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BlueCelluLab: Biologically Detailed Neural Network Experimentation API

Tuncel, Mustafa Anil  
•
Gevaert, Mike
•
Van Geit, Werner  
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August 17, 2024
The Journal of Open Source Software

The NEURON simulator, established in 1984 and continuously developed since, stands as the preeminent tool for neuron simulation within computational neuroscience. Its widespread adoption and compatibility with computational clusters and supercomputers underscore its pivotal role in large-scale neuronal research. However, its integration with the Python pro- gramming language has introduced complexities, particularly concerning memory management and object lifecycle. To conceal these challenges from the user and seamlessly interface with community standards for neural network representation data formats such as SONATA, we introduce BlueCelluLab. The high-level Python API simplifies the execution of neural simulations, ranging from single neurons to intricate networks, by managing complexities related to memory management and object lifecycle, thus providing a streamlined experience for users. Today, BlueCelluLab is powering various Python packages, command line interfaces, web applications, and data analysis workflows.

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10.21105.joss.07026.pdf

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