We are excited to release our first community tool, Benchtop -  an open-access software for validating results generated by scientific or bioinformatic tools. This tool compares an output file against a reference and provides users with informative metrics such as precision, recall and concordance.

Data reproducibility is a huge challenge in scientific studies. Every code change or release may affect the performance and results of a software. Currently, many bioinformatic developers and researchers rely on manual benchmarking and troubleshooting. This can drastically impede the software development process and any downstream analysis workflows.

Magna Labs provides the best-in-class development tools built specifically for scientists, including automated and interactive benchmarking and testing, data curation and synthesis, and advanced data intelligence and reporting capabilities.

Our mission is to accelerate the innovation and delivery of precision science & medicine by empowering scientists to build and test bioinformatics tools with ease.

As part of our mission and efforts towards open science, we will be providing community tools to help open-source developers and academic researchers to improve the quality of their research.  Benchtop is the first of these tools to be released to the community, and complements our comprehensive and customizable commercial software testing platform by providing quick, on-demand comparison tools that can be used by researchers and developers alike.

With Benchtop, you can generate key benchmarking statistics for paired and truth/result datasets in seconds, such as:

  • Overall and stratified result-level concordance and accuracy metrics
  • Percent of matching results that have additional attributes within a specified threshold (e.g. Matches with Difference in Allele Frequency Estimate < 10%)
  • Grouped stats and charts for easy issue identification and exploration
Try Benchtop now in the link below and let us know what other features you want to see!
  • Benchtop - our free output-file comparison tool quickly analyzes and visualizes differences in your bioinformatic results

You can also check out our:

  • Tutorial - an easy somatic variant calling demo dataset to get started with
  • Documentation - including hidden features and our recommendations for effective comparison and benchmarking

And stay tuned for more open-access research tools in our Community Tools Portal (access at the top right of the page)!