Tutorials are slow videos that allow you to follow along when using TinkerCell. They do not contain audio. For explanations of different TinkerCell features (with audio), see the Demos page.
This tutorial will show basic of creating diagrams, editing parameters, editing reaction rate equations for creating a simple biochemical bistable system. A bistable system is one where the system can come to rest (i.e. reach steady state) at two different points. Imagine a ball rolling on a surface with two wells -- it can come to rest in one of the two wells.
Light-induced System involving two Phosphorylation Steps
This tutorial will show how to create a diagram composed of a cell, receptor, and gene regulation. Specifically, the model will be that of a light-controlled system. The tutorial will also use basic simulation to show how light affects the final output. Note that in the new TinkerCell, you should use "activation" instead of the "phosphorylation" connection (this tutorial was made with an older version).
Light-induced gene activation
Genetic NOR Gate
This tutorial will show how to create a NOR gate using two genes, where the first gene produces a repressor for the second gene. The output is the green fluorescent protein (GFP). If your default TinkerCell view does not contain the "repressible promoter" symbol, use "Show/hide catalog items" option from the "Settings" menu to show all the promoter options.
Genetic NOR Gate
Oscillator & Eigenvalues
This tutorial will show how to create an oscillator by using two genes. The tutorial will also demonstrate the use of Eigenvalues for investigating how the system's stability is influenced by the parameters. This tutorial will also make use of hierarchical modeling, i.e. model within models, for demonstrating that modeling transcription and translation as two separate steps is needed for producing oscillations. The tutorial will also show how stochastic oscillations disagree with deterministic oscillations, which is common in genetic networks.
lac operon and bistability
This tutorial will show how to create the bistable lac operon. The system is bistable because the final value of lactose and LacZ within the cell depends on the amount of lactose that is inside the cell in the beginning. If there is not enough in the beginning, the amount of lactose stays low. If there is enough in the beginning, then lactose upregulates its own uptake.
Create New Symbols in TinkerCell
This tutorial will show how to create the above image using the TinkerCell NodeGraphics program. This program can be used to add new symbols in TinkerCell.
