculture, Food and Drink,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

URL http://bivi.co
 
Title BBSRC Biological Visualisation Network Website 
Description Biological Visuasliation Tools/Techniques Database and Website 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Widespread availability of biological visualisation techniques. 
URL http://bivi.co
 
Description Birkbeck College (Maya Topf) 
Organisation Birkbeck, University of London
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Our committee member from Birkbeck College ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcome activities are attached to the project.
Start Year 2014
 
Description Bringing together Biological Data Visualisation Practitioners and Researchers in Industry and Academia 
Organisation GlaxoSmithKline (GSK)
Department Respiratory Biology GSK
Country United Kingdom 
Sector Private 
PI Contribution Collaborated on a proposal and delivered a pitch for an EBI-Industry meeting "Innovations in Data Visualisation for Drug Discovery". Proposed topics, and selected academic speakers for meeting program.
Collaborator Contribution Collaborated on a proposal and delivered a pitch for an EBI-Industry meeting "Innovations in Data Visualisation for Drug Discovery". Proposed topics and suggested academic and industry speakers for meeting program.
Impact Engagement Activity: 2018 June - EBI Industry meeting on Innovations in Data Visualisation for Drug Discovery
Start Year 2017
 
Description Brunel University London (David Gilbert) 
Organisation Brunel University London
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Our theme leader and committee member from Brunel University London ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcome activities are attached to the project.
Start Year 2014
 
Description EMBL-EBI (Bren Vaughan) 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Our committee member from EMBL-EBI ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcome activities are attached to the project.
Start Year 2014
 
Description Elixir 
Organisation ELIXIR
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We have made our data (events, tools, presentations) available to Elixir via a customised RSS feed for import into their website.
Collaborator Contribution Elixir have raised awareness of the BiVi network.
Impact All outcomes are attached to the project.
Start Year 2014
 
Description Exeter Centre for the Study of the Life Sciences, University of Exeter (Sabina Leonelli) 
Organisation University of Exeter
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Our committee member from The University of Exeter ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcome activities are attached to the project.
Start Year 2014
 
Description Imperial College (Mike Sternberg) 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Our theme leader and committee member from Imperial College ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcome activities are attached to the project.
Start Year 2014
 
Description SICSA 
Organisation SICSA Scottish Informatics and Computer Science Alliance
Country United Kingdom 
Sector Academic/University 
PI Contribution In addition to providing a resource for members of the SICSA community, we administered the funding provided by SICSA for attendance at the BiVi AGMs, and raised awareness of the organisation at these events.
Collaborator Contribution Provided funding for SICSA members' attendance at BiVi AGMs and raised awareness of the BiVi network.
Impact All outcomes are attached to the project.
Start Year 2014
 
Description TGAC (Manuel Corpas and Vicky Schneider) 
Organisation The Genome Analysis Centre (TGAC)
Country United Kingdom 
Sector Public 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Theme leaders and committee members from TGAC ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcomes are attached to the project.
Start Year 2014
 
Description The Roslin Institute (Dave Burt and Tom Freeman) 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Theme leaders and committee members from The Roslin Institute ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcomes are attached to the project.
Start Year 2014
 
Description UCL (Bernard de Bono) 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Our committee member from UCL ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcomes are attached to the project.
Start Year 2014
 
Description University of Dundee, (Geoff Barton, Jim Procter) 
Organisation University of Dundee
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Theme leaders and committee members from The University of Dundee ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcomes are attached to the project.
Start Year 2014
 
Description University of Edinburgh (Martin Jones) 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Edinburgh Napier was responsible for Network co-ordination and infrastructure maintenance and development of the Network's website.
Collaborator Contribution The BiVi Network is a joint enterprise between a number of partner organisations. Our committee member from The University of Edinburgh ensured dissemination of information and growth of the Network by engaging the biology community and in helping with content creation for the website.
Impact All outcomes are attached to the project.
Start Year 2014
 
Title Professor Michael Sternberg - EzMol - a web-based wizard-driven program for the display of protein and nucleic acid structures 
Description A very simple-to-use web-based molecular visualisation tool developed by our group. It works via most browsers and is driven by a wizard interface. The program is web-based and works with most common browsers so there is no need for any installation or a licence. It is driven a wizard that directs the user through a focussed set of options with no need for any commands to be typed. It supports cartoon, stick and space-filling visualisation options for the protein chains, and the user selects residues for display, colouring and labelling from a presented list, similar to date selection tools on many web sites. The final visualisation model can be downloaded for publication or saved for subsequent use. The interface is particularly designed for the occasional user who does not want to remember command syntax or have to cope with a large number of menu options. Available at http://www.sbg.bio.ic.ac.uk/~ezmol/ 
Type Of Technology Webtool/Application 
Year Produced 2018 
Impact None yet as just launched 
URL http://www.sbg.bio.ic.ac.uk/~ezmol/
 
Description 2017 - June: Article in TheConversation.au - Data visualisation isn't just for communication, it's also a research tool 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact An article describing how basic principles of data visualisation and user interface design help researchers more effectively analyse and explore biological data, featuring an example of an analysis being performed with Jalview. The article also highlighted communities of biologists and biomedical researchers, computer scientists, artists and designers who are engaged in developing new visualisations and computational tools that allow researchers to understand new types of experimental data, and communicate insights to the public. The article was published in theconversation.au, and had been viewed over 5000 times by readers in Australia, the US, UK and France. Following its publication, material from it was included in an article on 'Big Data in Biology' that will be published in the March 2018 edition of "Contact", Dundee University's Magazine.
Year(s) Of Engagement Activity 2017
URL https://theconversation.com/data-visualisation-isnt-just-for-communication-its-also-a-research-tool-...
 
Description 2017 - May - Jalview 'Tips and Tricks' Tutorial as part of the 3rd UK Biological Visualisation Network Annual General Meeting 
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 A two hour workshop on experimental and technical aspects of the Jalview workbench for Multiple Sequence Alignment and Analysis was conducted on the 3rd Annual General Meeting of the UK Biological Visualisation Network's training day to a group of biological data visualisation researchers and practitioners. Aspects of this workshop included discussion about workarounds for technical limitations of existing web APIs for public datasets, and future web platform development directions in partnership with other ELIXIR-UK node resources.
Year(s) Of Engagement Activity 2017
URL http://bivi.co/page/3rd-bivi-annual-meeting-workshops#jalview
 
Description 2018 June - EBI Industry meeting on Innovations in Data Visualisation for Drug Discovery 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact An EBI-Industry meeting proposed by L. Edwards (GSK) and J. B. Procter (U. Dundee) aimed at users and developers of data visualisations working in drug discovery in Industry with invited speakers from Academia to learn about state of the art practices and research in the design and delivery of data visualisation and discuss barriers and future opportunities for engagement between academic and industry communities working on data visualisation in drug discovery and biomedical data science. The meeting took place at the Wellcome Trust conference centre at the EBI on 13-14th June 2018.
Year(s) Of Engagement Activity 2018
URL https://www.ebi.ac.uk/industry/private/industry-workshop/2018/06/innovations-data-visualisation-drug...
 
Description BiVi AGMs 
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 Three two-day long annual general meetings were organised to help researchers in biology, bio-bioinformatics, visualisation, and bio-visualisation keep in touch with what is happening within Bio-visualisation, connect with a community of researchers from the UK and worldwide, and get hands-on experience and training with the latest tools. Each AGM included an exciting programme of thought-provoking keynotes from highly regarded international researchers; workshop training sessions from leading UK and international bio-visualisation researchers and developers; short talks focusing on the latest in UK based bio-visualisation; and poster sessions and lightning talks presenting new and upcoming research in the field. The programme was specifically designed to facilitate networking, with many opportunities for discussions and making contact with others with an interest in bio-visualisation, throughout the meetings. The meetings were a great success: 90% of respondents to the 2017 questionnaire said they would like to come to a BiVi meeting again. The AGM opened up the community to new participants, with 59% of respondents stating that it was the first time they had attended a meeting of this type. When asked "what was the best thing about the meeting", along with the quality of talks and workshops on offer, respondents identified networking opportunities and cross-pollination of ideas: "mix of different disciplines, not just one type"; "interacting with people from different disciplines"; "a chance to discuss my research with biologists and experts in bioviz. Normally I go to HCI conferences, so the type of feedback/recommendations I get is different"; and "connecting to people", were just some of the responses we received.
Year(s) Of Engagement Activity 2014,2015,2016
URL http://bivi.co/event/3rd-bivi-annual-meeting-2017
 
Description Biological Visualisation Network overview 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Presentation of BIVI website and resource to the Elixir management team with the aim of receiving Elixir backing/support fo rhte continuation of hte website.
Year(s) Of Engagement Activity 2017
 
Description Information Design Principles and Biological Visualisation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Keynote Talk to biologists to introduce them to biological visualisaiton and educate them on how to better present their data. Sparked interest in collaboration and visiting researcher.
Year(s) Of Engagement Activity 2016
URL https://www.software.ac.uk/research-data-visualisation-workshop-rdvw
 
Description Jessie Kennedy - Distinguished Researcher Speaker, Taxonomy and Visualisation, Distinguished Lecture Series, Scientific Computing Institute, University of Utah, USA, 29/9/2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited talk on taxonomy and visualisation. Raised awareness of biological visualisation and the BiVi network, and sparked interest in future collaboration
Year(s) Of Engagement Activity 2017
 
Description Jessie Kennedy - Invited Speaker - Visualising Taxonomy, Opening Conference Centre for Medical Imaging and Visualization, Bergen Norway, 12/12/2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invited speaker at a medical imaging and visualisation conference. Sparked interest in the network and future collaborations.
Year(s) Of Engagement Activity 2017
URL https://mmiv.no/events/
 
Description Jessie Kennedy - Invited Speaker, Principles of Visualisation, James Hutton Institute, 7/2/2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Invited talk to biologists to introduce them to biological visualisaiton and educate them on how to better present their data. Raised awareness of the BiVi network and sparked interest in collaboration
Year(s) Of Engagement Activity 2017
 
Description Jessie Kennedy - Invited Talk, Biological Visualisation, Dept. Computer Science, St Andrews University, 7/11/2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Invited talk on biological visualisation. Raised awareness of biological visualisation and the BiVi network, and sparked interest in future collaborations.
Year(s) Of Engagement Activity 2017
 
Description Presentation at TDWG Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Slides of presentation given at the Taxonomic Databases Working Group (TDWG) Conference, Florence, Italy on Tuesday 29th November, 2013



http://www.tdwg.org/fileadmin/2013conference/slides/Graham_VESPER.ppt

no actual impacts realised to date
Year(s) Of Engagement Activity 2013
URL http://www.tdwg.org/fileadmin/2013conference/slides/Graham_VESPER.ppt
 
Description Professor Michael Sternberg - Imperial Festival 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Imperial Festival. We presented protein modelling. In 2016 and 2017 we also presented the protein docking game BioBlox.
Year(s) Of Engagement Activity 2014,2016
 
Description Professor Michael Sternberg - New Scientist Live - stand presentation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact New Scientist Live - stand presentation. Over 300 visitors to the stand saw protein modelling.
Year(s) Of Engagement Activity 2017
URL https://live.newscientist.com/
 
Description Professor Sabina Leonelli - Invited seminar at Data Visualisation Workshop, hosted by the Exeter Imaging Network and Big Data Challenges, 28 January 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was a one-day workshop attended by around 70 people, including researchers from different disciplines and several different universities as well as representatives of the BBSRC, aiming at exploring visualisation issues in biology. My talk was titled "Organising Data for Re-Use: Visualisations in Biological Databases". As part of the talk, I discussed the activities and remit of BIVI, and encouraged the audience to engage with the network.
Year(s) Of Engagement Activity 2015
URL http://www.exeter.ac.uk/news/events/details/index.php?event=2562
 
Description bio-IT world 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Opening Keynote Speaker at Data Visualization & Exploration Tools, Part of Bio-IT World & Expo, April 21-23, 2015, Seaport World Trade Center, Boston, USA
Year(s) Of Engagement Activity 2015
 
Description biojs conf 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation on the BBSRC biological visualisation network to the BioJS community.
Year(s) Of Engagement Activity 2015
URL http://conf.biojs.net/