Prof Gordon Smyth Wins 2024 ARDC Eureka Prize for Research Software

We are pleased to announce that Professor Gordon Smyth of the Walter and Eliza Hall Institute (WEHI) has won the 2024 ARDC Eureka Prize for Excellence in Research Software.

Awarded annually by the Australian Museum, the Eureka Prizes honour excellence across research and innovation, leadership, science engagement, and school science in Australia. In its second year, the ARDC-sponsored Eureka Prize for research software recognises the development, maintenance or extension of software that has enabled significant new scientific research.

Currently head of WEHI’s bioinformatics division, Prof Smyth leads the development of the open-source software limma, which helps identify and interpret changes in genomic or proteomic material. This is key to understanding how diseases arise and finding new treatments for them. Having contributed to more than 70,000 scientific papers, limma is the world’s most downloaded R software package for statistical bioinformatics.

“limma has been a huge effort over a long period of time, and it changed the way that genomic data was analysed. I am grateful to all the members of my lab who contributed to the project over the years,” said Prof Smyth.

Craig Roy, Chair, ARDC, and Nick Jenkins, Research Software Specialist, ARDC, presented the award at the Sydney Town Hall on Gadigal Country on 4 September.

“It was great to see the award recognising the contribution of an important piece of software that has been around for more than 20 years. It demonstrates how critical good software is to modern research practice,” said Mr Jenkins.

Transforming Genomic Data Analysis with limma

Prof Smyth started work on limma soon after he joined WEHI in 2001. His group has developed Limma to detect changes in gene activity, specifically how genes are turned on or off.

“limma uses advanced statistical methods, borrowing information between genomic features to significantly improve the confidence with which conclusions can be made in biomedical research,” said Prof Smyth.

Understanding gene expression can help scientists identify causes of diseases like cancer, diabetes and neurological disorders, leading potentially to new treatments.

“Our goal is ultimately to learn more about how diseases originate by examining genetic disruption and how this can be controlled, while freely providing the tools we develop to others around the world so they can do the same.

“limma is used for thousands of published results every year and has been used in probably over 200 of my own papers. One example I am very proud of was our work to identify the cell of origin for the most invasive type of breast cancer (Lim et al., 2009). This work used limma’s gene set testing functionality to correlate normal mammary cell populations with breast cancer subtypes.

“Software development is fundamental for modern research but has not always been fully recognised or rewarded – it is fantastic that the Australian Museum and the Australian Research Data Commons have created this prize to highlight its critical importance in driving discovery and innovation,” said Prof Smyth.

Congratulations to All Finalists

We would also like to thank the Eureka Prize judges and congratulate the other 2 finalists for the 2024 ARDC Eureka Prize for Excellence in Research Software:

• MiniZinc team, which has developed the open-source, easy-to-learn modelling language MiniZinc for engineers, mathematicians and scientists to solve optimisation problems like rostering, scheduling and resource allocation
• MRtrix3 team, which has developed the open-source MRtrix3 software for researchers to estimate from MRI scans the complex connectivity of the human brain white matter and its disturbance in disease.

Watch and read more about the finalists. Stay tuned for our in-depth interviews with them in the coming months by subscribing to the ARDC Connect newsletter. 

Read about the 2023 winners, Dr Minh Bui and Professor Robert Lanfear, and finalists.

Also read our ongoing interview series about leading Australian research software engineers (RSEs).

Recognising Research Software

Presented in partnership with some of the nation’s leading scientific institutions, government organisations, universities and corporations, the Australian Museum Eureka Prizes have celebrated since 1990 hundreds of Australian scientists and their world-leading, world-changing contributions. 

Since 2023, the ARDC has sponsored the Eureka Prize for Excellence in Research Software to recognise and celebrate the development and maintenance of software in Australia that underpins research and scientific discovery. The award is a key part of the ARDC’s work with the research community to strengthen recognition of software, a critical enabler of data-driven research.

The ARDC continues to sponsor the Eureka Prize for Excellence in Research Software in 2025 with applications expected to open next February. Stay tuned by subscribing to the ARDC Connect newsletter.

The ARDC also sponsors a range of other research software prizes, including the Venables Award for New Developers of Open Source Software for Data Analytics, which is now open. Learn more and apply by Friday 1 November.

This article is based in part on a press release by WEHI.

The ARDC is funded through the National Collaborative Research Infrastructure Strategy (NCRIS) to support national digital research infrastructure for Australian researchers.