ArticleBiophysical journal2017
Compartmental and Spatial Rule-Based Modeling with Virtual Cell.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- Protein interactions, calcium, phosphorylation, and cholesterol modulate CFTR cluster formation on membranes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SYK negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy.Journal of immunology (Baltimore, Md. : 1950) · 2025Article
- MxlPy-Python package for mechanistic learning and hybrid modelling in life science.Bioinformatics advances · 2025Article
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 2025Article
- Spleen Tyrosine Kinase (SYK) negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy.bioRxiv : the preprint server for biology · 2024Article
- bnglViz: online visualization of rule-based models.Bioinformatics (Oxford, England) · 2024Article
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.PLoS computational biology · 2024Article
- Building the next generation of virtual cells to understand cellular biology.Biophysical journal · 2023Review
- Reaction-diffusion models in weighted and directed connectomes.PLoS computational biology · 2022Article
- Hybrid modelling of biological systems: current progress and future prospects.Briefings in bioinformatics · 2022Review
- A kinetic model of phospholipase C-γ1 linking structure-based insights to dynamics of enzyme autoinhibition and activation.The Journal of biological chemistry · 2022Article
- An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability.PLoS biology · 2021Article
- Mechanistic dissection of spatial organization in NF-κB signaling pathways by hybrid simulations.Integrative biology : quantitative biosciences from nano to macro · 2021Article
- Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages.Bioinformatics (Oxford, England) · 2021Article
- A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis.Frontiers in genetics · 2021Review
- An inactive receptor-G protein complex maintains the dynamic range of agonist-induced signaling.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).Journal of integrative bioinformatics · 2020Article
- pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems.BMC bioinformatics · 2020Article
Corrections and comments
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Authors and funding
6 authors.
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Abstract
In rule-based modeling, molecular interactions are systematically specified in the form of reaction rules that serve as generators of reactions. This provides a way to account for all the potential molecular complexes and interactions among multivalent or multistate molecules. Recently, we introduced rule-based modeling into the Virtual Cell (VCell) modeling framework, permitting graphical specification of rules and merger of networks generated automatically (using the BioNetGen modeling engine) with hand-specified reaction networks. VCell provides a number of ordinary differential equation and stochastic numerical solvers for single-compartment simulations of the kinetic systems derived from these networks, and agent-based network-free simulation of the rules. In this work, compartmental and spatial modeling of rule-based models has been implemented within VCell. To enable rule-based deterministic and stochastic spatial simulations and network-free agent-based compartmental simulations, the BioNetGen and NFSim engines were each modified to support compartments. In the new rule-based formalism, every reactant and product pattern and every reaction rule are assigned locations. We also introduce the rule-based concept of molecular anchors. This assures that any species that has a molecule anchored to a predefined compartment will remain in this compartment. Importantly, in addition to formulation of compartmental models, this now permits VCell users to seamlessly connect reaction networks derived from rules to explicit geometries to automatically generate a system of reaction-diffusion equations. These may then be simulated using either the VCell partial differential equations deterministic solvers or the Smoldyn stochastic simulator.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.