ArticlePLoS computational biology2012
Hybrid models and biological model reduction with PyDSTool.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- PyRates-A code-generation tool for modeling dynamical systems in biology and beyond.PLoS computational biology · 2023Article
- Dynamics of hepatocyte-cholangiocyte cell-fate decisions during liver development and regeneration.iScience · 2022Article
- Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression.Nucleic acids research · 2022Article
- Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.NPJ systems biology and applications · 2021Article
- Excitatory-inhibitory tone shapes decision strategies in a hierarchical neural network model of multi-attribute choice.PLoS computational biology · 2021Article
- Multi-stability in cellular differentiation enabled by a network of three mutually repressing master regulators.Journal of the Royal Society, Interface · 2020Article
- Pericytes enable effective angiogenesis in the presence of proinflammatory signals.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows.PLoS computational biology · 2019Article
- A biophysical model explains the spontaneous bursting behavior in the developing retina.Scientific reports · 2019Article
- Article
- Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors.Cell systems · 2018Article
- Code Generation in Computational Neuroscience: A Review of Tools and Techniques.Frontiers in neuroinformatics · 2018Review
- Working Memory and Decision-Making in a Frontoparietal Circuit Model.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2017Article
- Numb prevents a complete epithelial-mesenchymal transition by modulating Notch signalling.Journal of the Royal Society, Interface · 2017Article
- A computational method for the investigation of multistable systems and its application to genetic switches.BMC systems biology · 2016Article
- Is realistic neuronal modeling realistic?Journal of neurophysiology · 2016Review
- Reproducibility in Computational Neuroscience Models and Simulations.IEEE transactions on bio-medical engineering · 2016Article
- Average activity of excitatory and inhibitory neural populations.Chaos (Woodbury, N.Y.) · 2016Article
- Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype.Journal of the Royal Society, Interface · 2016Article
- An ecocultural model predicts Neanderthal extinction through competition with modern humans.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
1 author.
Funding
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Abstract
The PyDSTool software environment is designed to develop, simulate, and analyze dynamical systems models, particularly for biological applications. Unlike the engineering application focus and graphical specification environments of most general purpose simulation tools, PyDSTool provides a programmatic environment well suited to exploratory data- and hypothesis-driven biological modeling problems. In this work, we show how the environment facilitates the application of hybrid dynamical modeling to the reverse engineering of complex biophysical dynamics; in this case, of an excitable membrane. The example demonstrates how the software provides novel tools that support the inference and validation of mechanistic hypotheses and the inclusion of data constraints in both quantitative and qualitative ways. The biophysical application is broadly relevant to models in the biosciences. The open source and platform-independent PyDSTool package is freely available under the BSD license from http://sourceforge.net/projects/pydstool/. The hosting service provides links to documentation and online forums for user support.
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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.