Summary

The era of whole genome sequencing (WGS) using high-throughput sequencing (HTS) technologies has arrived and is pouring out gigabases of reads (sequences) in a day. The wealth of knowledge held within this sequencing data brings with it the promise of true personalised medicine. Technological advances of HTS technologies have been pivotal in accelerating DNA sequencing and lowering the cost per genome. However, to fully benefit from such a profusion of data, high performance, tools and systems are needed to align the sequences from the base reads and extract the information hidden within.

Biological computation is highly intensive with a large computational load that grows exponentially with the dimension of the problem domain. General Processing Units (GPUs) have been employed to accelerate computations by enabling computations to be performed in parallel [4]. Ramdas and Egan (IEEE TENCON 2005) in highlighted that “Software implementation of some sequence alignment algorithms suffer quadratic time performance” while highly parallelised solutions “provide linear time performance”. FPGA hardware offers an enhanced speed up for parallel processing and have been used to enhance the genomics computational pipeline.

This PhD will investigate the use of FPGA Hardware for parallelising computation, development of new architectures for algorithm acceleration, and other key mechanisms such as networks-on-chip interconnect strategies, to enhance the computation throughput for HTS. Performance enhancement is critical to support HTS in personalised medicine and therefore compact/efficient FPGA designs are sought to provide desktop high-performance computing (HPC).

This project is a collaboration between Dr Harkin and Lightbody on FPGA Hardware Acceleration, and Dr Shukla on bioinformatics and clinical decision making tools/tests for personalised/stratified medicine of degenerative diseases. Dr Shukla  will guide the PhD student on the computational bottlenecks within the subject domain, and will provide intricate knowledge of algorithms and bioinformatics pipelines and Dr Lightbody and Dr Harkin will advise on scalable computation and interconnect implementation strategies for FPGA acceleration. External advice from Dr Blayney will provide the medical/biological expertise and knowledge on the project area with a focus on the analysis of omics data and clinico-pathological data.

The project has access to required resources including open-access data, modern FPGA design tools, hardware platforms and test equipment. The goals for the PhD student are:

1).  Develop deep knowledge of the problem domain – with a focus on sequence alignment and computational bottlenecks.

2).  Understand the state-of-the-art in HPC solutions for computational biology and determine which bottleneck(s) could be resolved through parallelism.

3).  Investigate tools and hardware solutions for FPGAs, note with advances in acceleration stack sets this may include a combination of CPU, GPU and FPGA processing.

4).  Investigate novel architectures (scalable) for these solutions and implement chosen architecture(s), optimising for performance and providing comparative metrics against relevant prior work.

Potential impact from the PhD resides in reducing the computational cost for processing HTS data, which eventually will help to push personalised medicine more into clinical practice.


Essential criteria

  • 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.
  • Experience using research methods or other approaches relevant to the subject domain

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.

  • First Class Honours (1st) Degree
  • Masters at 70%
  • For VCRS Awards, Masters at 75%
  • Publications - peer-reviewed

Funding

    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:

    Department for the Economy (DFE)

    The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £15,285 per annum for three years. 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


Other information


The Doctoral College at Ulster University


Reviews

Profile picture of Adrian Johnston

As Senior Engineering Manager of Analytics at Seagate Technology I utilise the learning from my PhD ever day

Adrian Johnston - PhD in Informatics

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Profile picture of Xin Wei

I received the bachelor’s of engineering degree in computer science and technology from Shangrao Normal University, Jiangxi, China, in 2013; and the master’s degree in computer application and technology from the School of Mathematics and Computer Science, Fujian Normal University, China. When I was pursuing a PhD degree at Ulster University, I continued my research on face recognition and image representation.This long journey has only been possible due to the constant support and encouragement of my first supervisor. I also like to thank my second supervisor for his patience, support and guidance during my research studies. My favourite memory was the days of exercising, gathering and playing with my friends here. If I could speak to myself at the start of my PhD, the best piece of advice I would give myself would be "submit more papers to Journals instead of conferences".

Xin Wei - PhD in Computer Science and Informatics


Profile picture of Jyotsna Talreja Wassan

In the whole PhD ordeal, my supervisory team played a tremendous role:- they are three in a million. They are perfect supervisors who perfectly know which milestones or pathways to be taken during research initiatives, and they understand the roles of virtually all stages in the journey of PhD. They showcased superior abilities in managing and motivating me evoking high standards; demonstrating a commitment to excellence. Jane and Haiying guided me as their daughter and Fiona turned out to be the best of friends.I heard from “Eleanor Roosevelt” that “The future belongs to those who believe in the beauty of their dreams.” The dream with which I grew up to become a Doctor one day, has finally come true. In the journey of PhD, I embraced that a PhD is not just the highest degree in Education but rather it is a life experience where perseverance is the key. I can never forget words from my external examiner Prof Yike Guo, from Imperial College London. His words

Jyotsna Talreja Wassan - PhD in Computer Science and Informatics