Platforms & Software
Platforms & Software
Platforms
Melbourne Bioinformatics has provided support for the development of the following platforms.
| Name | Description | Link |
|---|---|---|
| ABLeS (Australian BioCommons Leadership Share) | Compute, storage and tools for creating and sharing community data assets such as reference genome assemblies. Co-funded by Bioplatforms Australia, NCI and Pawsey. | Australian BioCommons |
| Galaxy Australia | An open, web-based platform for accessible, reproducible and transparent bioinformatics research. Melbourne Bioinformatics co-manages Galaxy Australia alongside Australian BioCommons, QCIF and AARNet. | Galaxy Australia |
| Genomics Virtual Laboratory (GVL) | A computational workbench providing a highly accessible cloud-based genomics analysis environment preconfigured with best practice genomics tools and supplemented with comprehensive tutorial materials and protocols, managed services and user support. | GVL is no longer supported |
| GenoVic | A system for managing and sharing clinical genomic data between laboratories, clinicians, patients and researchers, used by six laboratories for accredited testing and data management. Developed by the Melbourne Genomics Health Alliance; Melbourne Bioinformatics provided early support by hosting the GenoVic software development team. | Melbourne Genomics |
| Human Genomes Platform Project | An initiative to develop a common toolbox based on global standards for the sharing of human genomic data between Australian institutions. Part of the NCRIS-funded Human Genomes Informatics Initiative. | Australian BioCommons |
| Janis | A framework for creating specialised, simple workflow definitions that are then transpiled to Common Workflow Language or Workflow Definition Language. Developed as part of the Portable Pipelines Project, a Melbourne Bioinformatics collaboration with Peter MacCallum Cancer Centre and WEHI. | Janis |
| Microbial Genomics Virtual Laboratory (microGVL) | An easily instantiated computer image based around Galaxy with a defined set of microbial-specific tools and reference data is an ideal solution for enabling standardisation between laboratories. | microGVL is no longer supported |
| Seqera Platform | A pilot project investigating the viability of a fully subsidised centralised command post for Nextflow pipelines as a service for Australian researchers. An Australian BioCommons BYOD Project, supported by Pawsey, NCI, SIH, QCIF, and Melbourne Bioinformatics. | Australian BioCommons |
| ToolFinder | Resource for determining where bioinformatics tools and software are installed across the major Australian compute services. | Australian BioCommons |
| WorkflowFinder | Resource for determining where bioinformatics workflows are installed across the major Australian compute services. | Australian BioCommons |
Software
The following open source projects have either been designed by or had significant input into their design and implementation from Melbourne Bioinformatics experts.
| Name | Description | Link |
|---|---|---|
| Bioinitio | 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. Published in Gigascience, 2019. | Bionitio |
| Bpipe | A bioinformatics pipeline. Published in Bioinformatics, 2012. Collaboration with Murdoch Children’s Research Institute. | Bpipe |
| Degust | A web tool to help analyse, visualise and fully appreciate Differential Gene Expression data from RNA-seq experiments. Collaboration with VBC, Monash University. | Degust |
| Dovex | A web based tool to quickly provide an interactive overview and enable quick exploration of datasets. | Dovex |
| Gurita | A command line tool for analysing and visualising tabular data in CSV or TSV format. | Gurita |
| Janis | A framework for creating specialised, simple workflow definitions that are then transpiled to Common Workflow Language or Workflow Definition Language. Developed as part of the Portable Pipelines Project, a collaboration with Peter MacCallum Cancer Centre and WEHI. | Janis |
| sEst | An R-package for estimating sex from DNA methylation microarray data | sEst |
| SRST2 | Short Read Sequence Typing for Bacterial Pathogens. Published in Genome Medicine, 2014. Collaboration with Prof Kat Holt (Monash University) and Prof Mike Inouye (Baker Institute). | SRST2 |
| 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. | TotalPerspectiveVortex |
| Varlap | A tool aimed at quality control of DNA variants arising from sequencing alignments. | Varlap |
Software (archived)
The following open source projects have either been designed by or had significant input into their design and implementation from Melbourne Bioinformatics experts. (Attribution will sometimes refer to our previous name of VLSCI.)
The software listed here is no longer supported. Some information and links may be out of date.
| Name | Description | Link |
|---|---|---|
| ABRicate | Mass screening of contigs for antimicrobial and virulence genes. | ABRicate |
| Annokey | Gene-based search for key-terms in the NCBI gene database and associated PubMed abstracts. Published in Source Code for Biology and Medicine, 2014. Collaboration with the GEL lab, Department of Pathology, University of Melbourne. | Annokey |
| Burgene | An interactive web-server for prioritising genes by comparing burden of predicted pathogenic mutation in cases compared to a reference population (ExAC and gnomAD). | |
| Cpipe | A shared variant detection pipeline designed for diagnostic settings, published in Genome Medicine, 2015. | |
| FAVR | Filtering and Annotation of Variants that are Rare. Published in BMC Bioinformatics, 2013. Collaboration with the GEL lab, Department of Pathology, University of Melbourne. | FAVR |
| Genomics Virtual Laboratory | A practical bioinformatics workbench for the cloud. Published in PLOS ONE, 2015. | GVL Project |
| Hi-Plex | A streamlined highly-multiplexed PCR-based target-enrichment system for massively parallel sequencing suitable for an extensive range of clinical and research applications. Hi-Plex is complemented by software for primer design and variant calling. | |
| HiTIME | High-resolution Twin-Ion Metabolic Extraction. Collaboration with School of Chemistry, University of Melbourne. Published in Analytical Chemistry, 2015. | HiTIME |
| Methpat | A program for summarising CpG methylation patterns. Collaboration with the Ludwig Institute for Cancer Research. Published in Gigascience, 2015. | Methpat |
| MLST | For scanning contig files against PubMLST typing schemes. | MLST |
| Nullarbor | Pipeline to generate complete public health microbiology reports from sequenced isolates. | Nullabor |
| Predictein | Structure and function prediction of proteomes. | Predictein |
| Prokka | A software tool for the rapid annotation of prokaryotic genomes. Published in Bioinformatics, 2014. Collaboration with VBC, Monash University. This high-profile software has reached over 10,000 citations. | Prokka |
| Rover | Read-pair overlap considerate variant-calling software for PCR-based massively parallel sequencing datasets. Published in Source Code for Biology and Medicine, 2014. Collaboration with the GEL lab, Pathology, University of Melbourne. Part of the Hi-Plex project. Simple, low-cost, modular targeted DNA sequencing technology. Supported by NHMRC project grant APP 1025879. | Rover |
| Rubra | A bioinformatics pipeline. Presented at the Bioinformatics Open Source Conference, 2013 (BOSC2013). Used by many bioinformatics projects at Melbourne Bioinformatics. | Rubra |
| Snippy | Rapid haploid variant calling and core SNP phylogeny. | Snippy |
| UNDR ROVER | A fast and accurate DNA mutation detector for targeted DNA sequencing. Published in BMC Bioinformatics, 2016. Created by Melbourne Bioinformatics experts A/Prof Daniel J. Park, Roger Li, Edmund Lau, Peter Georgeson, Dr Tú Nguyen-Dumont and Dr Bernard J. Pope. | UNDR ROVER |
| Over 50 ‘recipes’ for Homebrew Science to make it easy for people to install bioinformatics software have been published by our experts. | Homebrew Science |