gencirc

Created: 2012-03-21 09:25
Updated: 2014-04-04 15:20

README.md

Genetic Circuits Builder

An HTML5 app that allows users to build genetic circuits. Live demo: http://gencirc.psyph.com

Features

  • UI to build circuits using drag-and-drop components.
    • Components and Interactions are intelligently placed.
    • Components
      • Drag a new component from the toolbox onto the canvas.
      • Drag a component off of the canvas to remove it.
      • Drag an existing component to rearrange it.
      • Rename a component by clicking on it's text.
    • Interactions
      • Select between activating and repressing interactions in the toolbox.
      • Draw a line between two components to create an interaction (invalid interactions marked in red).
      • Drag on the knob to adjust the line heights temporarily, or to remove the interaction.
    • Rename the circuit by clicking on the title.
  • Circuits are stored locally using HTML5 LocalStorage.
    • File menu provides save, open, and new options... presented with intelligent dialogs.

Running the server

Download a local copy of the repository. The contents of static can be placed in any web accessible directory, and then navigating to index.html. A light webserver is included for testing (requires Flask).

python server.py

And then browse to http://localhost:5000/

Building the source

While the source is functional, it is not optimized (loads in several files). To build, install node and r.js:

npm install -g requirejs

Within src/js, execute:

./build

while will create a build directory at the root.

Bugs/Notes

  • Backbone-localStorage and Backbone-relational do not play well together. I had to patch Backbone-localStorage to recursively assign ID's to models on create/update. This is not well tested.

  • The Circuit's SVG uses foreignObject to display a link, which should be replaced with svg:a and svg:text components.

  • Export as PNG is not yet implemented.

  • There are no restrictions on how one can draw an interaction, though a warning does show. This can instead be enforced.

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