Andrew Severin

Andrew Severin

His PhD was in Biophysics/NMR spectroscopy. He did a Bioinformatics Postdoc in Soybean genetics and now runs the Genome Informatics Facility at Iowa State University. He is passionate about evolution and the science behind the genome. There is so much we don't know about how the elements in a genome interact to create the fine balance of gene expression, modification and 3D structure that create the dynamic range of phenotypes we observe. As sequencing technology continues to improve and the cost continues to decrease, we will be able to ask more complex questions that increase our understanding via comparative and translational genomics.

Workflows

Workflow languages are becoming common practice in bioinformatics and many big data sciences to automate pipelines. As a person advances in your bioinformatics knowledge, they tend to create many scripts commonly in bash, python, perl, insert your favorite language, etc to make the processing of data easier. Longer scripts can be created in these languages but each project is unique and tend to have exceptions that would have to be accounted for resulting in more and more complicated script. Workflows permit the user to keep the scripts they have written in different languages or found on the internet and put them into processes that then can be called by the workflow script. This makes all those scripts we have written much more module. In addition, workflow languages abstract away the submission and tracking of jobs making the program more universally transferrable between computers.

nextflow

nextflow is a workflow framework that can be used by a bioinformatician to integrate all of her/his/their bash/python/perl/other scripts into a one cohesive pipeline that are portable, reproducible, scalable and checkpointed. Nextflow is its own DSL (Domain Specific Language) that extends a language called groovy which is an extension of Java that has language feature similarity to Python, Ruby and Smalltalk.