Multiscale modeling and interoperability in MOOSE

Introduction

MOOSE (Multiscale Object Oriented Simulation Environment; http://moose.ncbs.res.in) is a general biological simulator. It allows the simulation of models that span many levels of detail, from single molecules to neuronal networks. MOOSE is backward compatible with GENESIS [1] and has a similar set of objects of various types (channels, molecules, compartments) to represent biological concepts. We report current developments that combine to give MOOSE distinctive capabilities in multiscale modeling and interoperability.

Multiscale modeling and scalability

Specialized Numerical Engines

We have implemented Hines' solver for biophysical models of neurons and a GSL- (GNU Scientific Library-) based solver for kinetics of biochemical signaling networks. In terms of speed of execution, the Hines' solver matches the performance of GENESIS, whereas the kinetics' solver is 10×–50× faster than GENESIS. A Gillespie solver for stochastic chemical kinetics has been implemented.

SigNeur

SigNeur is a set of tools to specify multiscale neuronal models comprising of biochemical signaling and cellular biophysics. The user embeds reaction networks in different parts of a cell, and specifies an appropriate solver for each part of the model (e.g., a stochastic chemical solver for small volumes). Communication is managed seamlessly between solvers. A specific example is upregulation of AMPA receptors in a spine, which is conveyed from a chemical solver to a neuronal solver, and interpreted there as an increase in maximal synaptic conductance.

Parallelization

A developer- and user-friendly framework has been implemented using the MPI (Message Passing Interface) standard to allow MOOSE to run in parallel on a cluster. Both developers and users can think of their problem in a serial fashion, with the underlying framework managing cross-node communication and load-balancing. MOOSE has successfully cleared a large set of unit tests on a 64-node Linux based Opteron cluster.

Interoperability

PyMOOSE

PyMOOSE is a Python-based scripting interface to MOOSE implemented using SWIG (Scalable Wrapper Interface Generator). This lets us use Python to mediate communication among Python-aware simulators. For example [2], we have simulated a single neuron in NEURON [3], and an intracellular reaction network in MOOSE. Simulation state variables were communicated at runtime between the two simulators using Python.

MUSIC

MUlti SImulator Coordinator (MUSIC) [4] is a standard to allow multiple simulators to exchange data during a simulation. Each simulator is allowed to be a parallelized application. MUSIC compatibility was added to MOOSE and the NEST [5] simulators by their respective developers. A simulation was carried out with a cortical network model running in NEST sending spike-times via MUSIC to a striatal network model running in MOOSE.

SBML

The capability to read and write models of chemical signaling in the simulator-independent Systems Biology Markup Language (SBML) is currently being implemented and tested in MOOSE.