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README.md

VizGallery

About

Join the chat at https://gitter.im/Phinch2/Lobby

Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Davis. Whether it's genes, proteins, or microbial species, Phinch provides an interactive visualization tool that allows users to explore and manipulate large biological datasets.

Install

First, clone the repo via git:

git clone https://github.com/PhinchApp/Phinch.git your-project-name

Then install dependencies with yarn or npm install.

$ cd phinch
$ yarn

You'll also need to install hdf5 in order to be able to load hdf5 biom files. You can obtain it from the HDF Group, or from a package manager like brew:

$ brew install hdf5

Finally, here's the tricky part. Phinch uses a python script in the biomhandler folder to load hdf5 biom files. To make Phinch easy to install, we use PyInstaller to package that script into a standablone executable. Follow these steps to generate the executable:

cd biomhandler
virtualenv ./virtualenv
source ./virtualenv/bin/activate
cat requirements.txt | xargs -n 1 -L 1 pip install
pyinstaller biomhandler.spec

Run

$ npm run dev

Good to Know

Phinch's performance will depend on your system, but in general large biom files may take time to load. Files with a large number of selected samples (more than 500) may be sluggish in the filter and visualization views. Please be patient when working with large files, or consider pre-filtering your data for visualization.

Packaging

Package apps for the local platform with:

$ npm run package

Mozilla Global Sprint: Round 5 of Mozilla Open Leaders

Mozilla

Mozilla Open Leaders information

Code of Conduct

Check out our Code of Conduct

Contribution Guidelines

Check out our Contribution Guidelines

License

The BSD 2-Clause License