Nucleus v0.5 is now released. A lot has happened in the last few months–in addition to the main path work of developing and documenting PURE-compatible Modules for use in synthetic cells, we’ve spent a lot of effort in building out the infrastructure to support the Nucleus Ecosystem.
We now have four key pillars of the Nucleus Ecosystem, described in the Nucleus Beginner’s Guide. Each pillar serves a unique function within the community:
Forum. The primary place for community members to suggest new features, identify bugs, and otherwise have discussion about all aspects of Nucleus.
Developer Notes. Technical notes that support interoperable research. The primary mechanism to contribute to Nucleus.
Documentation. Documentation and protocols that work, and work together, to build synthetic cells.
Hub. A preconfigured, Jupyter-based computational platform that enables easy access to Nucleus software tools and data sharing. Use it for collaboration and writing DevNotes.
We are consolidating all of the sites into the nucleus.engineering domain. This is intended to create a clear distinction between Nucleus, the open platform, and b.next, maintainers of and contributors to that platform.
We look forward to continuing to support and grow shared development of synthetic cells in 2026.
-b.next team
Highlights¶
Nucleus Cytosol is announced via DevNote—Cytosol is an open-formulation and open-protocol alternative to PURE made from OpenMTA DNA that can be used and built by anyone. It performs at the same level as commercial kits and specifically supports modular extension and synthetic cell development.
Launch of new Documentation site to supersede nucleus.bnext.bio. Docs will house documentation and protocols based on Nucleus Cytosol.
Launch of Forum
Forum¶
The forum has been added to enable greater engagement with the tools available within the Nucleus Ecosystem. There are dedicated sections for each of the pillars of the Nucleus ecosystem.
Please use the forum to offer suggestions and feedback, identify bugs, or otherwise engage with anything and everything Nucleus. As a matter of course, a forum thread will be created whenever new DevNotes or Documentation pages are released. We’ve done this for the new DevNotes and Documentation pages described in this release below.
DevNotes¶
Since our previous release, several works in progress have been shared as Developer Notes.
ClpXP Control Module: Deployment in Cells: Yen-Yu Hsu validates the ClpXP protein degradation module in PURE cells.
Nucleus Base Cell Testing: Surendra Yadav characterizes the performance of liposome-encapsulated Nucleus Cytosol using pOpen deGFP.
ClpXP Control Module: Deployment in Cytosol: Yen-Yu Hsu validates the ClpXP protein degradation module in PURE cytosol.
DNA toolkit - The T7 promoter collection: Charlie Newell and Astrid Joergensen introduce a set of promoters to tune expression levels in PURE.
First Nucleus Cytosol Testing: Surendra Yadav characterizes the performance of Nucleus Cytosol using pOpen deGFP.
Cx43 Cell: DNA Validation: Yen-Yu Hsu shows that the OpenMTA pOpen-Cx43 and pOpen-Cx43-deGFP plasmids developed based on the contribution from Ahmed Shiorwala is functional in PURE encapsulated synthetic cells.
Integrating PPK Module in PURE Cells: Yen-Yu Hsu shows that an energy module based on PPK2 increases protein expression in PURE encapsulated synthetic cells.
Nucleus OnePot PURE workshop: The experimental results from a five day hands on workshop where participants learned how to make and troubleshoot OnePot PURE. Read more here.
Documentation¶
We have introduced the following specifications to the Docs:
PPK Energy Module: increase the available energy to PURE.
ClpXP Control Module: enables targeted degradation of ssrA-tagged proteins in PURE.
Going forward, our documentation (Docs) will now reside at https://
The new site is built with JupyterBook and MyST Markdown. This is the same tech stack underlying DevNotes and will allow for greater integration and interoperability between the two sites.
The new site will also have a streamlined structure that builds on our lessons over the last two years of organizing documentation for synthetic cells. The documentation is structured into four distinct categories:
DNA Distribution - documentation and protocols required for manipulating the Nucleus DNA Distribution. For example, the T7 promoter collection.
Process Protocols - foundational protocols that describe how to make and characterize Base Cytosol and Cells.
Module Specifications - documentation and protocols for modules that extend the functionality of Base Cytosol and Cells
Implementations - documentation and protocols that describe combinations of modules or the deployment of modules in unique environments.
Importantly, all documentation and protocols will be built on Nucleus Cytosol, introduced this release, enabling shared development and interoperability.
For the foreseeable future, https://
Hub¶
This release marks the transition of Nucleus Hub to a cloud-based deployment managed by 2i2c. Access to the hub remains by request only. If you would like to contribute to Nucleus by submitting a DevNote please reach out to build@bnext.bio or leave a comment on the Forum.
- Yadav, S. (2025). First Nucleus Cytosol Testing: Evaluation of Nucleus Cytosol v0.5 Through deGFP Expression. 10.63765/fppr8928
- Hsu, Y.-Y. (2025). Cx43 Cell: DNA Validation. 10.63765/xvxu3274