LabOP - an open specification for laboratory protocols, that solves common interchange problems stemming from variations in scale, labware, instruments, and automation.

Project idea 1: Software, hardware, and wetware building LabOP with simultaneous language & protocol development & test executions

• Topics: Software standard development, Laboratory automation, Biology
• Skills: Python, Semantic Web Technologies (RDF, OWL), interest to think about describing biological & chemical laboratory processes
• Difficulty: Moderate
• Size: Large (350 hours)
• Mentors:
  1. Tim Fallon
  2. Dan Bryce

About: The Laboratory Open Protocol Language (LabOP)

See link: https://bioprotocols.github.io/labop/

LabOP is an open specification for laboratory protocols, that solves common interchange problems stemming from variations in scale, labware, instruments, and automation. LabOP was built from the ground-up to support protocol interchange. It provides an extensible library of protocol primitives that capture the control and data flow needed for simple calibration and culturing protocols to industrial control.

Software Ecosystem

LabOP’s rich representation underpins an ecosystem of several powerful software tools, including:

• labop: the Python LabOP library, which supports:
  • Programming LabOP protocols in Python,
  • Serialization of LabOP protocols conforming to the LabOP RDF specification,
  • Execution in the native LabOP semantics (rooted in the UML activity model),
  • Specialization of protocols to 3rd-party protocol formats (including Autoprotocol, OpenTrons, and human readible formats), and
  • Integration with instruments (including OpenTrons OT2, Echo, and SiLA-based automation).
• laboped: the web-based LabOP Editor, which supports:
  • Programming LabOP protocols quickly with low-code visual scripts,
  • Storing protocols on the cloud,
  • Exporting protocol specializations for use in other execution frameworks,

About the Bioprotocols Working Group

The Bioprotocols Working Group is an open community organization developing a free and open standard for representation of biological protocols.

To join the Bioprotocols Working Group:

• Join the community mailing list at: https://groups.google.com/g/bioprotocols
• Join the #collab-bioprotocols channel on the Bits in Bio Slack.

Leadership

Elected Term: August 24th, 2022 - August 23rd, 2023

Chair: Dan Bryce (SIFT)

Finance Committee:

• Jeremy Cahill (Metamer Labs)
• Mark Doerr (University of Greifswald)
• Tim Fallon (UCSD)

Governance

Approved by community vote on August 16th, 2022

https://bioprotocols.github.io/labop/about#Governance

Mission:

The Bioprotocols Working Group is an open community organization developing free and open standards for representation of biological protocols. In support of that goal, the organization also develops tools and practices and works with other organizations to facilitate dissemination and adoption of these standards.

As an organization, the Bioprotocols Working Group holds the following values:

• The standards developed by the community should be available under permissive free and open licenses.
• Technical decisions of the community should be made following open and inclusive processes.
• The community is strengthened by fostering a culture of diversity and inclusion, in which all constructive participants feel comfortable making their voices heard.