ArticleFrontiers in neuroinformatics2013
Reaction-diffusion in the NEURON simulator.
Article in Frontiers in neuroinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 78 citations in OpenAlex.
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- Protein trafficking and synaptic demand configure complex and dynamic synaptome architectures of individual neurons.Scientific reports · 2026Article
- Differentiable simulation expands frontiers for biophysical neural models.Nature methods · 2025Article
- Computer models predict differential dendritic vulnerability with ischemia and spreading depression.bioRxiv : the preprint server for biology · 2025Article
- Pre- and Post-synaptic Mechanisms of Neuronal Inhibition Assessed Through Biochemically Detailed Modeling of GABAThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Downmodulation of Potassium Conductances Induces Epileptic Seizures in Cortical Network Models Via Multiple Synergistic Factors.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
- Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software framework.PLoS computational biology · 2024Article
- An electrodiffusive network model with multicompartmental neurons and synaptic connections.PLoS computational biology · 2024Article
- Impact on backpropagation of the spatial heterogeneity of sodium channel kinetics in the axon initial segment.PLoS computational biology · 2024Article
- Diffusive kinks turn kirigami into machines.Nature communications · 2024Article
- Multiscale model of primary motor cortex circuits predicts in vivo cell-type-specific, behavioral state-dependent dynamics.Cell reports · 2023Article
- Temperature modulates PVN pre-sympathetic neurones via transient receptor potential ion channels.Frontiers in pharmacology · 2023Article
- A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience.Neuroinformatics · 2022Article
- Efficient Simulation of 3D Reaction-Diffusion in Models of Neurons and Networks.Frontiers in neuroinformatics · 2022Article
- Modernizing the NEURON Simulator for Sustainability, Portability, and Performance.Frontiers in neuroinformatics · 2022Article
- NetPyNE Implementation and Scaling of the Potjans-Diesmann Cortical Microcircuit Model.Neural computation · 2021Article
- Article
- An electrodiffusive, ion conserving Pinsky-Rinzel model with homeostatic mechanisms.PLoS computational biology · 2020Article
- A Computational Model of the Cholinergic Modulation of CA1 Pyramidal Cell Activity.Frontiers in computational neuroscience · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics) on the dynamics of neuronal response in health and disease, NEURON's Reaction-Diffusion (rxd) module in Python provides specification and simulation for these dynamics, coupled with the electrophysiological dynamics of the cell membrane. Arithmetic operations on species and parameters are overloaded, allowing arbitrary reaction formulas to be specified using Python syntax. These expressions are then transparently compiled into bytecode that uses NumPy for fast vectorized calculations. At each time step, rxd combines NEURON's integrators with SciPy's sparse linear algebra library.
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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.