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PSICS: Parallel Stochastic Ion Channel SimulatorTextensor Limited
http://www.psics.org/
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PSICS: Parallel Stochastic Ion Channel Simulator | psics.org Reviews
https://psics.org
Textensor Limited
psics.org
PSICS: Input formats
http://www.psics.org/formats/index.html
Larr; → next. Please let us know of errors, unclear text or if you have suggestions form improvements:. Models and control parameters are read from a set of linked XML files. Each file covers a particular aspect of the model so that each file can be used in a range of different contexts and common modifications to the model often only involve switching one file for another. Overall specification of the simulation to be performed. Specification of cell structure. Larr; → next.
PSICS: FAQ
http://www.psics.org/faq.html
Larr; → next. Please let us know of errors, unclear text or if you have suggestions form improvements:. If you don't find what you want here, try the forum. The rate in the PSICS Hodgkin Huxley channels for n and m transitions looks to be ten times larger than the original model. Why is this? The documentation includes ranges for most variables. Are these hard limits or just suggestions? What effect do they have? How are the tips of compartments treated? Is the area included? Why another neural simulator?
PSICS: User guide
http://www.psics.org/guide/index.html
Larr; → next. Please let us know of errors, unclear text or if you have suggestions form improvements:. PSICS computes the behavior of neuron models in which the ion channels behave deterministically or stochastically. As well as the formats reference, there are a range of example models. Which can be used to learn about psics by running it or as a starting point for defining new models. Installation and getting started. How to install and run PSICS on Linux, Windows and MacOSX. The methods used for cont...
PSICS Overview
http://www.psics.org/about/index.html
Larr; → next. Please let us know of errors, unclear text or if you have suggestions form improvements:. PSICS is open source, covered by the GNU GPL license. It is developed by Textensor Ltd. Under contract to Dr Matt Nolan. At The Centre for Neuroscience Research. At the University of Edinburgh, UK with grant funding from the BBSRC. Is periodically updated and summarizes major changes and releases. PSICS has been extensively tested and validated. The RallPack. In conjunction with some of the examples.
ICING - interactive channel insertion gui
http://www.psics.org/icing/index.html
Larr; → next. Please let us know of errors, unclear text or if you have suggestions form improvements:. ICING - Interactive Channel INsertion Gui. Once the channel models and the morphology are available, the bulk of the work in specifying a complex neuron model is to relate the two together by specifying how the channels are distributed over the structure. This is the puropse of ICING. It allows the creation and editing of cell properties files. Showing the main features of the user interface.
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NeuroML - A Model Description Language for Computational Neuroscience
https://www.neuroml.org/tool_support
A Model Description Language for Computational Neuroscience. Specifications v1.8.1. Examples v1.8.1. Current Application Support For NeuroML. The following is a list of software applications which currently support NeuroML (last updated: March 2014). Note that not all tools support all parts of NeuroML. If you would like your application included on this list! It's only through user feedback that features like this will make it further up long TODO lists. Supports morphologically detailed single cells.
Installing and running neuroConstruct
http://www.neuroconstruct.org/docs/install.html
Installing and running neuroConstruct. NeuroConstruct has been tested on on WinXP/NT, Red Hat Linux and openSUSE and Mac OS (please let us know. If you've any other experiences on other systems). A local installation of NEURON. Compliant simulator will be needed to execute the simulation scripts generated by neuroConstruct. Details of the interaction with these environments is available here. For tips on improving graphics performance on slower machines. Install Java J2SE 5 or higher. Available here.
neuroConstruct: Software for developing biologically realistic 3D neural networks
http://www.neuroconstruct.org/index.html
NeuroConstruct: Software for developing biologically realistic 3D neural networks. NeuroConstruct is being developed in the Silver Lab. In the Department of Neuroscience, Physiology and Pharmacology. It uses the latest NeuroML. Specifications, including MorphML. Development of this software was made possible with funding from the Wellcome Trust. The Medical Research Council. And the EU Synapse Project. The latest version of neuroConstruct ( v1.6.0, Aug 2012. Is available for download here. And it describ...
Useful neuroConstruct related links
http://www.neuroconstruct.org/links/index.html
Useful neuroConstruct related links. Note that a list of software packages with support for NeuroML is maintained here. NeuroConstruct can interact with most of these tools through import/export. Silver Lab at University College London. Http:/ www.ucl.ac.uk/npp/as. Http:/ www.neuroml.org. Web application for validating MorphML/ChannelML files. Http:/ www.neuroml.org/NeuroMLValidator. Http:/ www.genesis-sim.org/GENESIS. MOOSE Simulator (reimplementation of GENESIS core). Http:/ www.psics.org.
Links
http://www.si-elegans.eu/links.html
Symposium on Neuro-Bio-Inspired Computation and Architectures (NeBICA 2015). International Joint Conference on Neural Networks (IJCNN 2015). The idea and endeavour of simulating. Is not new. It has been suggested several times (e.g., NemaSys. US, 1997), Virtual. Project (Japan, 2004) and is currently pursued by the openworm. With all of its cells) published by Grove and Sternberg (Grove and Sternberg, 2011). Currently two biological accurate 3D models of. A physics engine for biomedical applications (All...
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PSICS: Parallel Stochastic Ion Channel Simulator
Larr; → next. Please let us know of errors, unclear text or if you have suggestions form improvements:. Edinburgh Summer School 2012:. Tutorial and links, Wednesday 29th August. New: Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes. In PLoS Computational Biology 6(8): e1000886. doi:10.1371/journal.pcbi.1000886. Latest changes: psics-1.1.1. Explains how to install PSICS, set up models and run them. The examples. Apart from ...
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PSICS: Parallel Stochastic Ion Channel Simulator
Larr; → next. Please let us know of errors, unclear text or if you have suggestions form improvements:. Edinburgh Summer School 2012:. Tutorial and links, Wednesday 29th August. New: Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes. In PLoS Computational Biology 6(8): e1000886. doi:10.1371/journal.pcbi.1000886. Latest changes: psics-1.1.1. Explains how to install PSICS, set up models and run them. The examples. Apart from ...
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