🇦🇺 Senior Bioinformatician at the Sydney Informatics Hub and the Australian BioCommons 🇦🇺
I enjoy wearing many hats - most of which aim to improve the accessibility of computational and data-heavy research for scientists, and to develop technical resources that help translate bioinformatics findings to actionable insights towards epidemiology and conservation purposes.
Always keen to chat, and discuss open-source projects - feel free to get in touch, and take a peek at a few repos below!
🎓: Google Scholar
📧: frederick[dot]jaya[at]sydney.edu.au
Significant contributions to scientific libraries, packages, and tools during my time at the Australian National University. Mainly Python and R.
- 🧬 cogent3: A python library for analysis of genomic sequence data with a flexible plugin architecture to interface with other tools.
- PoolTools: An easy-to-use Shiny interface to R packages for the design and analysis of pooled data.
- PoolPower: An R package for power and sample size calculations for designing optimal pool testing surveys.
Development of scalable Nextflow pipelines, most are optimised for use on institutional or national HPCs. Some fortunate enough to have led to publications!
- 🧪 rec-bench: Nextflow pipeline for benchmarking tools that detect recombination in virus sequences.
- 🐨 phasco-genes: Pre-processing pipeline for finding genome-wide associations to environmental variables.
- 🦠 ONT-bacpac-nf: Nextflow pipeline to assemble bacterial genomes from Nanopore long read data and identify AMR genes.
Past workshop content to help lower the barrier to bioinformatics.
- 🔀 hello-nextflow: A hands-on introduction to Nextflow. Written for biologists, by biologists. Part of the National Bioinformatics Training Cooperative.
- 🌴 spw23_iqtree: What is IQ-TREE and how do you use it? Part of the Sydney Phylogenetics Workshop.
Non-bioinformatics miscellanea when a big coding/technical itch needs to be scratched.
- ⌨️ zmk-config: Key mappings to accompany custom mechanical keyboards.
- 📄 dotfiles: Lazy ass bash aliases and configs for F1 CLI-ing.
- 👾 chickenpy: Cooking is modular. OOP is modular. Why not try combine the two? Might be usable one day.