Software Development

The following open source projects have either been designed by or had significant input into their design and implementation from our experts. (See here for archived projects.)

Bionitio. A template for command line bioinformatics tools in various programming languages. The purpose of the tool is to provide an easy-to-understand working example that is built on best-practice software engineering principles. It can be used as a basis for learning and as a solid foundation for starting new projects. github.com/bionitio-team/bionitio. Published in Gigascience, 2019: academic.oup.com/gigascience/article/8/9/giz109/5572530

Bpipe. A bioinformatics pipeline. github.com/ssadedin/bpipe. Published in Bioinformatics, 2012: bioinformatics.oxfordjournals.org/content/early/2012/04/11/bioinformatics.bts167.abstract. Collaboration with Murdoch Children’s Research Institute.

Degust. A web tool to help analyse, visualise and fully appreciate Differential Gene Expression data from RNA-seq experiments. drpowell.github.io/degust. Collaboration with VBC, Monash University.

Dovex. A web based tool to quickly provide an interactive overview and enable quick exploration of datasets. github.com/supernifty/dovex

Gurita. A command line tool for analysing and visualising tabular data in CSV or TSV format. bjpop.github.io/gurita

Janis. A framework for creating specialised, simple workflow definitions that are then transpiled to Common Workflow Language or Workflow Definition Language. janis.readthedocs.io. Developed as part of the Portable Pipelines Project, a collaboration with Peter MacCallum Cancer Centre and WEHI.

sEst. An R-package for estimating sex from DNA methylation microarray data. github.com/jungch/sest

SRST2. Short Read Sequence Typing for Bacterial Pathogens. github.com/katholt/srst2. Published in Genome Medicine, 2014: genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0090-6. Collaboration with Prof Kat Holt (Monash University) and Prof Mike Inouye (Baker Institute).

TotalPerspectiveVortex. Provides an installable set of dynamic rules for the Galaxy application that can route entities (Tools, Users, Roles) to appropriate destinations based on a configurable yaml file. total-perspective-vortex.readthedocs.io

Varlap. A tool aimed at quality control of DNA variants arising from sequencing alignments. github.com/bjpop/varlap