This project aims to involve the wider biology community, especially wet lab biologists, in building and analyzing spatial mechanistic simulations at different levels of scale and connecting them in the context of whole cells. Our goal is to facilitate collaboration between experimental and computational biologists by building software tools and infrastructure to allow easy access to software packages written by computational biologists and easy visualization and sharing of results.
We have begun by building initial models for nucleating branched actin and growing microtubules as example systems, using the software package ReaDDy to simulate reaction-diffusion and dynamics and CytoSim to connect these coarse-grained molecular models to larger scale filament models of cytoskeletal networks. Our goal is to provide the resulting multiscale models to the community as a starting point for modeling their favorite aspect of cytoskeletal systems via a user interface on the web or programmatically through a python API. As we add more software packages and models, our long-term goal is to support mechanistic modeling of all cell systems at different levels of scale.
A visual user interface on a website allows biologists to create computational biological models by dragging and dropping components, either starting from scratch or reusing components that others have built. When they’re ready, they run their model and interact with the results in real time by navigating through a 3D “video game” world full of the cells and molecules they created. They pull up graphs and charts and configure them to help understand the results. When they want to share their findings with colleagues or provide supplemental materials for their next paper, they generate a link to their simulation playground where others can change parameters and explore their conclusions.
The backend application accepts inputs from this user interface and sends them to existing 3rd party simulation software packages for computation. As results are calculated on the server, they are collected and sent back to the viewport on the website so the user can see what is happening in 3D space and create graphs and other data visualizations. Computational biologists, who generally create these kinds of simulations by writing custom software, can upload the results of their simulations directly to the web viewport so they can easily be explored and shared, and also can contribute their software package as a 3rd party simulation engine.
Educators can peruse a library of simulations these researchers have published and use them to build interactive activities for their students. If you change the rate of a reaction, how does that affect the outcome of the simulation? These activities can be contributed back to a library that other educators can use. Some of these activities could also be published alongside news articles for the general public to explore