Software Working Group

Purpose:

To make it easy to do rigorous analysis of AIRR-seq data.

The goal of our working group is to encourage practices that enable software tools to work, and to work with one another. As such we have been assembling data sets that people can use to test functionality of various programs. We have also had discussions about containerization using Docker, which is a technology that allows a program to be self-contained and be mostly immune from differing versions of software dependencies. We have also discussed a Common Workflow Language (CWL) schema that would allow programs to be run with standardized input fields.

Our current first priority is standardized simulated data sets with known properties. We are currently working to define and implement summary statistics that can be used to characterize simulated data sets and compare them to real data sets. After that we can “benchmark the benchmarks” to decide how realistic the various simulations are.

Goals for 2018:

• Finalize list of summary statistics to use for validation of repertoire simulation tools and finish implementing these summary statistics in software
• Perform comparison of simulation tools using these summary statistics and write up results

Members

Leader: Frederick "Erick" Matsen

Members: Branden Olson, Duncan Ralph, Erick, Chaim Schramm, Christian Busse, Corey Watson, Inimary Toby, Jason Vander Heiden,  Mikhail Shugay, Simon Frost, Uri Laserson, Victor Greiff, William Lees, Jian Ye, Enkelejda Miho

Resources

Visit the Software Working Group Project.