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Benchling Creates Open Source Library of Lab Instrument Data Converters

publication date: May 17, 2023
author/source: Benchling



Benchling partners with Allotrope, backing industry standards and making library of open source industry data converters freely available to the scientific community

Benchling, the R&D Cloud powering the biotechnology industry, launched an initiative to standardize instrument data conversion in the scientific community at the Bio-IT World Conference. The company's efforts are twofold: Benchling is contributing to industry standards as an active member of the Allotrope Foundation Partner Network (APN) and is also creating a library of open source converters that format instrument-generated data to the Allotrope Simple Model (ASM) standard to help organizations to put these standards into practice. By making these converters available in the open source, companies of all sizes will be able to easily standardize and connect instrument data within and across their labs, ultimately driving greater industry adoption of findable, accessible, interoperable, and reusable (FAIR) data. 

Every company conducting scientific research and development, large or small, faces the same set of challenges when integrating lab instrument data into the scientific process. Lab instruments often produce proprietary data, leading to unnecessary and costly obstacles to data governance, standardization, and connectivity. Scientists are forced to manually transfer data and manage customized data pipelines, preventing them from using data at scale, creating burdens on IT and automation teams, and introducing regulatory compliance risk.

Industry leaders are showing support for Benchling's open source instrument data converters initiative.

“Today’s news illustrates the industry’s collective progress in reaching the goal of FAIR data in R&D,” said Corey Bakalarski, Chairman of Allotrope Foundation. “Earlier this year, Allotrope realized an important milestone, launching publicly available data standards using the Allotrope Simple Model, knowing that access and ease of use are critical in driving standardization. As an Allotrope partner, Benchling is furthering this mission, providing innovative, openly available tools that put standards into action.” 

“The traditional approach to lab instrument data integration, where scientists and IT teams manually build and maintain customized data pipelines is time consuming and resource-intensive,” said Mike Berke, Director of Automation at Amgen. “Benchling's announcement today shows the industry is making massive strides in standardizing the approach. IT teams can spend less time on maintaining the data infrastructure and focus more on making the data productive for science.”

"The proliferation of data formats across different lab instruments and different teams has been a major pain point. It requires lab IT to solve the same problems with data conversion again and again, ultimately slowing down process development and biomanufacturing," said Mark Southern, Senior Informatics Engineer at Resilience. "The approach Benchling is taking helps solve this pervasive challenge and makes the integrations more adaptable for future use cases."

This is the first element of Benchling’s Lab Automation product initiative to support wider adoption of FAIR data principles. Later this year, Benchling plans to build upon ASM and the open source converters to provide scientists with a complete solution to seamlessly communicate with instruments, ingest and harmonize data, and generate insights. As part of this, Benchling will continue to deliver high-demand instrument data converters for the scientific community. The first instrument data converters are for plate readers and will be available In July. Scientists and developers will also be encouraged to contribute to this open source library.

“The ability to effectively access and leverage the growing volume of R&D data is one of the most significant challenges that scientists face today. With the emergence of AI and ML, this has become even more pressing," said Shawna Wolverton, Chief Product Officer at Benchling. "Data standards from Allotrope are a great foundation. The data converters we’re putting into the open source library add another critical component. The real power comes when we have both together, along with the platforms that enable flexible, adaptable ease of use with data across the end-to-end R&D lifecycle.”



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