Study level

Honours

Vacation research experience scheme

Faculty/School

Science and Engineering Faculty

School of Computer Science

Topic status

We're looking for students to study this topic.

Supervisors

Dr Dimitri Perrin
Position
Senior Lecturer
Division / Faculty
Science and Engineering Faculty

Overview

CRISPR-Cas9 technology allows us to modify virtually any gene in any organism of interest. It has generated a lot of interest, both in the research community and the general population.

One of the crucial components of CRISPR experiments is the design of the “guide RNAs” that will control where modifications occur.

We have developed a software pipeline, named Crackling, to identify safe and effective guide RNAs across entire genomes. We're now seeking to develop a visualisation to communicate the results produced by the pipeline.

Research activities

This project will require you to apply your software engineering skills to biological data in order to produce an effective and interactive visualisation.

A starting point could be to integrate with the UCSC Genome Browser. For those with a creative mind, this project may provide you with the platform to express your ideas.

Outcomes

In this project, you'll review literature and existing visualisations in order to gain an understanding of what is currently available. You'll either expand upon these or create a new tool that can improve the communication of CRISPR guide RNA design.

During this, you will:

  • gain experience working with a bioinformatics pipeline
  • learn how to create visualisations for improving the communication of scientific results
  • have the opportunity to work alongside researchers working in the field of bioinformatics.

Skills and experience

This project requires that you have strong programming skills. Some experience with visualising data would be beneficial but not required. No prior experience with biology is necessary, but you must be willing to learn relevant concepts.

Keywords

Contact

Contact the supervisor for more information.