1- [ ![ 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 )
2-
3- This is the core computational engine of [ MOOSE simulator] ( https://github.com/BhallaLab/moose ) . This repository contains
4- C++ codebase and python interface called ` pymoose ` . For more details about MOOSE simulator, visit https://moose.ncbs.res.in .
1+ [ ![ Python package] ( https://github.com/BhallaLab/moose-core/actions/workflows/pymoose.yml/badge.svg )] ( https://github.com/BhallaLab/moose-core/actions/workflows/pymoose.yml )
52
63# Installation
74
@@ -18,3 +15,65 @@ Have a look at examples, tutorials and demo here https://github.com/BhallaLab/mo
1815# Build
1916
2017To build ` pymoose ` , follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md
18+
19+
20+ ----------
21+ # MOOSE
22+
23+ MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed
24+ to simulate neural systems ranging from subcellular components and biochemical
25+ reactions to complex models of single neurons, circuits, and large networks.
26+ MOOSE can operate at many levels of detail, from stochastic chemical
27+ computations, to multicompartment single-neuron models, to spiking neuron
28+ network models.
29+ MOOSE is multiscale: It can do all these calculations together. For example
30+ it handles interactions seamlessly between electrical and chemical signaling.
31+ MOOSE is object-oriented. Biological concepts are mapped into classes, and
32+ a model is built by creating instances of these classes and connecting them
33+ by messages. MOOSE also has classes whose job is to take over difficult
34+ computations in a certain domain, and do them fast. There are such solver
35+ classes for stochastic and deterministic chemistry, for diffusion, and for
36+ multicompartment neuronal models.
37+ MOOSE is a simulation environment, not just a numerical engine: It provides
38+ data representations and solvers (of course!), but also a scripting interface
39+ with Python, graphical displays with Matplotlib, PyQt, and VPython, and
40+ support for many model formats. These include SBML, NeuroML, GENESIS kkit
41+ and cell.p formats, HDF5 and NSDF for data writing.
42+
43+ This is the core computational engine of [ MOOSE simulator] ( https://github.com/BhallaLab/moose ) . This repository contains
44+ C++ codebase and python interface called ` pymoose ` . For more details about MOOSE simulator, visit https://moose.ncbs.res.in .
45+
46+ # ABOUT VERSION 4.0.0, Jalebi
47+
48+ Jalebi is an Indian sweet involving a golden twisting tube like a hyper-pretzel,
49+ of crunchy batter soaked in sugar syrup lightly flavoured with spices and
50+ sometimes lemon.
51+
52+ This release has the following major changes:
53+
54+ 1 . A major under-the-hood change to numerics for chemical calculations,
55+ eliminating the use of 'zombie' objects for the solvers. This simplifies
56+ and cleans up the code and object access, but doesn't alter runtimes.
57+
58+ 2 . Another major under-the-hood change to use pybind11 as a much cleaner
59+ way to interface the parser with the C++ numerical code.
60+
61+ 3 . Addition of a thread-safe and faster parser based on ExprTK
62+
63+ 4 . Resurrected objects for handling simulation output saving using HDF5
64+ format. There is an HDFWriter class, an NSDFWriter, and a new NSDFWriter2.
65+ The latter two implement storage in NSDF, Neuronal Simulation Data Format,
66+ Ray et al Neuroinformatics 2016. NSDF is built on HDF5 and builds up a
67+ specification designed to ensure ready replicability as well as self-
68+ description of model output.
69+
70+ 5 . Multiple enhancements to rdesigneur, including vastly improved 3-D
71+ graphics output using VPython.
72+
73+ 6 . Various bugfixes
74+
75+ # LICENSE
76+
77+ MOOSE is released under GPLv3.
78+
79+
0 commit comments