ArticleBioinformatics (Oxford, England)2016
Rule-based modeling with Virtual Cell.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Artificial Intelligence Virtual Organoids (AIVOs).Bioactive materials · 2026Review
- Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications.PLoS computational biology · 2026Article
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 2025Article
- bnglViz: online visualization of rule-based models.Bioinformatics (Oxford, England) · 2024Article
- A framework for multi-scale intervention modeling: virtual cohorts, virtual clinical trials, and model-to-model comparisons.Frontiers in systems biology · 2023Article
- A roadmap for translational cancer glycoimmunology at single cell resolution.Journal of experimental & clinical cancer research : CR · 2022Review
- Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry.Molecular biology of the cell · 2021Article
- Computational modeling of RNase, antisense ORF0 RNA, and intracellular compartmentation and their impact on the life cycle of the line retrotransposon.Computational and structural biotechnology journal · 2021Article
- NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale.Biophysical journal · 2020Article
- Article
- Pleione: A tool for statistical and multi-objective calibration of Rule-based models.Scientific reports · 2019Article
- Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? What Really Constitutes the Study of "Systems Biology" and How Might Such an Approach Facilitate Vaccine Design.Cold Spring Harbor perspectives in biology · 2018Review
- Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.PLoS computational biology · 2018Article
- SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.Bioinformatics (Oxford, England) · 2017Article
- Automated visualization of rule-based models.PLoS computational biology · 2017Article
- Compartmental and Spatial Rule-Based Modeling with Virtual Cell.Biophysical journal · 2017Article
- Quantitative computational models of molecular self-assembly in systems biology.Physical biology · 2017Review
- Finding your inner modeler: An NSF-sponsored workshop to introduce cell biologists to modeling/computational approaches.Cellular logistics · 2017Article
- Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology.International journal of molecular sciences · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
unlabelledRule-based modeling is invaluable when the number of possible species and reactions in a model become too large to allow convenient manual specification. The popular rule-based software tools BioNetGen and NFSim provide powerful modeling and simulation capabilities at the cost of learning a complex scripting language which is used to specify these models. Here, we introduce a modeling tool that combines new graphical rule-based model specification with existing simulation engines in a seamless way within the familiar Virtual Cell (VCell) modeling environment. A mathematical model can be built integrating explicit reaction networks with reaction rules. In addition to offering a large choice of ODE and stochastic solvers, a model can be simulated using a network free approach through the NFSim simulation engine. AVAILABILITY AND IMPLEMENTATION: Available as VCell (versions 6.0 and later) at the Virtual Cell web site (http://vcell.org/). The application installs and runs on all major platforms and does not require registration for use on the user's computer. Tutorials are available at the Virtual Cell website and Help is provided within the software. Source code is available at Sourceforge. CONTACT: vcell_support@uchc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.