Blue-Neuroscience-as-a-Service-SingleCell is an open source web application. It enables users to quickly visualize single cell model morphologies in 3D or as a dendrogram. Using a simple web user interface, single cell simulations can be easily configured and launched, producing voltage traces from selected compartments.
You can use the application on the EBRAINS platform at https://ebrains-cls-interactive.github.io/online-use-cases.html by selecting "Single Cell InSilico Experiments". You can also follow this direct link.
The user documentation for the service can be found here.
From version 2.0 we are using BlueCelluLab library to run simulations.
To get the code for legacy (neuron) version check out v1 branch
- After cloning or forking the repository, you can use poetry to install the dependencies:
poetry install- To start the backend server run the following command. This starts some docker services and then brings up the fastapi server:
make buildYou can upload your own models and run single cell simulations. The .zip file format must be:
model_name.zip
- model_name
- mechanisms /
- *.mod files
- morphology /
- morphology file loaded by cell.hoc
- cell.hoc
- mechanisms /
When you use the BlueNaaS-SingleCell software, we ask you to cite the following:
The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology and from the Human Brain Project's Specific Grant Agreement 3.
Copyright (c) 2022-2024 Blue Brain Project/EPFL