Overview¶
The purpose of this tutorial is to guide a newcomer through the complete Nucleus technology stack and supporting workflows.
At the end of this tutorial you will have used the Protocols in the Distribution to assemble Base Cytosol, characterize its performance using the Cell Development Kit (CDK) on Nucleus Hub, and finally post a Developer Note (DevNote) that reports on its performance.
This tutorial assumes that you have the necessary components of Base Cytosol: small molecule mix, tRNA, protein mix, ribosomes, and a suitable reporter plasmid such as pOpen-deGFP. The components of Base Cytosol can be obtained in two ways: you can make them yourself from scratch, or you can acquire a premade reagent kit from b.next.
If you are looking to get started quickly, we recommend acquiring a kit from b.next. If you prefer more control over the cytosolic system, the distribution contains materials, protocols, and documentation for making your own components from scratch.
Using the Distribution as a knowledge base¶
The Distribution contains numerous validated protocols and other documentation organized across four different categories: DNA Distribution, Processes, Modules, and Implementations. Assembling Base Cytosol is regarded as a fundamental process in the Distribution, so protocols and documentation for its assembly can be found in the Processes section. We recommend exploring the four Protocol category pages to get a sense for how the documentation is organized.
Now that we’re more oriented in the documentation let’s navigate to the protocol we’d like to implement:
If you follow the steps on that page, you should find yourself with some data in hand ready to be analyzed. Rather than firing up Excel or opening a Google Sheet, we’re going to sign into Nucleus Hub.
Analyzing Data with Nucleus Hub¶
If you follow the steps on that page, you shoud find yourself with some data in hand ready to be analyzed. Rather firing up Excel or opening a Google Sheet, we’re going to sign into Nucleus Hub.
Analyzing Data with Nucleus Hub¶
Nucleus Hub is an interactive computing platform built on Jupyter Hub. Like it or not, we have to interact with software to get our work done and share it with others. Nucleus Hub provides a way of accessing software tools that just work. No installs, no compiling, no environmental management. Of course if you want to modify your own environments and build code, that’s supported as well. The Nucleus CDK lives on GitHub, but the Hub is preconfigured to get you up and running without any additional work. And there’s templates.
Getting Started with Nucleus Hub
If you followed the steps on that page, you should not find yourself with a Nucleus Hub account and some nice looking plots. Let’s tell the Nucleus Community what you’ve been up to and write up a DevNote.
Sharing your results as a Developer Note¶
Nucleus is open source which means that we’re building something together. Developer Notes are the key way to contribute to the Nucleus Distribution and gain legend status in the community. Developer Notes are conveniently built ontop of Jupyter Notebooks and MyST Markdown (a flavor of markdown designed for technical communication). Since you’ve done your analysis in a Jupyter Notebook, you’ve already half-written your DevNote and you didn’t even know it.
Writing your first Developer Note
If you followed the steps on that page, you should have successfully posted a Developer Note. Not only does your data help us understand how good you are preparing base cytosols (and how well our reagents are performing), it helps expand the largest on-going interlab study on the expression of plamGFP. It also introduces you to the Developer Community, in a uniquely Nucleus Way.
Engage with the community on the Nucleus Forum¶
Once a DevNote goes live, a thread is opened on the Forum for others to discuss. People might ask you how to replicate what you did, tell you that you made an incredible mistake, or just say “hi”. These “Hello, World!” DevNotes go into a special channel and provide a place for people to introduce themselves.
Navigating the Nucleus Forum
Am I a Developer Now?¶
Well, not quite. To be a proper Nucleus Developer, you should probably have developed something. But don’t fret, you’re well on your way. You are now in command of a growing collection of validated Modules that you can build ontop of and equipped with the tools to analyze and share them. If you Develop something useful or something on the Nucleus Roadmap you should keep in mind the Nucleus Contribution Standards, they are the things you should keep in mind as you go about your work so that it’ll end up as part of the distribution.
Nucleus Distribution Standards
Once it’s in the Distribution, you can safely call yourself a Developer.