We are seeking a highly motivated Honours/Masters student to work on a two-semester long project to simulate DNA sequences using high performance computing. Opportunity for a further PhD study is possible depending on student’s performance in this project.
The student will work with a vibrant research team co-leaded by Dr. Minh Bui (School of Computing) and Prof. Robert Lanfear (Research School of Biology). The team is worldwide well known in the field of phylogenetics, i.e., using DNA sequence data to infer evolutionary relationships among organisms. Notably, we develop the widely used IQ-TREE software to investigate everything from understanding the origins of life on earth, to tracking the emergence and spread of the virus causing the COVID-19 pandemic.
Goals
The aim of this project is to improve the scalability of AliSim, a sequence simulator in IQ-TREE. This includes, for example:
- Improving the multi-threading implementation;
- Employing graphical processing units (GPUs);
- Adaptive combination of multi-node and multi-core parallelisation;
- Parallel I/O;
- Benchmarking on the Gadi supercomputer at the National Computational Infrastructure.
Requirements
Strong C++ programming skills and experiences in HPC. Basic knowledge of Evolutionary Biology is helpful but not required.
Background Literature
- AliSim: A fast and versatile phylogenetic sequence simulator for the genomic era; N Ly-Trong, S Naser-Khdour, R Lanfear, BQ Minh
- AliSim-HPC: parallel sequence simulator for phylogenetics; N Ly-Trong, G MJ Barca, BQ Minh