Contribution Guidelines

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 imperative phrases. See RFC 2119 for details.

• MUST: inclusion is an absolute requirement when submitting a Developer Note. Similarly, MUST NOT implies that exclusion is an absolute requirement.

• SHOULD: inclusion is considered best practice. Similarly, SHOULD NOT implies that exclusion is considered best practice. Inclusion may prove technically challenging in some situations, but will make your submission more likely to be onboarded into the Distribution by the Core Development Team. Use good judgment, and post on the Forum if you need guidance on feasibility.

• MAY. This word means that something is optional and permissible. Inclusion or exclusion is fully at your discretion.

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.

General Considerations¶

General¶

• SHOULD include Author(s) ORCID.

• SHOULD include a schematic of the contribution.

Bill of Materials¶

• MUST indicate critical materials used for your Process, Implementation, or Module. SHOULD include a formatted Bill of Materials listing these materials. Provide it as either:

  • an inline markdown table on the Process page, labeled bom-<process-slug> (where <process-slug> is the process’s directory name), or

  • an uploaded CSV at resources/<process-slug>-bom.csv beside the page.

• IF POSSIBLE, prefer using existing validated materials used elsewhere in the Distribution, rather than introducing new materials. Consult the Materials Reference to see al materials in use in the Distribution.

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.

• SHOULD be in pOpen backbone.

• 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 (e.g., DNA and proteins).

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 MAY 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.

• SHOULD take measurements as timeseries, not just single measurements at 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.

• SHOULD analyze data 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.

• SHOULD include raw files of all images included in the DevNote.

• SHOULD include raw data files for all graphs in the DevNote.

Find a typo? Want a feature?¶

If something is missing, lacking, or wrong on this site, submit an issue! We use GitHub to maintain our documentation and to track ongoing work. Just click the link above and describe what change you’d propose made to the site. If you are comfortable with git workflows, consider joining the core development team!