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- [ ![ Build Status - master] ( https://travis-ci.org/BhallaLab/moose-core.svg?branch=master )] ( https://travis-ci.org/BhallaLab/moose-core ) | [ ![ PyPI version] ( https://badge.fury.io/py/pymoose.svg )] ( https://badge.fury.io/py/pymoose )
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-
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- This is the core computational engine of [ MOOSE simulator] ( https://github.com/BhallaLab/moose ) . This repository contains
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- C++ codebase and python interface called ` pymoose ` . For more details about MOOSE simulator, visit https://moose.ncbs.res.in .
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+ [ ![ Python package] ( https://github.com/BhallaLab/moose-core/actions/workflows/pymoose.yml/badge.svg )] ( https://github.com/BhallaLab/moose-core/actions/workflows/pymoose.yml )
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# Installation
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@@ -18,3 +15,65 @@ Have a look at examples, tutorials and demo here https://github.com/BhallaLab/mo
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# Build
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To build ` pymoose ` , follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md
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+ ----------
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+ # MOOSE
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+
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+ MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed
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+ to simulate neural systems ranging from subcellular components and biochemical
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+ reactions to complex models of single neurons, circuits, and large networks.
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+ MOOSE can operate at many levels of detail, from stochastic chemical
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+ computations, to multicompartment single-neuron models, to spiking neuron
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+ network models.
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+ MOOSE is multiscale: It can do all these calculations together. For example
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+ it handles interactions seamlessly between electrical and chemical signaling.
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+ MOOSE is object-oriented. Biological concepts are mapped into classes, and
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+ a model is built by creating instances of these classes and connecting them
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+ by messages. MOOSE also has classes whose job is to take over difficult
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+ computations in a certain domain, and do them fast. There are such solver
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+ classes for stochastic and deterministic chemistry, for diffusion, and for
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+ multicompartment neuronal models.
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+ MOOSE is a simulation environment, not just a numerical engine: It provides
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+ data representations and solvers (of course!), but also a scripting interface
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+ with Python, graphical displays with Matplotlib, PyQt, and VPython, and
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+ support for many model formats. These include SBML, NeuroML, GENESIS kkit
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+ and cell.p formats, HDF5 and NSDF for data writing.
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+
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+ This is the core computational engine of [ MOOSE simulator] ( https://github.com/BhallaLab/moose ) . This repository contains
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+ C++ codebase and python interface called ` pymoose ` . For more details about MOOSE simulator, visit https://moose.ncbs.res.in .
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+
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+ # ABOUT VERSION 4.0.0, Jalebi
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+
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+ Jalebi is an Indian sweet involving a golden twisting tube like a hyper-pretzel,
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+ of crunchy batter soaked in sugar syrup lightly flavoured with spices and
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+ sometimes lemon.
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+
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+ This release has the following major changes:
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+
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+ 1 . A major under-the-hood change to numerics for chemical calculations,
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+ eliminating the use of 'zombie' objects for the solvers. This simplifies
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+ and cleans up the code and object access, but doesn't alter runtimes.
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+
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+ 2 . Another major under-the-hood change to use pybind11 as a much cleaner
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+ way to interface the parser with the C++ numerical code.
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+
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+ 3 . Addition of a thread-safe and faster parser based on ExprTK
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+
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+ 4 . Resurrected objects for handling simulation output saving using HDF5
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+ format. There is an HDFWriter class, an NSDFWriter, and a new NSDFWriter2.
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+ The latter two implement storage in NSDF, Neuronal Simulation Data Format,
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+ Ray et al Neuroinformatics 2016. NSDF is built on HDF5 and builds up a
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+ specification designed to ensure ready replicability as well as self-
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+ description of model output.
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+
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+ 5 . Multiple enhancements to rdesigneur, including vastly improved 3-D
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+ graphics output using VPython.
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+ 6 . Various bugfixes
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+
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+ # LICENSE
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+
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+ MOOSE is released under GPLv3.
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+
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