Open source simulation of the pyloric network
© Fourie and Andras; licensee BioMed Central Ltd. 2007
Published: 6 July 2007
Simulations of the pyloric network have been developed since the 1970s . However, these simulations do not include many of the known details about the pyloric network, and produce a behaviour that resembles at high level the behaviour of the biological network, but ignores the behavioural details. These earlier simulations are also application specific, and cannot be easily modified and re-used by researchers.
Methods and results
We present here a new open source simulation of the pyloric network. The simulation is developed using the Neuron simulation language . Each neuron is simulated using four compartments: soma, primary neurite, axon, dendrite. The primary neurite is connected to all three other compartments. The connections are implemented by linking the axon outputs of neurons to the corresponding dendrite inputs of other neurons. The effects of neuromodulation are implemented in form of changing characteristics of neural connections in response to changes in the values of a multi-dimensional modulation state variable (i.e. each component of the vector indicates the presence and concentration of a neuromodulator, the components being labeled by the corresponding modulator). The values of parameters for the neural compartments are set using the STG neuron database developed by Prinz et al . To determine the right setting of parameters for each cell type we used the simulator attached to STG neuron database  to check that the output of our model neurons matches the output of modeled neurons.
Our simulation is developed as open source software, allowing other users to download the source code and modify it. In this way other researchers may use this detailed simulation of the pyloric network to check experimental assumptions and also possibly to develop simulations of other related networks (e.g. gastric mill network).
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