Timothy R. Fallon¹,⁶*, Daniel Bryce²,⁶, Jacob Beal³, Jeremy Cahill⁴,⁶, Mark Dörr⁵,⁶ 1=University of California, San Diego, USA
2=SIFT LLC, USA
3=Raytheon BBN, USA 4=Metamer Labs, USA
5=University of Greifswald, Germany
6=Bioprotocols Working Group (http://bioprotocols.org)
*=presenter
Protocols are of foundational importance to biological research - every researcher implicitly learns how to write and interpret these documents. But, protocols receive surprisingly little formal attention: very few graduate curricula include instruction in writing protocols, and detailed protocol documents are typically private to a particular laboratory, making it difficult to compare protocol norms across laboratories. Although the inclusion of sufficient detail to enable independent reproducibility is the goal of all published materials and methods sections in scientific manuscripts, these sections often omit details that are necessary for others to be able to use the protocol effectively. Projects such as Protocols.io (https://protocols.io/) have provided a critical and timely resource for a lowered barrier to edit, share, and run biological
protocols. But Protocols.io protocols or similar alternatives, are not machine readable, making them unable to be run on laboratory automation platforms, and unable to be checked for completeness, meaning that shared protocols are still often insufficiently specified for use by others.
The Bioprotocols Working Group (http://bioprotocols.org/) is an open community working to address these problems by developing an open source, freely available, and widely interoperable software & protocol standard, known as the Laboratory Open Protocol (LabOP; formerly known as the Protocol Activity Modeling Language or PAML). Here we present recent advances in LabOP, such as in-development protocol prototype which uses the SiLA2 standard (https://sila-standard.com/) to execute operations on physical scientific instruments, and the “LabOP editor” a web-based low-code
GUI for editing and sharing LabOP protocols via visual scripting. Future directions include the ability to run the same LabOP protocol on two cloud lab providers, Strateos and Emerald Cloud Lab. The Bioprotocols Working Group encourages interest and feedback from the Global Biofoundry Alliance. Those wanting to participate in the open development process or use LabOP should visit http://bioprotocols.org.
This work was supported by a National Institute of Environmental Health Sciences (NIEHS) fellowship to T.R.F. (F32-ES032276), and by Air Force Research Laboratory (AFRL) and DARPA contract FA8750-17-C-0184. This document does not contain technology or technical data controlled under either U.S. International Traffic in Arms Regulation or U.S. Export Administration Regulations.
