Bioinformatics, data and the value of open science

26 Apr 2023

Dr Maria Doyle. Image: Alan Place

University of Limerick’s Dr Maria Doyle demystifies bioinformatics for and explains some of the many applications for this multidisciplinary field.

Bioinformatics, Dr Maria Doyle explains, “combines biology, computer science and statistics to analyse and interpret biological data”.

“It involves the development and application of computational tools and techniques to understand complex biological information such as genetic sequences, protein structures and gene expression patterns,” she tells

In a world where data is so abundant that it is beyond human capabilities to handle, the multidisciplinary field of bioinformatics has become increasingly important for scientific research.

Doyle is a bioinformatician with a bachelor’s degree in biochemistry and a PhD in molecular biology. She currently works at the University of Limerick (UL).

During her studies, Doyle found that she enjoyed the computational side of her research more than carrying out experiments, so she transitioned into bioinformatics.

“I loved the combination of biology and computers, and it was (and still is) an exciting area with a lot of potential for growth.”

Bioinformaticians were recently described as “hidden heroes of the Covid-19 pandemic” for the rate at which they adapted to the challenges of the crisis and came up with methods to “dramatically reduce experimental lab time and enabled the communication of key information”.

Doyle is UL’s community manager for Bioconductor, a global open-source software project that has more than 1,000 developers and is downloaded by more than 1m users every year. She works in Prof Aedín Culhane’s group and leads the Bioconductor global training programme, website redesign, community outreach and support.

Doyle describes Bioconductor as “a critical tool in bioinformatics and computational biomedical research”.

The value of open research

Doyle is keen to emphasise the importance of open-source tools and resources in research. She mentions the Lero Open Source and Open Science Programme Office as an exciting recent initiative launched to promote and support open science. Earlier this year, Lero was awarded a European prize in recognition of its commitment to open science principles.

Doyle lists many benefits of open science including that it promotes the democratisation of research, reduces barriers to entry, increases accessibility and diversity of researchers, and encourages collaboration.

“This collaborative approach accelerates innovation, leading to the development of more efficient and accurate methods for data analysis and interpretation,” Doyle says.

Another key benefit of open-source research, according to Doyle, is that “it promotes transparency and reproducibility by making the source code available for scrutiny and use by other researchers”.

“This transparency helps ensure that methods can be accurately replicated and that any errors or biases are more easily identified and addressed.”

Doyle moved into a role in education because she enjoys “helping others learn”. From an educational perspective, she views the Bioconductor open-source software as a valuable resource that makes it easier for students and early-career researchers “to get hands-on experience in applying computational methods to real-world genomics data”.

A diverse discipline

It is an understatement to suggest that bioinformatics has a broad range of research applications. Doyle describes just some of the areas where this discipline plays a key role.

In medicine, analysis of genetic information can lead “to more effective and personalised healthcare”. It also helps with drug discovery and design.

Although, Doyle says, human genomics receives the most attention, “bioinformatics is applied to a wide range of organisms, including plants, animals and microorganisms”.

In the agricultural sector, bioinformatics helps “breeders identify and develop crop varieties that are more resistant to pests and disease, and have higher yields”.

In environmental research, bioinformatics is used “to analyse the genomes of microorganisms present in different environments, enabling researchers to monitor biodiversity and assess the health of ecosystems”.

“This information can be used to develop strategies for environmental conservation and management,” says Doyle.

Data, data and more data

With such a diverse array of disciplines feeding into bioinformatics research, one of the major challenges is the “massive volume of data and its complexity”.

As Doyle puts it: “Managing, storing and analysing such large datasets requires significant computational resources and expertise.”

As with many tech fields currently, there is a skills deficit. The interdisciplinary nature of the field requires expertise in multiple areas, including biology, computer science and statistics. “Ensuring that there are enough qualified people to meet this demand is a challenge,” says Doyle.

However, for Doyle, “genomics and bioinformatics are exciting areas to work in”. For someone looking to address complex research questions in a dynamic, collaborative and rapidly evolving field, bioinformatics is an intriguing prospect.

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Rebecca Graham is production editor at Silicon Republic