Frameworks
The nanoBIO node has many apps and tools built from external frameworks. Please see the related webpages for more information.
PhysiCell
PhysiCell aims to provide a robust, scalable code for simulating large systems of cells in 3-D tissues on standard desktop computers. Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment. The ideal "virtual laboratory" for such multicellular systems simulates both the biochemical microenvironment (the "stage") and many mechanically and biochemically interacting cells (the "players" upon the stage). PhysiCell was developed to work in concert with BioFVM to fill this role as a virtual laboratory.
CompuCell3D
CompuCell3D allows biomodelers to effectively use a multi-scale, multi-cell simulation environment to build, test, run and post-process simulations of biological phenomena occurring at single cell, tissue or even up to single organism levels. Simulations of tissues, organs and organisms require one to simplify and adapt single cell simulations to apply them efficiently to study, in-silico, ensembles of several million cells. To be useful, these simplified simulations should capture key cell-level behaviors, providing a phenomenological description of cell interactions without requiring prohibitively detailed molecular-level simulations of the internal state of each cell. While an understanding of cell biology, biochemistry, genetics, etc. is essential for building useful, predictive simulations, the hardest part of simulation building is identifying and quantitatively describing appropriate subsets of this knowledge. In the excitement of discovery, scientists often forget that modeling and simulation, by definition, require simplification of reality.
v. 4 is now available here.
COVID 19 Virtual Tissue Model
Flexible framework based on CompuCell3D which simulates tissue and immune system interactions during a viral lung infection. It can be run as a standalone app using suggested parameters, or as a flexible modeling framework with a variety of adjustable methods.
This tool exemplifies the simulation used in our study here https://doi.org/10.1101/2020.04.27.064139. You can select from the parameters used in the paper in the "Steering Panel" window. After the simulation is loaded it will wait for the selection of a parameter in the "Steering Panel" (even if you wish to stay with the default parameters you need to select one -- you can select a value that is already selected -- for the simulation to start). During the simulation you can choose to change the parameters at will.
Development of predictive quantitative models of all aspects of COVID-19 is essential for understanding this complex disease. COVID-19 varies significantly among individuals in both chances of infection and disease severity once infected. There is a critical need to develop mechanistic understanding of all aspects of COVID-19 spread and infection to assist in the development of improved clinical interventions.
Fury
Fury is a Python library available for scientific visualization. The library is available via PyPi or Anaconda package system. Go here for more information.
Tellurium
A Python Environment for Reproducible Dynamical Modeling of Biological Networks
Tellurium provides the interfacial code to convert between standard formats and utilize powerful libraries without requiring technical expertise, allowing you to focus on what’s important: building better models. Tellurium also provides first-class support for exchangeability via COMBINE archives, allowing you to share your models and simulations with other tools.