This is the release of v0.4.0, which includes stable Nucleus content (i.e., passing our internal testing and generally working).
Release: 23 July 2025
General
- Nucleus is now Nucleus Distribution.
- The open science policy has been updated Open science.
- A dedicated FAQs page has been added
FAQs. - Developer Notes and
Nucleus Community Contributions is being sunset on Nucleus Distribution) Developer Notes will now appear on a dedicated site at https://devnotes.bnext.bio/. - A section for tutorials has been introduced that includes
Nucleus Hub, 
Developer Notes, and 
Making Synthetic Cells for Beginners. - The Development section is being renamed Software.
Synthetic Cell
- The “Hello, World” Liposome Protocol has been renamed
PURE Cell and is now categorized as a Synthetic Cell. - The protocol “Booting up a simple synthetic cell” has been renamed Making Synthetic Cells for Beginners and placed under Guides.
Content
- The
OnePot PURE workshop module includes new DNA content encoding for the 36 PURE proteins in the pET28a backbone.
Cytosol
-
Make OnePot Protein Mix is added as an alternative to the existing 36-pot protocol for making PURE protein mix. -
Make Ribosomes introduces a protocol for purifying E. coli ribosomes from A19 biomass.
-
Make tRNAs is updated to recommend purifying from A19 biomass over MRE600.
- The structure of
PURE Protocols has been re-arranged for clarity.
Container
- No updates in this release.
Tutorials
- Nucleus Hub is added to help users get started with Nucleus Hub.
- Developer Notes is added to help users get started with DevNotes. If you’re interested in learning more about DevNotes, read here.
Software
- The Cell Development Kit is now available via PyPI:
pip install nucleus-cdk.
Community
- OnePot Workshop at Nucleus Labs. Eight graduate students and postdocs learned how to make PURE from energy mix, protein mix, tRNAs, and ribosomes that they made themselves in five days at Nucleus Labs in San Francisco.