论文标题

Netpyne的实施和重新制作Potjans-Diesmanncortical Microcircuit模型

NetPyNE implementation and rescaling of the Potjans-Diesmanncortical microcircuit model

论文作者

Romaro, Cecilia, Najman, Fernando Araujo, Lytton, William W, Roque, Antonio C, Dura-Bernal, Salvador

论文摘要

Potjans-Diesmann皮质微电路模型是最初在巢中进行的广泛使用的模型。在这里,我们使用Netpyne(神经元模拟器的高级Python界面)重新实现了该模型,并复制了理论出版物的发现。我们还实施了一种基于网络理论上现有工作的第一阶和二阶统计信息的网络尺寸的方法。新的实现可以使用具有MUL-TICATMATMENT形态和多个生物物理逼真的通道的更详细的神经元模型。这为新研究开辟了模型,包括对树突处理的研究,单个通道参数的影响以及在网络中通常多尺度的相互作用。重新缩放方法在运行这些更真实的模拟时提供了灵活性,可以增加或减小网络大小。最后,Netpyne使用其声明性语言来促进模型进行改建或扩展模型。优化模型参数;运行有效的大规模并行模拟;并通过内置方法分析themodel,包括局部现场计算和信息流量测量。

The Potjans-Diesmann cortical microcircuit model is a widely used model originallyimplemented in NEST. Here, we re-implemented the model using NetPyNE, a high-level Python interface to the NEURON simulator, and reproduced the findings of theoriginal publication. We also implemented a method for rescaling the network sizewhich preserves first and second order statistics, building on existing work on networktheory. The new implementation enables using more detailed neuron models with mul-ticompartment morphologies and multiple biophysically realistic channels. This opensthe model to new research, including the study of dendritic processing, the influenceof individual channel parameters, and generally multiscale interactions in the network.The rescaling method provides flexibility to increase or decrease the network size ifrequired when running these more realistic simulations. Finally, NetPyNE facilitatesmodifying or extending the model using its declarative language; optimizing modelparameters; running efficient large-scale parallelized simulations; and analyzing themodel through built-in methods, including local field potential calculation and informa-tion flow measures.

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