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Reproducibility, portability, scalability

Leah Kemp’s passion about coding is making a difference. 

Leah Kemp

She and her ESR team have been developing pipelines to analyse the genomes of patients with rare genetic disorders that haven't been able to be diagnosed with the type of genetic testing currently available to New Zealanders. 

And although these pipelines were developed with this purpose in mind, they can also analyse genetic data from different species, with different reference genomes and databases

The work has a heavy focus on reproducibility, portability, scalability.  This means the pipelines are publicly available through open source software. 

“We actively encourage collaborative coding and New Zealand wide standardisation in the analysis of genetic data, and we employed tools and coding best practices to ensure the pipelines can be deployed on different compute infrastructures - a laptop, a server, a high-performance cluster,” she said. 

If you're lucky enough to have access to NVIDIA parabricks and graphics processing units (GPU's) (keep an eye on NeSi) you can use these same pipelines to analyse your data with insane speed! It's akin to this:

Use and contribute to the pipelines here: human genomics pipeline and vcf annotation pipeline

More recently, Leah has been analysing small RNA-Seq and RNA-Seq datasets in research looking into diseases such as type 2 diabetes. exploring data communication and data visualisation in this space.

About Leah

Leah trained in Ecology, completing a BSc and MSc in Ecology and Biodiversity at Victoria Universitty of Wellington - Te Herenga Waka. 
Her MSc thesis involved studying the population genetic structure and genetic diversity of one of New Zealand's culturally and commercially important fisheries species, Araara/Trevally, providing useful insights for sustainably fishing this species.

During her studies she spent time taking courses in statistics, taking up the quality free training from organisations such as software carpentry and data carpentry and undertaking self-directed learning in how to analyse and visualise data. “I didn't realise at the time, but I was naturally moving into the wonderful world of bioinformatics!”

“After university I was lucky to be snapped up by the amazing Human Genomics Group at ESR, here I've had a crash course in full on bioinformatics as I immersed myself in the Genomics Aotearoa bioinformatics capability and clinical genomics projects.”

Bioinformatics and coding are literally for anyone! I every much relate to Alana Alexander who eloquently describes how entering the bioinformatics field can happen through a non-conventional route and how some coding experience can open up a world of opportunities in research analyses and beyond, even if you don't want to go full bore into bioinformatics. As Alana mentions, stubbornness can become your most useful personality trait!

“I recon the next generation will all be coders to some degree, hooray!”

Leah's areas of expertise:
•    Bioinformatics
•    Population genetics
•    Clinical genomics
•    Exome analysis
•    Small RNA-Seq and RNA-Seq analysis
•    Data visualization