ArticleBioinformatics (Oxford, England)2013
The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
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- 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
- Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways.Scientific data · 2022Article
- A systems approach to investigate GPCR-mediated Ras signaling network in chemoattractant sensing.Molecular biology of the cell · 2022Article
- Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry.Molecular biology of the cell · 2021Article
- SBML Level 3: an extensible format for the exchange and reuse of biological models.Molecular systems biology · 2020Review
- The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling.NPJ systems biology and applications · 2020Article
- The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems.PLoS computational biology · 2020Article
- A software package for immunologists to learn simulation modeling.BMC immunology · 2020Article
- Mechanistic Models of Cellular Signaling, Cytokine Crosstalk, and Cell-Cell Communication in Immunology.Frontiers in immunology · 2019Article
- Application of targeted mass spectrometry in bottom-up proteomics for systems biology research.Journal of proteomics · 2018Review
- Anosmin1 Shuttles Fgf to Facilitate Its Diffusion, Increase Its Local Concentration, and Induce Sensory Organs.Developmental cell · 2018Article
- Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology.Proceedings. Euromicro International Conference on Parallel, Distributed, and Network-based Processing · 2018Article
- Automated visualization of rule-based models.PLoS computational biology · 2017Article
- Compartmental and Spatial Rule-Based Modeling with Virtual Cell.Biophysical journal · 2017Article
- IL-2 sensitivity and exogenous IL-2 concentration gradient tune the productive contact duration of CD8(+) T cell-APC: a multiscale modeling study.BMC systems biology · 2016Article
- Targeted Proteomics-Driven Computational Modeling of Macrophage S1P Chemosensing.Molecular & cellular proteomics : MCP · 2015Article
- Modeling for (physical) biologists: an introduction to the rule-based approach.Physical biology · 2015Review
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Authors and funding
3 authors.
Funding
Abstract
motivationBiochemical modeling efforts now frequently take advantage of the possibility to automatically create reaction networks based on the specification of pairwise molecular interactions. Even though a variety of tools exist to visualize the resulting networks, defining the rules for the molecular interactions typically requires writing scripts, which impacts the non-specialist accessibility of those approaches. We introduce the Simmune Modeler that allows users to specify molecular complexes and their interactions as well as the reaction-induced modifications of the molecules through a flexible visual interface. It can take into account the positions of the components of trans-membrane complexes relative to the embedding membranes as well as symmetry aspects affecting the reactions of multimeric molecular structures. Models created with this tool can be simulated using the Simmune Simulator or be exported as SBML code or as files describing the reaction networks as systems of ODEs for import into Matlab. AVAILABILITY: The Simmune Modeler and the associated simulators as well as extensive additional documentation and tutorials are freely available for Linux, Mac and Windows: http://go.usa.gov/QeH (Note shortened case-sensitive URL!).
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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.