What should standards for integrating new modules onto the distribution be?

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We’re going to begin onboarding new modules. What should our standards be for transitioning work from DevNotes onto the distribution? Baseline is data showing function in base Nucleus cytosol. Likely needs to include a reproducible unit test + replicates.

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Here is a draft of some guidelines that we’ve been working on, would love feedback!

Overview

This document provides guidelines for making a contribution to the Distribution. Since technical contributions are made by submitting a Developer Note, these contribution guidelines include both minimal requirements for submitting a DevNote and suggestions for increasing the likelihood that your contribution will be onboarded into the Distribution.

To clarify this distinction, we define several phrases:

  • Must. This word means that something is an absolute requirement when submitting a Developer Note.

  • Should. This word means that including something will make it more likely that the submission will be onboarded into the Distribution by the Core Development Team.

  • Where possible. This phrase means that including something may prove technically challenging and situation dependent. Use good judgment, and post on the Forum if you need guidance on feasibility.

Note: Before reading the following guidelines, we highly recommend reading the document titled From Zero to DevNote which describes how to prepare your first Developer Note for inclusion into the Distribution. It provides a concrete description of the key components of a submission.

Parts of a Submission

All Developer Notes, and by extension all Submissions,

General Consideration

General

  • Must include Author(s) orcid ID

  • Should include a schematic of the contribution

Bill of Materials

  • Must have a section titled “Critical Reagents” that contains a table describing reagents that are critical for the experiment. The table Must have the following form:
Reagent Product Name Manufacturer Part # Price Storage Conditions Link
Amino Acids L-Amino acids, analytical standard Sigma-Aldrich LAA21-1KT $558 1C to 4C link
  • Should have a complete reagent list. In most circumstances, submissions will be modifying Processes with existing reagent lists. You are encouraged to reuse and modify these lists as appropriate and exercise good judgement when reagent substitutions should be regarded as “Critical”

DNA Sequence Maps

  • Must include linear or plasmid DNA sequence maps.

  • Must include a statement attesting to sequence validity.

  • Must include a table containing names of sequences used and links to files in the project. The table should have the following form:

  • Should be in pOpen backbone

TODO: provide an example of a formatted table

  • Should include sequence verification data.

  • Should follow DNA Distribution design guidelines

Lab Notebook Entry

  • Must include a document (format as .pdf or .txt) that describes reaction preparation in sufficient detail to allow for their reproduction. At a minimum this includes the composition of stock solutions and master mixes.

  • Should include notes on handling or preparation that are non-obvious. For example, “preparing an aqueous stock solution of FITC requires first suspending in DMSO at 100 mM concentration” or “use of modified amino acid mixture requires EXTENSIVE vortexing, do not use until solution is completely transparent”.

  • Should include appropriate QC data on intermediate products like DNA, proteins, and so on…

Considerations for Cytosols

Testing and Experimental Design

  • Must be tested in reference to the PURE system, either from a commercial vendor or self-prepared.

    • If using a self-prepared PURE system results Must be tested across at least 2 batches.

    • Data involving other systems such as lysates can be included but Must be done in reference to the PURE system.

  • Must include at least >3 technical replicates for each reaction condition.

  • Must include an Appropriately Designed positive and negative control.

  • Should be tested in reference to version-specified Cytosol, the open-formulation flavor of PURE described on the Distribution.

  • Where Possible measurements are made as timeseries, not just endpoints.

Data

  • Must include raw data in a format that can be ingested by the Nucleus CDK

  • Must include a platemap in format that can be ingested by the Nucleus CDK

  • Where possible data is analyzed using Nucleus CDK tools

Considerations for Cells

Testing and Experimental Design

  • Must include appropriately designed controls

  • Must include >2 biological replicates to support each result

Data

  • Must be possible to determine the size of liposomes

  • Must analyze >100 liposomes to support conclusions

  • Where Possible, raw files of all images included in the DevNote should be included

  • Where Possible, raw data files for all graphs in the DevNote should be included

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It is important for DevNotes to have reference standards to quantify the amount of protein produced in the reactions.