Motif Studio is a browser-based tool for querying connectomes with the DotMotif motif query language.

Installation and Setup

This repository holds dependencies and dev-dependencies in requirements/. To install dependencies, run:

pip install -r requirements/requirements.in

To install dev-dependencies, run:

pip install -r requirements/dev-requirements.in

Configuring the Server

The server is configured using a config.json file in src/server. An example configuration file is provided in src/server/config.example.json.

Running the Server

To run the server in "development" mode, run:

uvicorn src.server:app --reload

To run the server in "production" mode, run:

uvicorn src.server:app

Running the Tests

To run the tests in "development" watch mode, run:

ptw

This will run the test suite and then wait for changes to the codebase. When changes are detected, the test suite will be run again.

To run the tests once, run:

pytest

Running the web application

This is a Next.js project bootstrapped with create-next-app.

Getting Started

First, run the development server:

npm run dev

Open http://localhost:3000 with your browser to see the result.

Citation

If this work is useful to your research, please cite the following paper:

Scalable graph analysis tools for the connectomics community Matelsky et al., 2022

@article{matelsky2022scalable,
  title={Scalable graph analysis tools for the connectomics community},
  author={Matelsky, Jordan K and Johnson, Erik C and Wester, Brock and Gray-Roncal, William},
  journal={bioRxiv},
  pages={2022--06},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}