Nucleus v0.6 marks a significant step forward across the platform. Since January, the DevNote ecosystem has grown substantially — with contributions from the b.next team, the Developer Cell community, independent researchers, and for the first time, workshops and courses. The documentation migration from nucleus.bnext.bio to nucleus.engineering is complete. The Cell Development Kit ships its first major version update. Here’s what’s new.
Developer Notes¶
ClpXP Control Module: Deployment in Nucleus Cytosol: Validation of the ClpXP protein degradation control module in Nucleus Cytosol reactions.
Characterizing the Limited Operational Lifetime of Cytosol Reactions: A systematic characterization of how incubation time before encapsulation affects Cytosol reaction performance.
SecYEG-Based Membrane Translation Module in Synthetic Cells: Development of a membrane translation module via reconstitution of the SecYEG translocon for enhanced membrane protein integration in liposomes.
Nucleus OnePot PURE: Protocol and results from the Nucleus OnePot PURE workflow.
Using platemaps to analyze and share data: Introduction of the first Nucleus platemap standard, enabling structured sharing of plate reader experimental data.
Intro to Kinetics Analysis of Plate Reader Experiments: A practical introduction to kinetics analysis of plate reader data using the CDK.
Double emulsion optimization: inner solution, lipid concentration, and composition: Optimization of the double emulsion encapsulation workflow for producing GUVs.
Theophylline-LacZ sensor validation in Nucleus Cytosol: Validation of a theophylline-responsive LacZ sensor in Nucleus PURE.
TetO-Catecholase sensor validation in Nucleus Cytosol: Validation of a TetR-regulated catecholase biosensor in Nucleus PURE.
BCECF pH Sensor: Adapting the ratiometric pH indicator BCECF to continuous, 24-hour kinetic pH tracking in cell-free reactions.
DNA toolkit — The T7 terminator collection: Characterization of a collection of T7 terminator variants in PURE, enabling tunable transcription termination.
Workshops and Courses¶
This release introduces a new Workshops and Courses category for DevNotes, capturing hands-on educational work with Nucleus. Contributions this cycle include a Build a Cell workshop, a Cold Spring Harbor course, an undergraduate course at Cal Poly SLO, and a Developer Cell meeting in London.
Documentation¶
The migration of Nucleus documentation from nucleus.bnext.bio (Notion-based) to nucleus.engineering (MyST Markdown) is now substantially complete. All active protocols and module specifications are now maintained on the new site.
This release also introduces the first Nucleus platemap standard, enabling structured, reproducible sharing of plate reader experimental layouts. The standard is introduced and demonstrated in the Using platemaps to analyze and share data DevNote and supported by the CDK.
The FAQ and License pages have been updated to reflect the current state of Nucleus governance and open-source licensing.
Cell Development Kit¶
CDK v0.6 is now available on PyPI:
pip install nucleus-cdkv0.6 introduces support for the Nucleus platemap standard, updated kinetics analysis tools, and improved interoperability with the DevNote workflow. See the CDK changelog for the full list of changes.