Study level

  • Honours

Faculty/School

Faculty of Science

School of Computer Science

Topic status

We're looking for students to study this topic.

Research centre

Centre for Data Science

Supervisors

Associate Professor Dimitri Perrin
Position
Associate Professor
Division / Faculty
Faculty of Science

Overview

The CRISPR-Cas9 technology allows the modification of 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 are seeking to expand and improve various aspects of our current method.

This project may entail the application of:

  • high-performance computing
  • cloud computing
  • visualisation
  • web application development.

Research activities

This project will require you to apply your computer science and engineering skills in order to improve upon the existing method. There are various aspects of our software that you could contribute, each equally as important as the others. One starting point could be to explore ways to minimise the size of our binary-encoded data structure. Another, could be using cloud technologies to deploy a highly available and scalable offering of the pipeline at low cost. Or, developing a web-based visualisation tool to be embedded on our research website.

Outcomes

In this project, you will review literature and the existing bioinformatics pipeline in order to gain an understanding of what is currently available. You will have the opportunity to be a contributor to an open source project where your work could be made publicly available soon after development. During this, you will gain experience in working with a bioinformatics pipeline and have the opportunity to work alongside researchers working in the expanding field of bioinformatics.

Skills and experience

This project requires that you have strong programming skills. Some experience with either Python, the C programming language, cloud computing or visualisation techniques would be beneficial but not required. Your creativity would be an important contribution no matter which aspect of the project you were to work on, including writing code.

No prior experience with biology is necessary, but you must be willing to learn relevant concepts.

Keywords

Contact

Contact the supervisor for more information.