Virtual Cell
The Virtual Cell has been specifically designed to be a web-based research tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. Likewise the creation of models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. Users can build complex models with a web-based Java interface to specify compartmental topology and geometry, molecular characteristics, and relevant interaction parameters. The Virtual Cell automatically converts the biological description into a corresponding mathematical system of ordinary and/or partial differential equations.
COPASI
COPASI is a stand-alone software application for simulation and analysis of biochemical networks and their dynamics. COPASI supports models in the SBML standard and can simulate them using ODEs, SDEs, or Gillespie's stochastic simulation algorithm. COPASI provides a set analysis methods and parameter estimation.
SpringSaLaD
SpringSaLaD is a stand-alone software tool to explicitly model binding events and state changes among multivalent molecules. It is one of the first algorithms to account for crowding effects within multimolecular clusters. Spring SaLaD models proteins as sets of reactive sites (spheres) connected by stiff springs. The impenetrable spheres capture excluded volume and steric hindrance effects. Langevin dynamics are used to model diffusion of each reaction site, and binding reactions are governed by probability based on diffusion coefficients of the sites, the site radii and the macroscopic on rate.
Vivarium Collective
The Vivarium Collective is a registry for open-source Vivarium-compatible simulation modules. These can be wired together to generate novel multi-scale simulations, with the most appropriate algorithm for each biological mechanism.
FIJI/ImageJ VCell Simulation Results Viewer Plugin
The VCell FIJI/ImageJ Plugin enables the remote viewing and analysis of the VCell simulation results data sets in ImageJ, without the need to download data to your computer and import it to Fiji/ImageJ. It supports ImageJ compatible remote storage image format *.N5. New VCell features include, spatial simulation results in VCell can be prepared for export in N5 formats but still stored on the remote server, the link to simulation results enabled them to be opened by imaging software supporting N5, and the ImageJ/FIJI VCell Simulation Results Viewer Plugin can import VCell simulation results directly into Fiji.
Virtual FRAP Tool
Accessed through the VCell modeling and simulation environment (vcell.org), the Virtual FRAP tool is designed to analyze FRAP, Fluorescence Recovery after Photobleaching, experiments. It is available as a tool within the VCell software, and can be used to analyze experiments that collect all of the fluorescence associated with the cell, and where the bleach region does not vary through the Z dimension. Currently, Virtual FRAP can be used to fit D and %R for either one or two diffusing components of cytosolic (soluble) proteins, or to fit off rates for binding to immobile components. It does not analyze lateral diffusion within the plasma membrane.
Octane (Super-resolution imaging and single molecule tracking software.)
Please see additional software information and download information at Yu Lab>Software
The Octane is a program we developed to facilitate works involved in super-resolution optical imaging (PALM, STORM, etc.). By providing an intuitive graphical user interface front end, we hope it can serve as a useful tool for a wide range of scientists, including experimental biologists as well as physicists. The program runs as a plugin of the (extremely versatile) ImageJ software, thus can be used on any image format that is supported by ImageJ.
BaSDI (Bayesian super-resolution drift inference)
Please see additional software information and download information at Yu Lab>Software
Single-molecule localization based super-resolution microscopy requires accurate sample drift correction in order to achieve good results. BaSDI implements a Bayesian statistical algorithm that estimate amount of the sample drift for every image frame from the raw dataset. The inference requires no fiducial marker but requires the assumption that the drift is mostly smooth over time. A detailed description of the statistical framework for this algorithm is published, Elmokadem A, Yu J, Optimal Drift Correction for Super-resolution Localization Microscopy with Bayesian Inference, Biophys J, 2015 Nov 3;109(9):1772-80. doi: 10.1016/j.bpj.2015.09.017. PubMed Link
BioNetGenLanguage (BNGL) code visualizer
Usage and limitations of BNGL code visualizer:
- Non-visual parts of BNGL code such as parameter's block and actions are omitted in visualization for clarity, but all comments for molecules, species, rules and observables are displayed.
- No code validation is provided: the BNGL is visualized as is. There are rare instances when we note some errors in the code and provide guidance, but users should not rely on it.
- cBNGL is not supported, but compartmental export from VCell is supported. In VCell, a compartment is assigned to the whole reactant or product, while in cBNGL a compartment can be assigned to different sites of a molecule.
- There are many extensions and undocumented/semi-documented features in BNGL. We do not guarantee that all of them are supported. Please email Michael Blinov and we'll try to accommodate the visualization of more features.
MolClustPy
MolClustPy is a Python package to perform multiple stochastic simulation runs using NFsim (Network-Free stochastic simulator, Sneddon et al, 2011) and characterize distribution of cluster sizes, molecular composition, and bonds across molecular clusters and individual molecules of different types. Please note that NFsim is a non-spatial simulator, so it does not account for excluded volume and non-physical crosslinking when generating molecular complexes.
ModelBricks
ModelBricks is a database of well-annotated, reusable component mechanisms that can be assembled into fully annotated mathematical models for cell biology.