Visualising high dimensional data is challenging and a significant constraint is the need to render in 2D for the screen or page. With the arrival of virtual reality (VR) and augmented reality (AR) comes the opportunity to explore and share biomedical data in new ways. VR/AR can extend 2D analyses intuitively to higher dimensions, providing richer interaction with data. Critically, they also provide us with new ways to explore the topological structure of data, particularly valuable for network graphs of arcs and vertices. 2D renders of network graphs are inherently ambiguous due to the crossing of arcs, something that grows polynomially with graph size, making large graphs unintelligible. 3D rendering eliminates this problem completely.
Network graphs are routinely used to depict the Interactome: the networks of interactions that drive physiological function. We will develop the first VR tools to facilitate 3D rendering, navigation and manipulation of the pathways of cell, gene, protein and small molecule interactions that drive the interactome. The tools will be enable the interactome to be embedded in other renderings, such as the spatial structure of cells, tissues, organs or organisms and can be reused across diseases. As an exemplar, the tools will be first applied to disrupted cellular processes in the motor neuron disorder, Amyotrophic Lateral Sclerosis (ALS). By cross-relating the structure of the human molecular interaction network against genomic data, we have previously identified clusters of interacting genes with newly identified mutations that we believe are involved in the development of ALS. 3-D modelling will greatly help us to understand their role in disease development.
Pathways of the interactome are routinely described using the Systems Biology Graphical Notation (SBGN), an open, community-driven 2D mapping standard1 adopted by many software tools2. We propose to develop it for 3D visualisation. SBGN3D will exploit the Google Cardboard framework3, facilitating visualisation using cheap viewers and phone apps, or as interactive models embedded in 2D digital content.
Aims & Objectives
Aim 1 – Translation of SBGN from 2D to 3D
* Develop 3D glyphs corresponding to 2D glyphs.
* Define compartment structure and text orientation.
* Extend current SBGN file formats to SBGN3D.
Aim 2 – Development of SBGN3D viewer in Google Cardboard
* Develop import/export libraries for SBGN3D files.
* Build navigation interface for controlling SBGN3D maps.
* Export interface as phone app.
Aim 3 – ALS application.
* Curate new ALS interactome maps to SBGN3D.
* Identify topological structure of ALS interactome.
* Export ALS SBGN3D maps to public repositories for reuse.
This will yield:-
* The first schema for 3D mapping of the pathways of the interactome.
* The first toolset for viewing 3D pathway structures in VR environments.
* A richer understanding of ALS interactome topology VR schema/tools are the first step to AR modelling, the goal of follow up work.
Researcher will be based at C-TRIC (Altnagelvin Hospital site).
 Le Novere N, et al., Nat Biotech (2009) 27(9), 864-864.
If the University receives a large number of applicants for the project, the following desirable criteria may be applied to shortlist applicants for interview.
- Demonstrable programming skills and mathematical ability.
- Familiarity with biomedical science is desirable, but not essential.
- Completion of Masters at a level equivalent to commendation or distinction at Ulster is desirable, but not essential.
- A background in computer science, mathematics, physics, bioinformatics, biomedical science, stratified/personalised medicine, biomedical engineering, or another quantitative science.
- To hold, or expect to achieve by 15 August, an Upper Second Class Honours (2:1) Degree or equivalent from a UK institution (or overseas award deemed to be equivalent via UK NARIC) in a related or cognate field.
- Sound understanding of subject area as evidenced by a comprehensive research proposal
The University offers the following awards to support PhD study and applications are invited from UK, EU and overseas for the following levels of support:
Vice Chancellors Research Studentship (VCRS)
Full award (full-time PhD fees + DfE level of maintenance grant + RTSG for 3 years).
This scholarship will cover full-time PhD tuition fees and provide the recipient with £15,500 (tbc) maintenance grant per annum for three years (subject to satisfactory academic performance). This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.
Vice-Chancellor’s Research Bursary (VCRB)
Part award (full-time PhD fees + 50% DfE level of maintenance grant + RTSG for 3 years).
This scholarship will cover full-time PhD tuition fees and provide the recipient with £7,750 maintenance grant per annum for three years (subject to satisfactory academic performance). This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.
Vice-Chancellor’s Research Fees Bursary (VCRFB)
Fees only award (PhD fees + RTSG for 3 years).
This scholarship will cover full-time PhD tuition fees for three years (subject to satisfactory academic performance). This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.
Department for the Economy (DFE)
The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £ 15,500 (tbc) per annum for three years (subject to satisfactory academic performance). EU applicants will only be eligible for the fee’s component of the studentship (no maintenance award is provided). For Non-EU nationals the candidate must be "settled" in the UK. This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.
Due consideration should be given to financing your studies; for further information on cost of living etc. please refer to: www.ulster.ac.uk/doctoralcollege/postgraduate-research/fees-and-funding/financing-your-studies
The Doctoral College at Ulster University
My experience has been great and the people that I have worked with have been amazing
Kieran O'Donnell - 3D printing of biological cells for tissue engineering applicationsWatch Video
Kamin Hau - PhD in Biomedical Sciences
Completing the MRes provided me with a lot of different skills, particularly in research methods and lab skills.
Michelle Clements Clements - MRes - Life and Health SciencesWatch Video
I completed my undergraduate studies at Ulster University, where I graduated in 2017 with first class honours in Biomedical Science with a Diploma in Professional Practice . I joined the Diabetes Research group as a PhD researcher in September 2017 and completed my PhD studies in June 2020.I am proud to say I not only completed my PhD studies within 3 years, but also became the World Champion (with a perfect score!) in Irish Dance during my PhD studies. My favourite memory was the opportunity to present my PhD work at the EASD conference in 2019. If I could speak to myself at the start of my PhD, the best piece of advice I would give myself would be to enjoy every single minute as the time flies in. I really would do another PhD!
Sarah Craig - PhD in Biomedical Sciences
I completed my undergraduate studies in America at Texas Woman’s University where I majored in Kinesiology. I then moved to Scotland to successfully complete my Masters with Merit in Human Anatomy at the University of Dundee.My proudest moment was when I passed my viva! My favourite memory was …the dissections. I’ll never forget the friends I made and the good times we had together. I couldn’t have got through this without the support of my family, friends, lab colleagues, supervisors, and my boyfriend. If I could speak to myself at the start of my PhD, the best piece of advice I would give myself would be to write up after every experiment, keep a lot of back up copies of the work, and to enjoy the experience.
Natalie Klempel - PhD in Biomedical Sciences
Throughout my PhD I’ve been provided with continuous support and guidance by my supervisors and the staff at the University.I’ve also received many opportunities to further enhance my professional development in the form of teaching experience and presenting my work at conferences which will aid in my pursuit of a career in academia or industry.
I studied Medical Neuroscience at the University of Sussex followed by a year working in Industry and then a Master's in Genetics at the University of Lyon in France, before coming to Ulster University for my PhD in Biomedical Sciences.I want to thank my fantastic supervisors Declan McKenna and Colum Walsh for teaching me so much and for being so supportive. I had a brilliant PhD experience, made all the better by my lovely supervisors, office-buddies, tearoom-buddies, and other friends. I also want to thank the amazing staff at the Coleraine campus gym for being so much fun and for giving me my love of fitness. I am so glad that I decided to join in the first year - it was really the thing that kept me sane during the stressful periods and I so enjoyed being part of that community. My best wishes to the rest of my cohort and good luck for the future.
Charlotte Zoe Angel - PhD in Biomedical Sciences
I am originally from Nepal, having received my undergraduate and master's degree from Bangladesh. During my Master's degree, I chose area of diabetes research and then I was offered a PhD in the School of Biomedical Sciences on Diabetes Research. Currently, I'm working as a Scientist at Randox Laboratories Ltd. Thus, I would like to thank my supervisors, without them I wouldn't be in this position today.My proudest moment was when I presented my research outcomes to an international symposium. My favorite memory was the love of university staff and colleagues during my PhD tenure. I’ll never forget my supervisors, and especially Professor Peter Flatt, who has guided me in each step of my PhD life. I couldn’t have got through this without Professor Peter Flatt and Dr Yasser Abdel-Wahab and the University’s staff support.If I could speak to myself at the start of my PhD, the best piece of advice I would give myself would be after all the hard work, you will receive a
Prawej Ansari - PhD in Biomedical Sciences
I joined Ulster university in Jan 1990 after completing Postdoctoral research in Germany (1986-88) and PhD in India (1985). DSc degree in Applied Microbial-Biotechnology has been awarded after the evaluation of my thesis based on Research, Publication & related activities, completed as a research-active academic member of staff (1990-2019). DSc thesis summarised my scientific outputs and contributions (183 research papers, 3 biotechnology reference-books, 43 research-informed book-chapters, 26 research-informed review-articles, 90 conference-abstracts,1 European Patent and 2 Technology-transfers; Supervision of National & International researchers-18 Postdoctoral/Exchange and 12 PhD; and affiliations as Examiner of 58 PhD researchers globally, and Fellow & Member of nine scientific & academic societies.My message to all researchers is that "Chase your Aspirations and Never Give up". I couldn’t have got through my long academic & Professional journey without
Poonam Singh Nigam - DSc in Biomedical Sciences
I started my PhD after I completed my undergraduate in Biology at Ulster University in 2016, with a dissertation project that focused on genetic variations in bacterial species. I continued using some of these techniques in my doctoral research, which primarily involved the investigation and development of mass spectrometry imaging in vitamin D treated prostate cancer, looking at the metabolic and genetic variations upon treatment. I worked with international collaborators at the University of Edinburgh and Maastricht University, where I got to learn and develop mass spectrometry techniques that have not previously been carried out in Northern Ireland. I now work as a postdoctoral researcher at the National High Magnetic Field Laboratory at Florida State University in Tallahassee, Florida, where I am helping to develop and implement a mass spectrometry imaging facility for users across the world with the super powerful 21T FT-ICR mass spectrometer.A PhD is a demanding process but when
Karl Smith - PhD in Biomedical Sciences
I graduated Ulster University in 2016 with a degree in Biomedical Science with DPP (Pathology). I was then offered a PhD studentship with Dr Catriona Kelly and Professor Neville McClenaghan at CTRIC which I started in September 2016. My PhD explored the pathophysiology of Cystic Fibrosis-Related Diabetes, the most common co-morbidity associated with Cystic Fibrosis.My proudest moment was undoubtedly passing my Viva (via Skype!), but I was also proud to be given the opportunity to present my work at the UK Cystic Fibrosis Trust Conference in 2018. Through this conference, I was able to meet with people with CF and the challenges they face which was important reminder that the research I was doing mattered. I couldn't have got through this without the unwavering support of my family, who were always there for me in the good times and the bad. I am also extremely grateful for the support and mentorship of my supervisors Dr Catriona Kelly, Professor Neville McClenaghan and Dr Dawood Khan
Ryan Kelsey - PhD in Biomedical Sciences
My proudest moment was when I knew the possibility of the full transfer of my PhD project to Ulster University, the University which I loved and started my first steps towards my PhD in, and also being a PhD graduate from one of the highly reputable universities such as Ulster is a big thing which I should always be proud of. I think there is no that word that can ever express my deepest thanks and sincere appreciation to my supervisor Professor Kathryn Burnett for her ideal supervision, valuable guidance, encouragement, generous help and ultimate support throughout my PhD project. I have been really lucky to have her as a supervisor. Also my deepest gratitude to Mr Linden Ashfield, Principal Clinical Pharmacist, Antrim Area Hospital (NHSCT) for his help and endless support throughout the whole research project. Also, I could not have got through this without the support of my beloved family (my father ”Sayed”, my mother ”Gamila”, my wife “Nermeen”
Ahmed Abuelhana - PhD in Biomedical Sciences
I graduated from Queen's University Belfast with a Master's in pharmacy in 2014 and subsequently began working as a community pharmacist in the Greater Belfast area. My career began to take an unusual turn when I got involved with a small startup company who developed a novel blood glucose monitor for diabetic patients. From here, my interest in diabetes was piqued and I applied for a PhD project (somewhat optimistically!) in the Diabetes Research Group at Ulster. Nearly four years later, I'm still there working as a postdoctoral researcher. Not bad considering I never thought I had a chance of getting a PhD spot!My time within the DRG has been, and still is, fantastic. I've made life-long friends (and surprisingly few enemies!) who have been patient, helpful and a joy to collaborate with. I couldn't have got through it without them (you know who you are). Likewise, the guidance from my supervisors, Prof. Peter Flatt and Dr. Nigel Irwin, has been invaluable. I'm probably most proud of
Ryan Lafferty - PhD in Biomedical Sciences