ArticlePloS one2012
Python as a federation tool for GENESIS 3.0.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- SpikingJelly: An open-source machine learning infrastructure platform for spike-based intelligence.Science advances · 2023Article
- BindsNET: A Machine Learning-Oriented Spiking Neural Networks Library in Python.Frontiers in neuroinformatics · 2018Article
- Software for Brain Network Simulations: A Comparative Study.Frontiers in neuroinformatics · 2017Article
- Reproducibility in Computational Neuroscience Models and Simulations.IEEE transactions on bio-medical engineering · 2016Article
- Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON.Neural computation · 2016Article
- Modeling the Cerebellar Microcircuit: New Strategies for a Long-Standing Issue.Frontiers in cellular neuroscience · 2016Review
- Towards real-time communication betweenJournal of computational surgery · 2014Article
- A flexible, interactive software tool for fitting the parameters of neuronal models.Frontiers in neuroinformatics · 2014Article
- Stimfit: quantifying electrophysiological data with Python.Frontiers in neuroinformatics · 2014Article
- Reaction-diffusion in the NEURON simulator.Frontiers in neuroinformatics · 2013Article
- Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS.Frontiers in computational neuroscience · 2013Article
- The Virtual Brain: a simulator of primate brain network dynamics.Frontiers in neuroinformatics · 2013Article
- A federated design for a neurobiological simulation engine: the CBI federated software architecture.PloS one · 2012Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be 'glued' together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience.
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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.