Background
Nucleus is a platform for sharing synthetic cell modules and tools for their development. The goal of the platform is to make available a set of core synthetic cell modules and methods for their use that are well-documented and accessible such that can be readily used and adapted by other practitioners.
Nucleus has a two-tier approach. The Nucleus Core includes contributions that have been validated by b.next for robustness and interoperability. The Nucleus Contributor page is where external contributions are made. This two-tiered approach makes it easy to contribute without compromising the quality and focus of the Core distribution. Over time, we want to facilitate integration of community contributions into the Core, but this process will take time to get right and will be an act of co-creation between b.next and the community.
Our goal is to facilitate the growth of a thriving and collaborative synthetic cell industry. These practices will help to ensure that people can compete on creative things to do with synthetic cells and not on getting synthetic cells working in the first place.
This document is an active conversation. Feel free share your questions, comments, and concerns at build@bnext.bio
Sharing information
It is understood that if you are sharing information with b.next you agree that it is acceptable for us to share it with the rest of the synthetic cell community.
Sharing module DNA
All Module DNA should be shared publicly, free of any patent-based restrictions that would prevent others from using that module for any purpose.
Strongly recommended practices
- Module DNA should be described by a digital design file that is stored in an appropriate repository. Waiving such rights can be accomplished by sharing under a Creative Commons Public Domain Dedication (CC0) or Open Data Commons License equivalently permissive tool.
- Module DNA used in validation experiments should be sequence verified and the sequence data should be stored next to the design file.
- Design files and sequence verification should be assigned a persistent identifier.
- Module DNA should be submitted to AddGene and, if possible, be made available under OpenMTA.
Sharing module data
Module Data - meaning data supporting results about the expected behavior of the contributed module - should be shared publicly, free of any intellectual property or contractual restrictions that would prevent others from using that data.
Strongly recommended practices
- Module Data should link characterization data with experimental conditions unambiguously.
- Module Data should be stored in an appropriate domain specific repository in such a way as to waive any intellectual property rights in that data to the extent allowed by law. Waiving such rights can be accomplished by sharing under a Creative Commons Public Domain Dedication (CC0) or equivalently permissive tool.
- Module Data should be assigned a persistent identifier (DOI).
- Module Data should be shared using open, machine-readable formats. If an appropriate format exists within the Nucleus CDK, that format should be used.
- Module Data should adhere to FAIR principles.
Sharing open methods
Module methods - meaning the protocols and tools necessary to replicate the described behavior of the Module - should be shared publicly free of any intellectual property or contractual restrictions that would prevent others from using the module.
Strongly recommended practices
- Where possible, protocols should adhere to standard Nucleus formats.
- Where compatible with high standards of research practice, projects should use open source software. And, where possible, projects should use existing Nucleus software. Where this is not possible, the methods used should be described in sufficient detail to enable others to replicate experiments and that description shared publicly.
- Where compatible with high standards of research practice, projects should use open methods (e.g., kits, assays, and experimental procedures that are not subject to intellectual property rights). And, where possible, projects should use existing Nucleus methods. Where this is not possible, the methods used should be described in sufficient detail to enable others to replicate experiments and that description shared publicly.
- Where compatible with high standards of research practice, projects should use open materials and reagents (e.g., probes, cell lines, plasmids, antibodies). And, where possible, projects should use existing Nucleus plasmids. Where this is not possible, the materials used should be described in sufficient detail to enable others to replicate experiments and that description shared publicly.
Sharing data narratives
Data narratives are descriptive texts that provide contextual information about expected behavior of modules and protocols. They serve to tie together the components described above (e.g. module DNA, data, protocols) into a cohesive whole.
Strongly recommended practices
- Where possible, protocols should adhere to standard Nucleus formats.
- Where possible, references to component DOIs should be made within the document.
- Narratives should be submitted to the Nucleus contributor page.
b.next can help!
If you have any questions concerning this policy please contact b.next for further information. We can assist you in identifying and implementing appropriate open science strategies and accessing open resources.