https://github.com/damourchris/msb1013_computationalneuroscience

Simulation-Based Inference of Neuronal Models
https://github.com/damourchris/msb1013_computationalneuroscience

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Simulation-Based Inference of Neuronal Models

• Host: GitHub
• URL: https://github.com/damourchris/msb1013_computationalneuroscience
• Owner: damourChris
• License: mit
• Created: 2023-09-13T11:43:06.000Z (over 1 year ago)
• Default Branch: master
• Last Pushed: 2024-08-03T10:13:47.000Z (5 months ago)
• Last Synced: 2024-08-03T11:28:59.398Z (5 months ago)
• Language: Jupyter Notebook
• Homepage: https://damourchris.github.io/MSB1013_ComputationalNeuroscience/
• Size: 43.2 MB
• Stars: 3
• Watchers: 1
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
 Multi-layered neural input simulation-based inference 





    


        

            

        

        

            

        

    


Computational Neuroscience - MSB1013

Systems Biology

Maastricht University

2023




This project aims to infer the different layers that were given as input to a neuronal model. The output of the model is then transformed into a BOLD model. Finally, the [SBI toolbox](https://sbi-dev.github.io/sbi/) is used to infer the different simulation parameters.

---

Table of contents


- [Project](#project)

- [Installation](#installation)

- [Contributing](#contributing)

- [License](#license)

## Project 

The project is divided intro three modules: 

1. Neuron simulations, where the initial training data is generated

2. BOLD Signal, where the data from the neuron simulation is transformed into a BOLD signal 

3. Neural Net inference, where a neural net is used to perform inference to extract to original neuron simulation parameters. 

## Installation

This project uses Python and pip. Go check them out if you don't have them locally installed.

```sh

$ python --version

$ pip --version

```

To install the project, you can clone it locally and install the required packages:

```sh

$ git clone https://github.com/damourChris/MSB1013_ComputationalNeuroscience.git

$ cd MSB1013_ComputationalNeuroscience

$ pip install -r requirements.txt

```

We recommend using a conda environment for managing the dependencies. If you don't have conda installed, you can get it from here. Once you have conda installed, create a new environment and install the required packages:

```sh

$ conda create --name myenv

$ conda activate myenv

$ pip install -r requirements.txt

```

## Contributing

This project originates from the MSB1013 - Computational Neuroscience course of 2023. The codebase is not under active development, however feel free to fork this repo and work on it. Pull request are warmly welcomed. 

*Note: if you find some errors in the documentation, feel free to open up an issue or a PR.*

## License

The source code and documentation are released under the MIT License. See the LICENSE file for more details.