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

PGR-P-292

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Key facts

Type of research degree
PhD
Application deadline
Ongoing deadline
Country eligibility
International (open to all nationalities, including the UK)
Funding
Non-funded
Supervisors
Professor Roy Ruddle
Schools
School of Computing
<h2 class="heading hide-accessible">Summary</h2>

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 />

<h2 class="heading">How to apply</h2>

<p>Formal applications for research degree study should be made online through the&nbsp;<a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees">University&#39;s website</a>. Please state clearly in the research information section&nbsp;that the research degree you wish to be considered for is &lsquo;Data visualization with gigapixel displays for comparative genomics&rsquo; as well as&nbsp;<a href="https://engineering.leeds.ac.uk/staff/257/professor_roy_ruddle">Professor Roy Ruddle</a> as your proposed supervisor.</p> <p>If English is not your first language, you must provide evidence that you meet the University&#39;s minimum English language requirements (below).</p> <p>&nbsp;</p>

<h2 class="heading heading--sm">Entry requirements</h2>

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.

<h2 class="heading heading--sm">English language requirements</h2>

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.

<h2 class="heading">Funding on offer</h2>

<p><strong>Self-Funded or externally sponsored students are welcome to apply.</strong></p> <p><strong>UK</strong>&nbsp;&ndash;&nbsp;The&nbsp;<a href="https://phd.leeds.ac.uk/funding/209-leeds-doctoral-scholarships-2022">Leeds Doctoral Scholarships</a>, <a href="https://phd.leeds.ac.uk/funding/53-school-of-computing-scholarship">School of Computing Scholarship&nbsp;</a>, <a href="https://phd.leeds.ac.uk/funding/198-akroyd-and-brown-scholarship-2022">Akroyd &amp; Brown</a>, <a href="https://phd.leeds.ac.uk/funding/199-frank-parkinson-scholarship-2022">Frank Parkinson</a> and <a href="https://phd.leeds.ac.uk/funding/204-boothman-reynolds-and-smithells-scholarship-2022">Boothman, Reynolds &amp; Smithells</a> Scholarships are available to UK applicants. &nbsp;<a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary">Alumni Bursary</a> is available to graduates of the University of Leeds.&nbsp;</p> <p><strong>Non-UK</strong>&nbsp;&ndash; The&nbsp;<a href="https://phd.leeds.ac.uk/funding/53-school-of-computing-scholarship">School of Computing Scholarship&nbsp;</a>&nbsp;is available to support the additional academic fees of Non-UK applicants. The&nbsp;<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>&nbsp;is available to nationals of China. The&nbsp;<a href="https://phd.leeds.ac.uk/funding/73-leeds-marshall-scholarship">Leeds Marshall Scholarship</a>&nbsp;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>

<h2 class="heading">Contact details</h2>

<p>For further information regarding your application, please contact Doctoral College Admissions by email:&nbsp;<a href="mailto:EMAIL@leeds.ac.uk">p</a><a href="mailto:phd@engineering.leeds.ac.uk">hd@engineering.leeds.ac.uk,</a>&nbsp;or by telephone: +44 (0)113 343 5057</p> <p>For further information regarding the project, please contact Professor Roy Ruddle by email:&nbsp;&nbsp;<a href="mailto:R.A.Ruddle@leeds.ac.uk">R.A.Ruddle@leeds.ac.uk</a></p>


<h3 class="heading heading--sm">Linked research areas</h3>