Systems and Computational Biology
This page provides an overview of the projects I have undertaken with the University of Melbourne’s Systems Biology Laboratory since commencing my Ph.D in 2013, with particular focus on tools and techniques of general interest to computational biologists and bioinformaticians.
For information about my research outcomes regarding eukaryotic transcription, chromatin architecture, epithelial-mesenchymal plasticity and other molecular biology, please check out my research or contact me.
Predictive modelling of gene expression
From transcriptional regulatory elements
Virtual reference environments
A simple way to make research reproducible
NAIL (Network Analysis and Inference Library)
A software toolset for inferring, analysing and visualising regulatory networks
The NAIL project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results. These methods are designed as self-contained platform-independent components which can be called either from another program, or from a command line.
Modelling biological systems as networks (graphs) is becoming a common approach in the life sciences. However, different algorithms typically use different input and output data types, are implemented using different technologies, and are demonstrated by application to different biological problems. Because of this, the primary goal of the NAIL project is to provide a straightforward way to use network approaches in the life sciences, and to apply a variety of techniques quickly and easily on the same data.
- Download NAIL from SourceForge.net
- Read about NAIL in Bioinformatics