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@Bioprotocols

Biological Protocols Working Group

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

Welcome to the Bioprotocols Community landing page!

A image showing that PAML is combined from the Unified Modeling Language (UML) for the Activity model, the Synthetic Biology Open Language (SBOL) for Object model and materials, Aquarium, the Laboratory Operating System for Sample Typing, Autoprotocol for Atomic action libraries, PROV-O (from W3C) for the execution history

An open community developing a free and open standard for representation of biological protocols, which we call the Protocol Activity Modeling Language or PAML.

Please join our Bioprotocols Google Group, if you would like to see our mailing list, get access to our working documents and slides, or participate in our weekly scrums via Zoom: https://groups.google.com/g/bioprotocols

Please also see the collab-bioprotocols channel on the Bits-In-Bio Slack to participate in ongoing discussions. (details to join Bits-In-Bio here) https://app.slack.com/client/T02RKFYQV5L/C02UJJ3AND8

The last major workships on PAML took place in April 2022 at the HARMONY 2022 virtual converence: https://combine-org.github.io/events/

Workshop slides for Session 1: Demonstrating the Protocol Activity Modeling Language (PAML), are here.

Workshop slides for Session 2: Steering Development of the Protocol Activity Modeling Language (PAML), are here.

Workshop recordings are here.

See the repositories below for our ongoing code development.

Feel free to reach out with questions if you'd like to learn more about PAML & the Bioprotocols Community. We hope you'll join our initiative!

Pinned

  1. paml Public

    Protocol Activity Modeling Language

    Python 23 7

  2. Specification for Protocol Activity Markup Language (PAML)

    TeX 11 3

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