Introduction

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 a simulation environment, not just a numerical engine. It provides the essentials by way of object-oriented representations of model concepts and fast numerical solvers, but its scope is much broader. It has a scripting interface with Python, graphical displays with Matplotlib, PyQt, and OpenGL, and support for many model formats.

MOOSE can read kinetic models in SBML and GENESIS kkit formats, from BioModels.net and DOQCS. MOOSE also supports electrical models specified in NeuroML and Genesis .p formats, and can load over 30,000 morphology files from NeuroMorpho.org (.swc format).

About Moose version 4.1.1 – Incremental Release over v4.1.0 "Jhangri" 

This version builds upon the v4.1.0 (Jhangri) release and includes important internal improvements, documentation enhancements, and binding support.
 

ABOUT VERSION 4.1.1, Jhangri

Jhangri is an Indian sweet in the shape of a flower. It is made of white-lentil (Vigna mungo) batter, deep-fried in ornamental shape to form the crunchy, golden body, which is then soaked in sugar syrup lightly flavoured with spices.

This release has the following changes:
 

Installation:

Installing released version from PyPI using pip. 

run: pip install pymoose
 

Post installation You can check that moose is installed and initializes correctly by running:

python -c "import moose; ch = moose.HHChannel('ch'); moose.le()"

This should show:

Elements under 

/ 

/Msgs 

/clock 

/classes 

/postmaster

/ch

Now you can import moose in a Python script or interpreter with the statement: 

>>> import moose

New Features 

  • Formula-based versions of HH-type channels 
  • Added HHChannelF and HHGateF for formula-based evaluation of Hodgkin-Huxley type gating parameters 
  • Added a formula interface for HHGate: Users can now assign string formula in exprtk syntax to alphaExpr, betaExpr, tauExpr and infExpr to fill up the tables. These can take either v for voltage or c for concentration as independent variable names in the formula. 
  • Added moose.sysfields to display system fields like fieldIndex, numData etc. 
  • Reintroduced moose.neighbors() function to retrieve neighbors on a particular field. This allows more flexibility than element.neighbors[fieldName] by allowing the user to specify the message type ("Single", "OneToOne", etc.) and direction (1 for incoming, 0 for outgoing, otherwise both directions).

API Updates 

  • API changes in moose.vec and moose.element, including updated documentation. 
  • moose.showfields updated to:
    • skip system fields like fieldIndex, numData etc. These can now be printed using sysfields function. 
    • print common but informative fields like name, className, tick and dt at the top. 
    • return None instead of the output string to avoid cluttering the interactive session.
  • moose.pwe() returns None to avoid output clutter. Use moose.getCwe() for retrieving the current working element. 
  • children field of moose elements (ObjId) now return a list of elements instead of vecs (Id). This brings consistency between parent and children fields. 
  • moose.le() returns None to avoid output clutter. Use element.children field to access the list of children. 
  • path field for elements (ObjId) now includes the index in brackets, as in the core C++. This avoids confusion with vec (Id) objects. 
  • moose.copy() now accepts either str path or element or vec for src and dest parameters. 
  • Attempt to access paths with non-existent element now consistently raises RuntimeError. 
  • moose.delete now accepts vec (Id) as argument. 

 

Bug Fixes

  • bool attribute handling added to moose.vec 
  • More informative error message for unhandled attributes in moose.vec 
  • Fixed issue #505 
  • moose.setCwe() now handles str, element (ObjId) and vec (Id) parameters correctly 
  • Fixed moose.showmsg() mixing up incoming and outgoing messages. 

Documentation

  • Updated Ubuntu build instructions for better clarity. 
  • Enhanced documentation for HHGate, including additional warnings. 
  • Updated documentation for Stoich, with improved code comments and clarifications.

LICENSE

MOOSE is released under GPLv3.