Investigating how to exploit ultra-high definition (UHD+) displays to visualize genomics data

Next generation sequencing makes it feasible to sample thousands of individuals to understand the causes and development of life-threatening diseases such as cancer. Today it is the scientists themselves rather than sequencing technology that is the bottleneck in the analysis of such sequencing data. This is due to a lack of suitable interactive visualization tools and, as a consequence, scientists overreliance on automated processing methods. Where visualization is used, scientists tend to rely on ordinary computer displays, despite UHD (4k) displays being a commodity and even higher definition displays (UHD+; i.e., Powerwalls with multiple 4k displays, etc.) being readily available. Therefore, the overall aim of this PhD is to investigate how UHD displays can transform how scientists use visualization to analyse genomics data.<br /> <br /> That aim has several facets, which may be divided into investigations with the following objectives (NB: any single PhD will focus on some of the objectives, not all! Similarly, a PhD will focus on a particular type of genomic analysis, not the analysis of all genomic data):<br /> <br /> 1. Investigate scientists workflow to understand the data analysis pipeline, barriers that scientists face, assumptions/simplifications they are forced to make, and where visualization is (not) currently used.<br /> 2. Determine how scientists use visualization, including characterising the tasks they perform and quantifying the amount of interaction (pan, zoom, filter, select, etc.). This will identify where inefficiencies occur and, therefore, where UHD+ displays should be beneficial.<br /> 3. Investigate the scale at which conventional visualizations break down (e.g., become inefficient to use or difficult to gain insights from). This will involve user experiments that identify the circumstances under which users become overwhelmed by the quantity of data, the extent to which the problems are addressed by: (a) increasing display resolution, (b) particular visual encodings, (c) certain interaction methods (pan, zoom, filter, select, etc.), and (d) analysis aids (analysis wear, algorithms to find patterns like this, etc.).<br /> 4. Investigate how information-rich visualizations should be designed to address the barriers, simplifications, inefficiencies and breakdowns (see above). This includes analysing the design space of information-rich visualizations for different data analysis tasks, and conducting user experiments to gather evidence about factors in the design space.<br /> 5. Develop and evaluate proof of concept software that implements solutions from the above objectives, to show how UHD+ visualization can transform scientists analysis of genomics data<br /> <br />

<p>Formal applications for research degree study should be made online through the <a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">University's website</a>. Please state clearly in the Planned Course of Study section that you are applying for <em><strong>PHD Computer Science FT,</strong></em> in the research information section that the research degree you wish to be considered for is <em><strong>Investigating how to exploit ultra-high definition (UHD+) displays to visualize genomics data</strong></em> as well as <a href="https://engineering.leeds.ac.uk/staff/257/professor_roy_ruddle">Professor Roy Ruddle</a> as your proposed supervisor and in the finance section, please state clearly <em><strong>the funding that you are applying for, if you are self-funding or externally sponsored</strong></em>.</p> <p>If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below).</p> <p style="margin-bottom:11px"><em>As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability.</em></p> <p class="MsoNoSpacing" style="text-align:start; margin-bottom:24px">Applications will be considered after the closing date.  Potential applicants are strongly encouraged to contact the supervisors for an informal discussion before making a formal application. We also advise that you apply at the earliest opportunity as the application and selection process may close early, should we receive a sufficient number of applications or that a suitable candidate is appointed.</p> <p style="margin-bottom:11px"><strong>Please note that you must provide the following documents in support of your application by the closing date of Monday 6 January 2025 if applying for the China Scholarship Council-University of Leeds Scholarship, Monday 3 February 2025 if applying for Leeds Doctoral Scholarship or Tuesday 1 April 2025 for Leeds Opportunity Research Scholarship.</strong></p> <p>If you are applying with external sponsorship or you are funding your own study, please ensure you provide your supporting documents at the point you submit your application:</p> <ul> <li>Full Transcripts of all degree study or if in final year of study, full transcripts to date</li> <li>Personal Statement outlining your interest in the project</li> <li>CV</li> </ul> <p> </p>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree. Applicants are advised to check with the relevant School prior to making an application. Applicants who are uncertain about the requirements for a particular research degree are advised to contact the School or Graduate School prior to making an application.

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.5 overall with at least 6.5 in writing and at 6.0 in reading, listening and speaking or equivalent. The test must be dated within two years of the start date of the course in order to be valid. Some schools and faculties have a higher requirement.

<p style="margin-bottom:11px"><strong>Self-Funded or externally sponsored students are welcome to apply.</strong></p> <p><strong>UK</strong> – The <a href="https://phd.leeds.ac.uk/funding/138-leeds-doctoral-scholarship-2025-faculty-of-engineering-and-physical-sciences#:~:text=Key%20facts&text=One%20Leeds%20Doctoral%20Scholarship%20is,rata%20for%20part%2Dtime%20study.">Leeds Doctoral Scholarship</a> <strong>(closing date: Monday 3 February 2025)</strong> and <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2022">Leeds Opportunity Research Scholarship</a> <strong>(closing date: Tuesday 1 April 2025)</strong> are available to UK applicants.  <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.</p> <p><strong>Non-UK </strong>– The <a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021">China Scholarship Council - University of Leeds Scholarship</a> is available to nationals of China <strong>(closing date: Monday 6 January 2025)</strong>. The <a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a> is available to support US citizens. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.</p> <p>You will be responsible for paying the overtime fee in full in your writing up/overtime year (£320 in Session 2024/25), but the scholarship maintenance allowance will continue to be paid for up to 6 months in the final year of award.</p> <p><strong>Important: </strong>Please note that that the award does <em><strong>not</strong></em> cover the costs associated with moving to the UK.  All such costs (<a href="https://www.leeds.ac.uk/international-visas-immigration/doc/applying-student-visa">visa, Immigration Health Surcharge</a>, flights etc) would have to be met by yourself, or you will need to find an alternative funding source. </p> <p>Please refer to the <a href="https://www.ukcisa.org.uk/">UKCISA</a> website for information regarding Fee Status for Non-UK Nationals.</p>

<p>For further information about your application, please contact PGR Admissions by email to <a href="mailto:EMAIL@leeds.ac.uk">p</a><a href="mailto:phd@engineering.leeds.ac.uk">hd@engineering.leeds.ac.uk</a></p> <p>For further information about this project, please contact Professor Roy Ruddle by email to <a href="mailto:R.A.Ruddle@leeds.ac.uk">R.A.Ruddle@leeds.ac.uk</a></p>