Learner Profiles
Olivia Henderson
Olivia Henderson is a graduate student in Genetics who is about to starting a four year PhD program in Cancer Genetics. She has attended Unix, git and R/Python Software carpentries as part of her PhD training induction.
Olivia’s supervisor is studying the effect of a drug on the transcriptome of cancer cells. She will generate 6 samples (3 control and 3 drug treatment) in a lab experiment. These samples will be sent to a local research facility for RNA sequencing.
The research facility sends a link to the raw data files to Olivia once the sequencing is completed. Olivia will download the files and perform pre-processing. Pre-processing will be done by running a series of bioinformatics programs on the University’s compute cluster. She will then assess the quality of data and uses R to analyse the processed data.
Olivia is new to Unix and has never run and RNA-Seq analysis before or worked on a compute cluster. She is very nervous about working on the cluster and feels overwhelmed about managing the software she will need to use for the analysis.
Workflow management with Nextflow and nf-core will teach Olivia how to run reproducible workflows and how to track the software she is working with so that her work can be reproduced.
Isabelle Craig
Isabelle is a PostDoc working on the genetic causes of severe abnormalities that occur in early human development.
She writes her own analysis pipelines using shell scripts that she has developed over years and is comfortable running bioinformatics programs on the University compute cluster.
She has sent her scripts to a collaborator in another research institute and they are having problems running her pipeline as it is heavily tied to her own research environment.
Isabelle needs to publish her own pipeline for the detection of pathogenic variants so that others can use her work and so she can publish. Her PI has heard good things about Nextflow and wants her to migrate her existing pipline from a shell script to nextflow.
Isabelle is wary about migrating pipeline to a new techology and wants to publish asap.