Community-led design helps create Galaxy Australia’s Proteomics Lab

Galaxy Australia’s Proteomics Lab interface.

The new Galaxy Australia Proteomics Lab is now offering a customised, user-friendly view of Galaxy Australia that provides rapid access to a range of sophisticated proteomics resources alongside the compute proteomics researchers need.

Analysing proteomics data within Proteomics Lab is a smooth experience, with common tools conveniently sorted into categories. Each tool comes with descriptions and examples of required inputs, and includes links to tutorials and support. There’s also pre-organised test data available for key tools, making it faster to get started!

The Australian Proteomics Bioinformatics Community championed the development of Galaxy Australia’s Proteomics Lab, sharing their needs in quarterly meetings, including an in-person community forum held earlier this year. Assoc Prof Matt Padula, Director of the Lipidomics and Metabolomics Core Facility within the School of Life Sciences and Proteomics at University of Technology Sydney, and proteomics community member, found the community-led design approach particularly valuable:

It’s helped us realise the breadth of requirements from researchers with varying levels of proteomics knowledge. This field's complexity has led to misunderstandings about its capabilities and how to analyse data effectively. We’ve been able to design Proteomics Lab to assist researchers analyse proteomics data appropriately, with rapid access to guidance.

Matt expects Proteomics Lab will particularly benefit researchers who are beginning their proteomics journey:

The Lab will be an efficient training tool for both researchers and coursework students learning proteomics. It provides a lower barrier to entry, and the interfaces are streamlined compared to those of the desktop versions of the software, hiding complicated and potentially unnecessary settings that should often be left alone.

Proteomics Lab pairs perfectly with the computing power of Galaxy Australia, which is underpinned by computational resources provided by AARNet, ARDC Nectar Research Cloud, the University of Melbourne, QCIF, Pawsey Supercomputing Research Centre, National Computational Infrastructure, and Microsoft Azure. Access to this fully-subsidised compute via the Galaxy Australia Proteomics Lab is expected to improve efficiency for researchers using proteomics services like those accessing Matt’s Facility:

Now researchers at my Facility won’t have to wait for desktop computers to become free, and facility staff won’t have to manage access, freeing up everyone’s time.

Proteomics Lab is the latest release in a series of Labs that support different research domains. If you are an Australian researcher with an interest in proteomics, be sure to try out the new Galaxy Australia Proteomics Lab now!

Community forum helps to shape research infrastructure for computational proteomics

The “Connections in Computational Proteomics” forum recently brought together local and international experts to network, discuss and learn. Capitalising on the convergence in Melbourne for the annual Lorne Proteomics conference, 27 researchers and service providers discussed the latest trends, challenges and advances in computational proteomics.  

The forum was open to all, plus hosted the first in-person gathering of the Proteomics Bioinformatics community. BioCommons engages with this coordinated interest group to collaboratively address community-identified challenges, including resolving gaps in the digital infrastructure available for proteomics research. The open invitation was taken up by international visitors, students and plenty of new voices who joined the ongoing conversations.

Participants explored how they could tackle challenges inherent in computational proteomics, and shared how they are addressing current problems. Dr Nikeisha Caruana, Research Fellow in Bioinformatics at the Bio21 Institute, said that: 

The forum provided an environment where those in computational proteomics and the surrounding fields could come together and brainstorm solutions to current technological obstacles. The field is relatively new professionally and many of us are scattered around Australia, and it created a fantastic environment for networking and building potential collaborations.

Paula Burton, CEO and Co-Founder of Mass Dynamics, enjoyed “talking all things computational proteomics” at the forum, especially the “great talks by [international experts] Stefan Tenzer and Mathias Wilhelm, and the vibrant discussions had on the challenges we’re facing as a field.” 

The group collaboratively identified several key challenges related to proteomics experiments, particularly in terms of ensuring experiments are well-designed and reproducible. Output data must be clear, organised, and include metadata that provides sufficient context for others to reuse or repurpose the dataset.

Participants were offered a preview of the Galaxy Australia Proteomics Lab, a customised view of Galaxy Australia that provides rapid access to a range of sophisticated proteomics resources while retaining the full power of Galaxy Australia. The preview was “my favourite aspect of the forum,” according to Dr Rohan Lowe, Facility Manager of the La Trobe La Trobe Proteomics and Metabolomics Research Platform. Rohan particularly enjoyed “the chance to suggest improvements before it is fully launched for all Australian researchers to use." Stay tuned for more on Proteomics Lab in the coming months!

The forum closed with a discussion on the next steps for the Proteomics Bioinformatics community. The group have prepared a forum report, and are excited to get to work addressing the challenges they identified! 

If your work is in computational proteomics or a related field, you are invited to join the conversation and start collaborating! Head to the Proteomics Bioinformatics webpage to learn more and get involved.

Support from the Australasian Proteomics Society (APS) for this community event is warmly acknowledged. BioCommons thanks the APS for inviting international guests, and for sharing the event details on the Lorne Proteomics conference registration page to assist in getting the word out.