Usage

BioNetGen modelling language is a language for writing rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks, see here for more information.

This VS Code extension is designed to help write BNGL models by adding syntax highlighting and snippet support, do rapid tests of the model as you write with the help of a built-in run button and basic plotting features.

Syntax highlighting and snippets

Once the extension is installed you can create a new file with `.bngl`. This file extension will be automatically detected and you should see a run button at the top right corner of the file if the extension is running correctly. This extension will also do syntax highlighing on files with `.net` extension.

Next you can start writing your model. This VS Code extension supports a large list of snippets that can help you write your model. For a full list, see here, we will update this with a snippet guide in the future.

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Using the correct theme

If you notice that there is no highlighting on certain parts of the model or if the colors don’t match with the figures presented here, please make sure you have the `dark-bngl` theme activated (see here to learn how to select color themes). Currently only a dark theme is supported, we will include a light version in the future.

Running a model

Once you finished writing the model, you can try running it. For the run button to work, the default terminal window VS Code opens should have access to Perl, Python3 (preferably anaconda python) and the PyBioNetGen library. See here for more instructions on how to install the library. You can test if you have the library correctly installed by opening a new terminal and running `bionetgen -h`.

Once you press the run button (or use the shortcut `CTRL/CMD+SHIFT+F1`), the extension should create a new folder with the same name as the model. A time stamped folder will also be created and the current model will be copied under there and the extension will use the terminal and the PyBioNetGen library to run the model. Once the run completes, if the run created a `.gdat` file, it should open automatically.

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Plotting results

Once you have some `gdat/cdat/scan` files to look at, you can open one and you should see two new buttons instead of the run button. The white and red button on the right should plot your file into a png with some basic defaults (options to change these options will be provided in future releases).

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The blue button on the left should open a new window with an interactive plot (thanks to plotly.js). You can also use the `CTRL/CMD+SHIFT+F1` shortcut. The plotly window also allows you to save the image as a png as well as a svg file and has interactive features. You can also change the plotting type to markers or lines+markers and use one of the selection tools to sub-select time series. If you select a region on the plot with no data points, every time series in the original dataset will be shown again.

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