Galaxy Australia has two new interactive tools — one for proteomics, the other to help users meet European Nucleotide Archive’s (ENA) metadata regulations.
LFQ-Analyst is an analysis and visualisation tool to automate downstream statistical analysis of label-free quantitative proteomics data. It was developed by Monash University and wrapped for Galaxy by QCIF.
ENA Upload Builder helps users build metadata tables compliant with the ENA’s data submission requirements. Users can upload Galaxy data sets directly to the ENA.
Collectively, QCIF’s Bioinformatician Dr Cameron Hyde and Computational Biologist Mike Thang and Galaxy Australia Project Lead Dr Gareth Price created these tools to improve the experience of Galaxy Australia users. The ELIXIR BioHackathon 2023 was the focal point for the QCIF and international efforts to develop this tool.
“Interactive tools are a special kind of tool on Galaxy because they allow you to take an independent web application and effectively plug it into Galaxy, which empowers users to explore their data and can lead to some quite interesting results,” said Cameron.
LFQ Analyst was designed to work with MaxQuant, a popular tool on Galaxy Australia for proteomics users. Research data from MaxQuant can be fed directly into LFQ Analyst to create an interactive output.
“This cuts down the data analysis time quite considerably and shows the value of national collaboration in tool development and tool deployment into an easily accessible analysis service such as Galaxy Australia,” said Cameron.
Galaxy Australia makes genome assembly a routine activity for researchers, however the process of publishing genomic data to the ENA can, for a researcher, be unclear. Galaxy already has an existing tool to help users upload Galaxy data sets to ENA, however Cameron said it was causing “quite a bit of pain for users as they will create these tables for upload and get the metadata schema wrong.”
“There’s a very specific format that the data has to be in [for ENA]; there are required fields and controlled vocabularies, which makes it a very tedious process to do if you’re just writing these tables out in Excel and trying to upload them… It can take quite a long time for a user to figure that out,” said Cameron.
“With the ENA upload template builder, we have all these templates to help users do that. This interactive tool stays up-to-date by ingesting these templates from Github and then gives users an interactive table they can use to populate those data. They can see in real time whether their data is valid for upload to the ENA.”
Users experiencing any issues with the LFQ-Analyst and ENA Upload Builder tools can contact the Galaxy Australia support team for help.
7 million jobs and counting!
In other Galaxy Australia news, the seven millionth job was submitted to the site in October this year.
The lucky seven-millionth job was submitted by a student in Dr Kylie Munyard’s undergraduate course ‘Introduction to Bioinformatics’ at Curtin University.
Rapid uptake of Galaxy Australia by researchers, trainers and trainees demonstrates the platform’s versatility across a range of fields. Its popularity amongst bioinformatics teachers is just one of the reasons that it has been only a few months since Galaxy Australia celebrated reaching 6 million jobs!
Read more about the seven-millionth Galaxy Australia job on Australian BioCommons’ website.