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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 LabOP 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 Laboratory Open Protocol language or LabOP, formerly known as 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://bitsinbio.org) https://app.slack.com/client/T02RKFYQV5L/C02UJJ3AND8

If you'd like to financially support the community & the development of LabOP, check out our Open Collective page: https://opencollective.com/bioprotocols (And read up on our governance to see how we ensure support is well spent! https://bioprotocols.github.io/labop/about)


IWBDA 2022 Notebooks:


The last major workshops on LabOP took place in October 2022 at the COMBINE 2022 virtual converence: https://combine-org.github.io/events/

Recordings of the LabOP Sessions are available here:


The previous major workshop on LabOP/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 LabOP & the Bioprotocols Community. We hope you'll join our initiative!

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  1. labop labop Public

    Laboratory Open Protocol (LabOP) Language

    Python 40 11

  2. labop-specification labop-specification Public

    Specification for the Laboratory Open Protocol Language (LabOP)

    TeX 12 3

Repositories

Showing 10 of 11 repositories
  • labop Public

    Laboratory Open Protocol (LabOP) Language

    Bioprotocols/labop’s past year of commit activity
    Python 40 MIT 11 62 5 Updated Oct 7, 2024
  • Bioprotocols/labware-databank’s past year of commit activity
    Python 4 MIT 1 8 0 Updated Jul 11, 2024
  • device-databank Public

    An ontology and database for laboratory devices

    Bioprotocols/device-databank’s past year of commit activity
    Python 0 MIT 0 1 0 Updated Apr 27, 2023
  • Bioprotocols/Bioprotocols.github.io’s past year of commit activity
    HTML 0 MIT 0 0 0 Updated Feb 22, 2023
  • container-ontology Public

    Container ontology for use with PAML (Protocol Activity Markup Language)

    Bioprotocols/container-ontology’s past year of commit activity
    Jupyter Notebook 3 Apache-2.0 3 14 4 Updated Feb 10, 2023
  • Bioprotocols/labop-documentation’s past year of commit activity
    0 MIT 0 1 0 Updated Jan 17, 2023
  • labop-specification Public

    Specification for the Laboratory Open Protocol Language (LabOP)

    Bioprotocols/labop-specification’s past year of commit activity
    TeX 12 3 9 0 Updated Jan 16, 2023
  • labop-check Public
    Bioprotocols/labop-check’s past year of commit activity
    Python 0 MIT 1 2 0 Updated Jan 15, 2023
  • .github Public

    (Special repository to allow a README.md landing page)

    Bioprotocols/.github’s past year of commit activity
    0 0 0 0 Updated Nov 28, 2022
  • laboped Public

    LabOP Editor

    Bioprotocols/laboped’s past year of commit activity
    JavaScript 4 MIT 1 9 0 Updated Oct 27, 2022

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