ArticleComputation (Basel, Switzerland)2014
SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology.
Article in Computation (Basel, Switzerland), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 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.
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Who cites it
5 citing papers in PubMed.
- A tool for modeling gene regulatory networks (GRN_modeler) and its applications to synthetic biology.Molecular systems biology · 2025Article
- Visualizing metabolic network dynamics through time-series metabolomic data.BMC bioinformatics · 2020Article
- Combined in silico and 19F NMR analysis of 5-fluorouracil metabolism in yeast at low ATP conditions.Bioscience reports · 2019Article
- Construction of integrated gene logic-chip.Nature nanotechnology · 2018Article
- SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.BMC systems biology · 2015Article
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Authors and funding
4 authors.
Funding
Abstract
The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration. In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to identify parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the parameter space and for the large-scale model calibration and estimation of uncertain parameter values.
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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.