Leveraging Galaxy Australia to teach proteomics
The complete set of proteins expressed by a living organism is known as its proteome. Studying the proteome is vital to being able to understand the role of proteins within an organism and how they react to changes in their environment. It can include evaluating how changes might relate to outcomes like a particular condition, disease, or pharmaceutical treatment. The study of proteomes - proteomics - involves the analysis of all proteins, including their composition, structure, modifications, location and functions. Heavily reliant on mass spectrometry, proprietary software is commonly used to turn output data into valuable insights. This can be an impediment for newcomers, who need well designed training materials that are simple and specific for the software they will use in the lab once they learn proteomics techniques and tools.
Dr Matt Padula from the University of Technology Sydney (UTS), is a Senior Lecturer at their School of Life Sciences, and Director of the UTS Proteomics Core Facility, a facility responsible for providing the technical support and instrumentation to study proteomics. At the recent Biocommons showcase, Dr Padula shared his experience using Galaxy Australia and how it simplifies how he teaches proteomics.
‘When it comes to actually training students in proteomics you have to develop a whole lot of materials that are specific for certain pipelines and then along comes Galaxy… Galaxy has made life a little bit simpler’ – Matt
There are a number of difficulties when it comes to teaching students proteomics. Firstly, access to proprietary software is a real problem when teaching large numbers of students. To add to the challenge, many university desktops aren’t powerful enough to run the programs smoothly, often resulting in analyses taking several days. To tackle these challenges, Matt turned to MaxQuant - an open source proteomics software designed to analyse large mass spectrometric data sets. While it requires no proprietary licence, MaxQuant’s desktop version still takes considerable time to process, while also being complicated with the setting of different searches and parameters proved problematic for students.
Matt began using MaxQuant through Galaxy Australia because it removes the need for a super powerful desktop and potentially messy software installations, simplifies analysis, and can be run from anywhere, allowing for easier remote learning and access. When using the tool through Galaxy Australia, your hard drive isn’t filled with unnecessary input or output files, and workflow creations are able to continue well into the night without interruption.
For Matt, choosing to use MaxQuant for his analysis and teachings has taken the complexity out of setting up searches, and the abundance of training materials on offer means he can simply direct students over to the Galaxy Training Network website. The tutorials have come in handy for both Matt and his students:
‘I use the excellent online Galaxy tutorials to guide me in the creation of a workflow, which I can just save and call it up when I need it’ - Matt
Matt also made use of Galaxy’s new internal Training Infrastructure as a Service (TIaaS). Providing Matt with clear and live insights into the progress of concurrent tasks, it facilitated tailored support of individual students. TIaaS also allowed the administrators of Galaxy Australia to anonymously monitor the training event and fine-tune any resourcing required to provide the students with the best experience possible. The service will soon be rolled out for use by anyone interested in using Galaxy Australia for their training.
In addition to providing tools, workflows and training infrastructure, Galaxy also comes with an active community. For proteomics, the Galaxy-P community supports a multi-omics platform that provides integrative analysis and promotes collaboration. The supportive communities are made up of global partners with diverse backgrounds and perspectives, who are extremely passionate about open-source research. They are crucial in creating a supportive and engaging environment that stimulates research and encourages training opportunities for its members. Learn more about Galaxy’s proteomics community or take advantage of the proteomics training materials on the Galaxy Training Network.
Dr Matt Padula at University of Technology Sydney