Introduction

mozaik is an integrated workflow framework for large scale neural simulations, intended to relieve users from writing boilerplate code for projects involving complex heterogenous neural network models, complex stimulation and experimental protocols and subsequent analysis and plotting.

It is built on top of the following tools:

• PyNN (for simulator independent neural network model definition)
• neo (for exchange and internal representation of data)
• matplotib (for plotting)

Mozaik currently covers the following main areas of the neural simulation workflow:

• High-level components for definition of topologically organized spiking networks (built on top of PyNN)
• Experiment control (description and execution of experiments)
• Stimulus definition framework
• Data storage (storage of recordings and analysis results)
• Data manipulation (a query based system for performing high-level filtering operations over the datastore)
• Analysis module
• Plotting module

Tasks that we would like to cover in mozaik in future are:

• Support of FACETS-like benchmarks within the experiment control framework
• Versioning system built on top of Sumatra
• GUI for recording and analysis browsing and plotting

mozaik is currently subdivided into the core package and 10 subpackages:

• mozaik API - contains the core of the mozaik:

  • core - The core API objects

  • controller - the control center of mozaik workflows
  • space - the input space handling

• sheets Package - Code defining 2D sheets of neurons, one of the basic building blocks of mozaik networks

• connector Package - Defines various connections between sheets

• experiments Package - Defines the experiment interface

• models Package - code encapsulating a mozaik network consisting of sheets and connectors and providing

  an ‘I/O’ interface to it. Currently it also contains retinal models (these might be reorganized in future).

• stimuli Package - definition of stimulus interfaces

• storage Package - data storage and data querying code

• analysis Package - analysis code

• visualization Package - plotting code

• meta-workflow Package - code supporting meta-workflows, such as parameter searches

• tools Package - utility code

This might change as mozaik grows, and code in the framework is likely to get separated into new sub-packages as it matures.

Scetch of how the control flows between the mozaik elements: