DendroTweaks

DendroTweaks is a Python toolbox designed for creating and validating single-cell biophysical models with active dendrites.

It is available both as a standalone Python package and as a web-based application. This repository contains the code for the web-based application.

Table of Contents

• Learn More
• Publication
• Repository Structure
• Installation

Learn More

• Standalone Library: Explore the official documentation for detailed tutorials and API reference.
• Web Application: Access the GUI online via our platform at dendrotweaks.dendrites.gr.
• Quick Overview: Check out our e-poster, including a video demonstration, presented at the FENS Forum 2024 in Vienna.

Publication

For an in-depth understanding of DendroTweaks, refer to our publication in eLife:

Roman Makarov, Spyridon Chavlis, Panayiota Poirazi (2024).
DendroTweaks: An interactive approach for unraveling dendritic dynamics.
eLife 13:RP103324. https://doi.org/10.7554/eLife.103324.1

If you find DendroTweaks helpful for your research, please consider citing our work:

@article{Makarov2024,
    title={DendroTweaks: An interactive approach for unraveling dendritic dynamics},
    author={Makarov, Roman and Chavlis, Spyridon and Poirazi, Panayiota},
    journal={eLife},
    volume={13},
    pages={RP103324},
    year={2024},
    doi={10.7554/eLife.103324.1}
}

Repository Structure

This repository is organized as follows:

dendrotweaksapp/
│
├── app/
│   ├── presenter/                # Coordination of app components
│   │   ├── presenter.py          # Main presenter class
│   │   └── ...                   # Mixins for the presenter class
│   │
│   ├── static/                   # Static files (e.g., CSS, JS, user data)
│   ├── templates/                # HTML templates for the app
│   ├── view/                
│   │   ├── view.py               # Main view class
│   │   └── ...                   # Code to initialize GUI elements
│   │
│   ├── main.py                   # Main script to launch the Bokeh app
│   ├── bokeh_utils.py            
│   ├── default_config.json       # App configuration
│   ├── user_config.json          # User preferences
│   ├── bokeh_utils.py            
│   ├── utils.py                  
│   └── logger.py
│
├── environment.yml               # Conda environment configuration
├── requirements.txt              # Python dependencies for pip
├── README.md                     # Documentation and setup instructions
└── LICENSE                       # Project license

Installation

In this section, we will explain how to locally install DendroTweaks and run it in GUI mode via a Bokeh server.

Set Up a Conda Environment (recommended)

Create and activate a conda environment using the provided environment.yml file:

conda env create -f environment.yml
conda activate dendrotweaksapp

Install Dependencies Using PIP (optional)

Alternatively, install required packages using pip:

pip install -r requirements.txt

Install more graph layouts (optional)

sudo apt-get install graphviz graphviz-dev

Run the Bokeh Server

To run the Bokeh server and launch the app locally, use the following command:

bokeh serve --show app

This will start the Bokeh server and automatically open your default web browser to display the app.