BIOM02 Improving and benchmarking software tools for microbiome data

Overview

This is an interdisciplinary topic, at the intersection of bioinformatics and microbiome sciences.

Microbiome data is complex, high-volume data and keeps evolving, requiring novel computational method development as the wetlab approaches changes and databases grow. Thus, novel computational methods are required to take advantage of them. We have already developed several methods that are already widely used: SemiBin, macrel, NGLess, argNorm, and others. However, we also have several needed improvements to these that we wish to implement and test.

Specific projects can be designed around each student's current skill level and learning goals and interested students are encouraged to contact Luis Pedro Coelho to discuss potential ideas.

Research engagement

Method development and evaluation

Research activities

The student will primarily be developing scripts in Python and bash

Outcomes

Benchmark data on improved performance or usability of existing tools.

Skills and experience

Some experience with Python and/or bash scripting is required, but specific projects can be designed each student's interest. An ideal student would be familiar with the Software Carpentry curriculum, including version control, but it is also possible to learn those topics by following the tutorials and with practical training. Nonetheless, students are expected to have a desire to improve their bioinformatics skills.

All potential projects will be developed in a collaborative research environment that uses open science principles and interacting with others within the group as well as users is an expected part of the work.

Start date

1 November, 2024

End date

21 February, 2025

Location

Translational Research Institute, Woolloongabba

Keywords

• microbiome
• bioinformatics
• computational biology

Contact

Luis Pedro Coelho: luispedro.coelho@qut.edu.au