diff --git a/README.md b/README.md index 6d24f26326..468a7d597c 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,4 @@ -[![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) - -This is the core computational engine of [MOOSE simulator](https://github.com/BhallaLab/moose). This repository contains -C++ codebase and python interface called `pymoose`. For more details about MOOSE simulator, visit https://moose.ncbs.res.in . +[![Python package](https://github.com/BhallaLab/moose-core/actions/workflows/pymoose.yml/badge.svg)](https://github.com/BhallaLab/moose-core/actions/workflows/pymoose.yml) # Installation @@ -18,3 +15,65 @@ Have a look at examples, tutorials and demo here https://github.com/BhallaLab/mo # Build To build `pymoose`, follow instructions given here at https://github.com/BhallaLab/moose-core/blob/master/INSTALL.md + + +---------- +# MOOSE + +MOOSE is the Multiscale Object-Oriented Simulation Environment. It is designed +to simulate neural systems ranging from subcellular components and biochemical +reactions to complex models of single neurons, circuits, and large networks. +MOOSE can operate at many levels of detail, from stochastic chemical +computations, to multicompartment single-neuron models, to spiking neuron +network models. +MOOSE is multiscale: It can do all these calculations together. For example +it handles interactions seamlessly between electrical and chemical signaling. +MOOSE is object-oriented. Biological concepts are mapped into classes, and +a model is built by creating instances of these classes and connecting them +by messages. MOOSE also has classes whose job is to take over difficult +computations in a certain domain, and do them fast. There are such solver +classes for stochastic and deterministic chemistry, for diffusion, and for +multicompartment neuronal models. +MOOSE is a simulation environment, not just a numerical engine: It provides +data representations and solvers (of course!), but also a scripting interface +with Python, graphical displays with Matplotlib, PyQt, and VPython, and +support for many model formats. These include SBML, NeuroML, GENESIS kkit +and cell.p formats, HDF5 and NSDF for data writing. + +This is the core computational engine of [MOOSE simulator](https://github.com/BhallaLab/moose). This repository contains +C++ codebase and python interface called `pymoose`. For more details about MOOSE simulator, visit https://moose.ncbs.res.in . + +# ABOUT VERSION 4.0.0, Jalebi + +Jalebi is an Indian sweet involving a golden twisting tube like a hyper-pretzel, +of crunchy batter soaked in sugar syrup lightly flavoured with spices and +sometimes lemon. + +This release has the following major changes: + +1. A major under-the-hood change to numerics for chemical calculations, +eliminating the use of 'zombie' objects for the solvers. This simplifies +and cleans up the code and object access, but doesn't alter runtimes. + +2. Another major under-the-hood change to use pybind11 as a much cleaner +way to interface the parser with the C++ numerical code. + +3. Addition of a thread-safe and faster parser based on ExprTK + +4. Resurrected objects for handling simulation output saving using HDF5 +format. There is an HDFWriter class, an NSDFWriter, and a new NSDFWriter2. +The latter two implement storage in NSDF, Neuronal Simulation Data Format, +Ray et al Neuroinformatics 2016. NSDF is built on HDF5 and builds up a +specification designed to ensure ready replicability as well as self- +description of model output. + +5. Multiple enhancements to rdesigneur, including vastly improved 3-D +graphics output using VPython. + +6. Various bugfixes + +# LICENSE + +MOOSE is released under GPLv3. + +