Developing Capability in Bioimaging Research Software Engineering with National Programs and Partnerships

Dr Paula Andrea Martinez1,2,3,4

1National Imaging Facility, Brisbane, Australia, 2The University of Queensland, Brisbane, Australia, 3Centre for Advance Imaging, Brisbane, Australia, 4The Characterisation Community, , Australia


TheĀ  Characterisation Community is a project that underpins national capability by connecting national infrastructure and expertise. The project lead partners are three Australian national institutions (NIF, Microscopy Australia and ANSTO), plus five Australian Universities (UQ, UoM, Monash, UWA, SydUni and UoW). This project is co-funded by the Australian Research Data Commons (ARDC).

The Characterisation Community cases data-intensive science, in which informatics infrastructure, expertise and best practice are essential to turning data into new discoveries. As a collective, this community has been planing and implement strategies to overcome these challenges (first drafted strategy 2017).

Last year’s program (2019) developed and improved effective and networked relationships across Australia. By advocating a collaborative climate of innovation, we managed a series of events to outreached users at the beginner, intermediate and advanced levels. The event highlighted for this presentation is an intermediate-advanced tutorial, titled: “Automating Neuroimaging Workflows” and the target is research software engineers, and neuroscientists.

With this training, we accomplished goals and lesson learned which are worth sharing with the community:

– Automating workflows are still a key requirement from the community to advance science. This training did not only provide examples of existing workflows but also encourage attendees to develop their own workflows with the community.

– Giving participants accessibility to computational capacity. Containers and access to the Characterisation Virtual Laboratory (CVL).

– Build community and collaborations amongst practitioners and end-users by providing opportunities for professional development. We delivered in-person training connecting members of the Victorian Biomedical Imaging Capability (VBIC), and guests.


Dr Paula Andrea Martinez is leading the National Training Program for the Characterisation Community since 2019. She works for the National Image Facility (NIF) which is present in ten Australian universities and research institutes. Last year she worked at ELIXIR Europe coordinating the Bioinformatics and Data Science training program in Belgium and collaborated with multiple ELIXIR nodes in the development of Software best practices. Her career, spanning Sweden, Australia and Belgium nurtured her experience in Bioinformatics and Research Software development for complex and data-intensive science in the last 6 years. She started a career in Computer Science, later on, interested in research methods development and now outreach and advocacy in data and software best practices.



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