We receive support from the Australian Biocommons Apollo project and have used this to create genome browsers for new genomes generated by our group.

Reproducible analysis for publications

We work with large genomic, transcriptomic and proteomic data, often combining outputs from multiple analyses to generate inferences. A typical project will involve many small shell scripts, some command-line tools written in Python and lots of R code. We use github to manage this complexity, collaborate and share our work. For new projects we suggest starting with our project template.

Examples of publications with associated code repositories:

  • Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum
  • Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts.
  • Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common Octopus Octopus vulgaris
  • Comparative Proteomic Analysis of Slime from the Striped Pyjama Squid, Sepioloidea lineolata, and the Southern Bottletail Squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae)