Led by our software expert Anthony Marty, Melbourne Bioinformatics’ role in the Australian Genomics Health Alliance has extended to providing a technical assessment of several well-developed, prototyped tools which enable sharing of curated genomic variant data. The preferred tool will be adopted across Australian pathology laboratories for use in research and clinical diagnoses. When known […]
Dr Natalie Thorne, Project Manager, Clinical Bioinformatics & Genomics (Program 2, Project 4)
|Australian Genomics Health Alliance (Australian Genomics)||LEAD INSTITUTE|
$25m from the NHMRC Targeted Call for Research into Preparing Australia for the Genomics Revolution in Healthcare
Melbourne Bioinformatics is one of 80 partners across Australia and internationally who are participating in this exciting project which aims to integrate genomic medicine into Australian healthcare. Members include clinical genetics services, research institutes, public pathology laboratories, hospitals, universities, professional bodies and patient advocacy groups. Their task? How can this relatively new practice of genome sequencing to aid in diagnoses be implemented into clinical practice in a responsible, reliable way?
Our involvement in this project is through our existing relationship with Dr Natalie Thorne, Clinical Bioinformatics and Genomics Project Manager and Stream Lead, Innovation and Adoption, Melbourne Genomics. Andrew Lonie and Bernard Pope have led our effort to assist in curating a registry of clinical pipelines already in use throughout Australia with the aim of developing a standard vocabulary for pipeline comparison, and a structured representation for improved pipeline elucidation and visualisation. This involves finding out what is being used around the country, making sure these tools are searchable and findable and that they are documented in language which is uniform. For each workflow, the aim is to establish what version of a software is being used, what databases are being accessed and what filtering processes are being employed.
In May 2017, Melbourne Bioinformatics hosted a talk and workshops for Melbourne researchers by Community Engineer and co-founder of the Common Workflow Language (CWL) Project, Michael R. Crusoe. CWL is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high-end computing environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL has been developed by an informal, multi-vendor working group consisting of organisations and individuals aiming to enable scientists to share data analysis workflows.
In the field of bioinformatics, we are helping to bring the discipline and practices of computer scientists into the world of our life scientists, to ensure clinical practices arising from the new biology are FAIR: findable, accessible, interoperable and reusable.
To gain a familiarity with CWL, work through “A Gentle Introduction to the Common Workflow Language”.
Michael’s one-hour talk and two-hour workshop were both recorded and are now accessible via our Video archive.
Australian Genomics is Australia’s link to the Global Alliance for Genomics and Health.
In early August, Bernie Pope, Maillie Gall and Melbourne Genomics’ Natalie Thorne attended the inaugural AGHA conference in Brisbane and presented a poster on their current Australian Genomics project. The poster was featured at the following Human Genetics Society of Australasia conference, also held in Brisbane.