• PAML Pilot
  • 2021-12-16 Meet
    • Agenda
    • Notes
    • To Discuss with BBN, etc.:
  • 2021-12-04 Meet
    • Recap
    • Agenda
    • Notes
    • Action Items

tags: comms

PAML Pilot

Anyone can edit this note.
Click on the pencil icon or open https://hackmd.io/@friendzymes/paml/edit.
Associated GitHub issue: https://github.com/friendzymes/community/issues/14.

2021-12-16 Meet

Agenda

• Sanity check and confirm/coordinate current protocol plan
• Set high-level OKRs and milestones.
  • Bumped to Meeting 2
  • Medium-term goal for BioProtocols: Get an alpha out by April 2022
  • "LIMS-less interlab coordination"

Notes

• Reviewing the protocols.io draft

  • Steps 18 and 19 raise questions about how much to abstract
    • One option is to explode "recovery" into multiple explicit steps
    • Another option is to abstract "recovery" into another protocol for modularity
  • Step 1
    • 60 mass percent is suboptimal representation

• PAML config

  • install flow needs work
  • graphviz dependency isn't documented
  • inconsistent results with pip/pip3
  • PAML colab notebooks need plumbing as well

• Luiza notes on PAML_GG_protocol

  • https://docs.google.com/document/d/1AupzE_OLUqp-3mfgJ47NplMxqvzMAK5I/edit#heading=h.gjdgxs

To Discuss with BBN, etc.:

• Ontology is unclear for primitives.
  • How are schemas for parameters resolved? When are they resolved?
  • Are they expected to be stored in a "canonical" way in a central place like bioprotocols.org?
    • If so, to what degree is it expected that people will "homebrew" their own?
    • And also, we probably need to set that up, right?
  • What is the intended difference in practice of a SampleArray and a SampleCollection?
• PAML spec questions
  • Needed: exhaustive list of primitives
  • Needed: list of recommended changes and additions

2021-12-04 Meet

Recap

At COMBINE 2021, we heard about a new lab modeling language.
Jake Beal led an exploratory workshop on this spec.

Its description was as follows:

Defining a Common Protocol Representation
This session is a working session for stakeholders to discuss needs, requirements, and opportunities for a common protocol representation, leveraging the current protocol specification and implementation of the Protocol Activity Markup[sic] Language (PAML).
Jacob BealWed, Oct 13, 2021

This led to a planning session for preliminary working groups.
The aim of this second session was stated as follows:

Implementation and Roadmap for Common Protocol Representation
This session is a working session that will use the outcomes of the prior “Defining a Common Protocol Representation” session to work on the specifics of implementation of a common protocol representation, leveraging the current prototype specification and implementation of the Protocol Activity Markup[sic] Language (PAML), and to determine priorities and next steps.
Thu, Oct 14, 2021 Jacob Beal

By the end of this session, the rough contours of three groups were defined.

1. GUI dev
2. iGEM interlab - iGEM engineering
3. Friendzymes and friends - practical pilot

Niches for which no group yet exists include:

1. Protocol dev
2. Core "data curation" - ontology dev, knowledge representation
3. Non-GUI toolchain dev

We are here to initiate discussion of group 3: Friendzymes and friends

Agenda

1. Define our challenge problem more concretely.
2. Set high-level OKRs and milestones.
3. Coordinate further comms and project management.

Notes

• Objectives

  • Define our challenge problem more concretely.
    • Scope: Known-good reproducibility demo of a Golden Gate protocol
    • Options:
      • Marburg with BsmBI
        • https://www.protocols.io/view/golden-gate-lvl-0-8edhta6
      • Marburg with BsaI-HFv2
        • https://drive.google.com/file/d/1TIfXaeupHi2ZGUXDSk8RGXE9tC3q9e_w/view?usp=sharing
      • Intended Goal: Marburg with BsaI, forked from the Marburg with BsmBI protocol:
        • Our fork is here
        • https://www.protocols.io/view/golden-gate-lvl-0-b2k4qcyw
  • Coordinate further comms and project management.
    • Friendzymes has github and discord-oriented comms
    • We need to get added to the bioprotocols github org as well
    • Jeremy suggests we work where we're admins / it's easy (friendzymes) and deposit deliverables over there (bioprotocols)
      • ^Ya boy Tim isn't an admin though
      • Can add. If scoped to one main repo there shouldn't be too much spam / problems. <- Ok, sure (https://github.com/tsdobbs)
    • Google Group exists but nobody's in it
      • https://groups.google.com/g/bioprotocols
  • Set high-level OKRs and milestones.
    • Bump to Meeting 2
    • Medium-term goal for BioProtocols: Get an alpha out by April 2022
    • "LIMS-less interlab coordination"

• Links

  • PAML basics
    • https://github.com/bioprotocols/paml
    • https://github.com/bioprotocols/pamled
    • https://github.com/bioprotocols/paml-specification
    • https://github.com/rpgoldman/container-ontology
    • Data Representation in the DARPA SD2 Program
    • Process-Level Representation of Scientific Protocols with Interactive Annotation
    • 2021-10-14_COMBINE2021_Standards-Meeting.pdf
  • This working group
    • friendzymes/community #14 - Meeting: PAML Pilot
    • friendzymes project board - PAML

Action Items

• isaacG update forked protocol
• forked protocol to PAML (github)
• research and summary updates on other enzymes
• Scott to talk to Jenny / Nico to build a list of tested combinations to express GFP
• isaacG whenisgood for next meet, prior to christmas and preferably 2021-12-11 - 2021-12-18