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Developer Notes

Build synthetic cells that work

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Developer Notes (DevNotes) document how synthetic cell work gets done: the protocols, code, data, and decisions behind a result. Each DevNote centers on a single result or insight, and together they form the working record of a project as it develops. DevNotes are built on Jupyter Notebooks, so code, data, and other files sit alongside the text. The full workflow travels as one package that others can rerun, adapt, and build on. DevNotes come from b.next’s Core Development Team, from residents and fellows at Nucleus Labs, and from developers across the wider community. New developments to the Nucleus platform appear here first, before they are integrated.

If you work on synthetic cells or related systems, or build with the Nucleus platform, we invite you to submit a DevNote. DevNotes are open access and open source, published under Nucleus terms. Each one is a direct contribution to the platform: the Core Development Team at b.next integrates results and insights that prove broadly useful into Nucleus.

layer-group Browse by Collection

Core, Developer Cells, Community, Workshops and Courses, and AI Scientist.

diagram-project See the Network

Find yourself, and see who’s working with whom.

Latest¶

What is a Cytosol Landscape?

ClpXP Control Module: Deployment in Nucleus Cytosol

Development of a Control Module in Nucleus Cytosol Reactions

Characterizing the Limited Operational Lifetime of Cytosol Reactions

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

Using platemaps to analyze and share data

Intro to Kinetics Analysis of Plate Reader Experiments

Nucleus OnePot PURE

Nucleus OnePot PURE Protocol and Results

Collections¶

Nucleus Developer Notes hosts several collections of DevNotes that represent contributions from across the Nucleus Developer Ecosystem.

Core¶

DevNotes from the Core development team at b.next.

What is a Cytosol Landscape?

See all Core DevNotes here

Developer Cells¶

DevNotes from the Developer Cell Network, a group of multi-team nodes building shared capacities for engineering synthetic cells at scale.

Node: Chicago¶

Developer Notes from the Chicago Node.

Theophylline-LacZ sensor validation in Nucleus Cytosol

See all Node: Chicago DevNotes here

Node: London¶

Developer Notes from the London Node.

Diffusion Kinetics

See all Node: London DevNotes here

Community¶

Community Developer Notes are independent contributions from across the Nucleus Developer Community.

BCECF pH Sensor

Adapting the ratiometric pH indicator BCECF to continuous, 24-hour kinetic pH tracking in myTXTL cell-free reactions

See all Community DevNotes here

Workshops and Courses¶

DevNotes from workshops and courses that build on and contribute back to Nucleus

Developer Studio

A three-week event bringing together 12 labs to reproduce, integrate, and document synthetic cell engineering demonstrations at Nucleus Labs.

See all Workshop and Course DevNotes here

AI Scientist¶

AI Scientist DevNotes are developed with an AI Scientist in the loop.

AI Scientist: Base Module Report

See all AI Scientist DevNotes here