PhD Study : Interactome visualisation of ALS using virtual reality

Summary

Background

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.

Methods

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.

Outputs

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).

References

[1] Le Novere N, et al., Nat Biotech (2009) 27(9), 864-864.

[2] https://sbgn.github.io/.

[3] https://developers.google.com/cardboard.

Desirable Criteria

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.

Essential criteria

Applicants should hold, or expect to obtain, a First or Upper Second Class Honours Degree in a subject relevant to the proposed area of study.

We may also consider applications from those who hold equivalent qualifications, for example, a Lower Second Class Honours Degree plus a Master’s Degree with Distinction.

In exceptional circumstances, the University may consider a portfolio of evidence from applicants who have appropriate professional experience which is equivalent to the learning outcomes of an Honours degree in lieu of academic qualifications.

• Sound understanding of subject area as evidenced by a comprehensive research proposal

Funding and eligibility

The University offers the following levels of support:

Vice Chancellors Research Studentship (VCRS)

The following scholarship options are available to applicants worldwide:

• Full Award: (full-time tuition fees + £19,000 (tbc))
• Part Award: (full-time tuition fees + £9,500)
• Fees Only Award: (full-time tuition fees)

These scholarships will cover full-time PhD tuition fees for three years (subject to satisfactory academic performance) and will provide a £900 per annum research training support grant (RTSG) to help support the PhD researcher.

Applicants who already hold a doctoral degree or who have been registered on a programme of research leading to the award of a doctoral degree on a full-time basis for more than one year (or part-time equivalent) are NOT eligible to apply for an award.

Please note: you will automatically be entered into the competition for the Full Award, unless you state otherwise in your application.

Department for the Economy (DFE)

The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £19,000 (tbc) 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.

• Candidates with pre-settled or settled status under the EU Settlement Scheme, who also satisfy a three year residency requirement in the UK prior to the start of the course for which a Studentship is held MAY receive a Studentship covering fees and maintenance.
• Republic of Ireland (ROI) nationals who satisfy three years’ residency in the UK prior to the start of the course MAY receive a Studentship covering fees and maintenance (ROI nationals don’t need to have pre-settled or settled status under the EU Settlement Scheme to qualify).
• Other non-ROI EU applicants are ‘International’ are not eligible for this source of funding.
• Applicants who already hold a doctoral degree or who have been registered on a programme of research leading to the award of a doctoral degree on a full-time basis for more than one year (or part-time equivalent) are NOT eligible to apply for an award.

Due consideration should be given to financing your studies. Further information on cost of living