Ensuring a suitable slice of the computational pie for Australian proteomics
Creators: name: Gustafsson, Ove Johan Ragnar
name: Price, Gareth
name: Padula, Matthew P
name: Thang, Mike WC
name: Pukala, Tara L
name: Crossett, Ben
name: Schittenhelm, Ralf B
name: Sadowski, Pawel
name: Butterworth, Nathaniel P
name: Chew, Tracy
name: Young, Clifford
name: Carroll, Luke
name: Lowe, Rohan GT
name: Hyde, Cameron J
name: Shah, Anup D
name: Downton, Matthew
name: Winter, Uwe
name: Manos, Steven
name: Christiansen, Jeffrey H
Publisher: name: Zenodo
Year: 2023
Subjects: subject: Proteomics
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Galaxy Australia
subject: Cloud
subject: HPC
subject: Community engagement

description: <em>The lightning talk and poster included here were presented at the 28th Annual Lorne Proteomics Symposium, February 2023. </em> Traditional high performance computational infrastructure in Australia has not been designed for bioinformatics, and this presents challenges to many researchers in the life sciences, including proteomics. The Australian BioCommons has been engaging with members of the national proteomics community, including the Australasian Core Facilities group, since 2020 to understand the specific bioinformatics challenges facing researchers. Challenges noted include a lack of sufficient compute (memory, cores), an imbalance between the software available for model and non-model organisms, the constant tension presented by the need for both open source and proprietary software, and the presence of high intellectual barriers that prevent the community from adopting new solutions to their challenges, whether these solutions are software, hardware or policy based. In this presentation we will introduce the current scope of activities that the Australian BioCommons is coordinating in consultation with the Australian proteomics community that are aimed at addressing the challenges noted above. These activities range from development of discovery services for tools and workflows on local systems, deployment of tailored software and infrastructure that address proteomics requirements, establishing processes to allow information sharing with the broader community, and the beginnings of a collective national informatics training effort that supports the proteomics community. Specific examples include creating reusable/scalable DIA-NN workflows for use on a variety of computational infrastructures, and work with the freely accessible Galaxy Australia online bioinformatics workbench (https://usegalaxy.org.au/) to increase the size and complexity of possible MaxQuant analyses, make popular interactive tools like LFQanalyst available and expand the proteomics tool set available. Finally we are collectively exploring the use of the ARDC Nectar Cloud (https://ardc.edu.au/services/ardc-nectar-research-cloud/) for proteomics and development of a hosted proteomics-specific instance of Galaxy Australia. We invite the Australian proteomics community to join us in the on-going effort to make sure that they have a fit-for-purpose and meaningful slice of the computational pie: the right tools, workflows and reference data, accessible on suitable compute systems, so that we can collectively empower both experts and end users within Australian proteomics. If you would like to join the conversation, you are welcome at our new quarterly meeting series, where we discuss current community challenges and feature presentations from both local and international proteomics researchers. You can also join our Google Group: https://www.biocommons.org.au/proteomics