Mentor program breaking down barriers with Nextflow/nf-core

Dr Georgina Samaha, Bioinformatics Group Lead at the Sydney Informatics Hub and BioCommons team member.

A mentorship in the Nextflow and nf-core program has been awarded to Australian BioCommons bioinformatician Dr Georgina Samaha, Bioinformatics Group Lead at the Sydney Informatics Hub. The highly competitive Nextflow/nf-core mentorship program will pair Georgie with an experienced developer to work closely on a project that she is particularly passionate about: breaking down barriers that prevent life sciences researchers from using high performance computing (HPC). 

The ever-increasing scale of life sciences data means that researchers need to process or analyse their data with large-scale compute resources. This can be a daunting process, particularly for those with less experience writing code or interacting with computers on the command-line interface. Georgie plans to address these challenges:

“I will create new resources and share my learnings about Nextflow/nf-core with the broader life science research and bioinformatics communities to make their lives easier, give them a starting point and increased confidence in approaching the difficult and intimidating aspects of their work on HPCs.”

Georgie is heavily involved in improving access to command-line infrastructure for life sciences researchers as part of the BioCommons Bring Your Own Data Expansion Project. She applied to the Nextflow/nf-core mentorship program as she frequently encounters researchers who need her help to run bioinformatics pipelines on HPCs. nf-core offers community-supported reproducible pipelines that simplify data processing. These pipelines are popular in the bioinformatics community, but researchers still face challenges in using them such as understanding the resource requirements and running the pipelines efficiently. Georgie’s project aims to address these challenges to make life sciences researchers’ lives easier. She also aims to demonstrate to national HPC providers that there is significant value in improving access to large-scale compute resources for life sciences researchers.

Georgie expects that her involvement in the mentorship program will greatly increase the level of support she can offer to researchers, plus provide her valuable experience coding in Nextflow. Georgie will bring this newfound expertise to her role at Sydney Informatics Hub and the BioCommons to empower the researchers she works with, plus share her knowledge with partners including QCIF, NCI and Pawsey.

Georgie’s mentorship started in June and will run until the end of September 2023. You can find out more about the Nextflow/nf-core mentorship program at the nf-core website, and stay tuned to hear from Georgie later in the year!