Important
We are no longer actively maintaining this repository. All active work by the Allen Institute for Cell Science is located under the AllenCell organization.
a simulation framework for molecular modeling
our goal is to create a system that:
- simulates molecules spatially with volume exclusion
- has the ability to form spatial complexes of molecules that each have a position and orientation within the complex
- takes common molecular model definitions as input, starting with BioNetGen and possibly also SMBL
- can define shapes of molecule containers based on 3D microscopy data
- calculates in real time so that users can change parameters on the fly
- eventually runs in a web browser, with an easy-to-use UI for defining models and changing parameters
currently prototyping in Unity WebGL, eventually will use C++ or something for speed
chart of current architecture: https://www.lucidchart.com/documents/view/25a4e766-d7fe-4a87-b33f-157feaca604d/0
Unity version: 2017.2.0f3 (download here https://unity3d.com/get-unity/download/archive)
To run sample models, once project is open in Unity:
- open Scenes/Reactor
- press play!
To load a different model:
- with Reactor scene open, select Reactor object in Hierarchy
- drag a model file of your choice from Data/Models to the model slot on Reactor
- press play!