Learner Profiles

Olivia Henderson

Olivia Henderson is a graduate student in genetics who is about to begin a four-year PhD program in Cancer Genetics. As part of her training, she has attended workshops on Unix, Git, and R/Python Software Carpentry.

Olivia’s supervisor is studying the effect of a drug on the transcriptome of cancer cells. For her project, she will generate six samples: three control and three drug-treated, in a lab experiment. These samples will be sent to a local research facility for RNA sequencing.

Once the sequencing is complete, the research facility will send Olivia a link to the raw data files. She will download the files and perform pre-processing using a series of bioinformatics programs on the University’s compute cluster. She will then assess the data quality and use R to analyze the processed data.

Olivia is new to Unix and has never run an RNA-Seq analysis or worked on a compute cluster before. She is understandably nervous and feels overwhelmed about managing the software she needs for the analysis.

The Nextflow and nf-core workshop will teach Olivia how to run reproducible workflows and track the software she uses, ensuring her work can be easily replicated.

Background knowledge and skills:

• Recently attended Unix, Git and R Software carpentries workshops
• Can install software using GUI’s
• Comfortable using Windows interface

Goals:

• Run an RNA-Seq pipeline using current best practices in the community
• Documenting her analysis

Isabelle Craig

sabelle Craig is a postdoctoral researcher studying the genetic causes of severe abnormalities in early human development.

Isabelle writes her own analysis pipelines using shell scripts that she’s developed over the years and is comfortable running bioinformatics programs on the University’s compute cluster.

She sent her scripts to a collaborator at another research institute, who struggled to run the pipeline because it’s heavily tied to her own research environment.

Isabelle needs to publish her own pipeline for detecting pathogenic variants to both share her work and fulfill publication requirements. Her PI has heard positive things about Nextflow and suggests she migrate her existing pipeline from shell scripts to it.

Isabelle is apprehensive about switching to a new technology and wants to publish as soon as possible.

Background knowledge and skills:

• Proficient in Unix and shell scripting
• Uses Git to manage her code
• Can install software using conda and write her own environment files

Goals:

• Convert her existing pipeline to Nextflow
• Specify her pipeline’s software requirements
• Publish her pipeline on her Github repository for broader research use