OpenWorm Foundation, USA
MetaCell Limited, UK.
Philos Trans R Soc Lond B Biol Sci. 2018 Sep 10;373(1758):20170380. doi: 10.1098/rstb.2017.0380.
Geppetto is an open-source platform that provides generic middleware infrastructure for building both online and desktop tools for visualizing neuroscience models and data and managing simulations. Geppetto underpins a number of neuroscience applications, including Open Source Brain (OSB), Virtual Fly Brain (VFB), NEURON-UI and NetPyNE-UI. OSB is used by researchers to create and visualize computational neuroscience models described in NeuroML and simulate them through the browser. VFB is the reference hub for neural anatomy and imaging data including neuropil, segmented neurons, microscopy stacks and gene expression pattern data. Geppetto is also being used to build a new user interface for NEURON, a widely used neuronal simulation environment, and for NetPyNE, a Python package for network modelling using NEURON. Geppetto defines domain agnostic abstractions used by all these applications to represent their models and data and offers a set of modules and components to integrate, visualize and control simulations in a highly accessible way. The platform comprises a backend which can connect to external data sources, model repositories and simulators together with a highly customizable frontend.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling at cellular resolution'.
盖比特是一个开源平台，为构建可视化神经科学模型和数据以及管理模拟的在线和桌面工具提供通用中间件基础设施。盖比特是许多神经科学应用程序的基础，包括开源大脑 (Open Source Brain，OSB)、虚拟果蝇大脑 (Virtual Fly Brain，VFB)、NEURON-UI 和 NetPyNE-UI。OSB 被研究人员用于创建和可视化在 NeuroML 中描述的计算神经科学模型，并通过浏览器对其进行模拟。VFB 是神经解剖和成像数据的参考中心，包括神经突、分段神经元、显微镜堆栈和基因表达模式数据。盖比特还被用于为神经元模拟环境 NEURON 和使用 NEURON 进行网络建模的 Python 包 NetPyNE 构建新的用户界面。盖比特定义了所有这些应用程序用于表示其模型和数据的领域无关抽象，并提供了一组模块和组件，以高度可访问的方式集成、可视化和控制模拟。该平台包括一个后端，该后端可以与外部数据源、模型存储库和模拟器连接，以及一个高度可定制的前端。本文是“从连接组到行为：在细胞分辨率下进行建模”讨论会议议题的一部分。
