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https://github.com/zakandrewking/escher

Build, share, and embed visualizations of metabolic pathways.
https://github.com/zakandrewking/escher

bioinfomatics biology d3js escher javascript python visualization

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Build, share, and embed visualizations of metabolic pathways.

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# Escher



Escher is a web-based tool to build, view, share, and embed metabolic maps. The

easiest way to use Escher is to browse or build maps on the

[Escher website](http://escher.github.io/).



Visit the [documentation](http://escher.readthedocs.org/) to get started with

Escher and explore the API.



Check out the

[developer docs](https://escher.readthedocs.org/en/latest/development.html),

the [Gitter chat room](https://gitter.im/zakandrewking/escher), and the

[Development Roadmap](https://github.com/zakandrewking/escher/wiki/Development-Roadmap) for information

on Escher development. Feel free to submit bugs and feature requests as Issues,

or, better yet, Pull Requests.



Follow [@zakandrewking](https://twitter.com/zakandrewking) for Escher updates.



You can help support Escher by citing our publication when you use Escher or

EscherConverter:



Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan

E. Lewis, and Bernhard O. Palsson (2015) *Escher: A web application for

building, sharing, and embedding data-rich visualizations of biological

pathways*, PLOS Computational Biology 11(8):

e1004321. doi:[10.1371/journal.pcbi.1004321](http://dx.doi.org/10.1371/journal.pcbi.1004321)



Escher was developed at [SBRG](http://systemsbiology.ucsd.edu/). Funding was

provided by [The National Science Foundation Graduate Research Fellowship](https://www.nsfgrfp.org)

under Grant no. DGE-1144086, The European Commission as part of a Marie Curie

International Outgoing Fellowship within the EU 7th Framework Program for

Research and Technological Development ([EU project AMBiCon, 332020](http://ec.europa.eu/research/mariecurieactions/node_en)),

and [The Novo Nordisk Foundation](http://novonordiskfonden.dk/)

through [The Center for Biosustainability](https://www.biosustain.dtu.dk/)

at the Technical University of Denmark (NNF10CC1016517)



# Building and testing Escher



## JavaScript



First, install dependencies with [npm](https://www.npmjs.com) (or you can use

[yarn](https://yarnpkg.com)):



```

npm install

```



Escher uses webpack to manage the build process. To run typical build steps, just run:



```

npm run build

```



You can run a development server with:



```

npm run start

# or for live updates when the source code changes:

npm run watch

```



To test the JavaScript files, run:



```

npm run test

```



## Python



Escher has a Python package for generating Escher visualizations from within a

Python data anlaysis session. To learn more about using the features of the

Python package, check out the documentation:



https://escher.readthedocs.io/en/latest/escher-python.html



You can install it with pip:



```

pip install escher

```



## Jupyter extensions



When you `pip install escher`, the Jupyter notebook extension should be

installed automatically. If that doesn't work, try:



```bash

# The notebook extenstion should install automatically. You can check by running:

jupyter nbextension list

# Make sure you have version >=5 of the `notebook` package

pip install "notebook>=5"

# To manually install the extension

jupyter nbextension install --py escher

jupyter nbextension enable --py escher

# depending on you environment, you might need the `--sysprefix` flag with those commands

```



To install the Jupyter lab extension, simply install Escher with `pip install escher` then

install the extension:



```bash

jupyter labextension install @jupyter-widgets/jupyterlab-manager

jupyter labextension install escher

```



## Python/Jupyter Development



For development of the Python package, first build the JavaScript package and

copy it over to the `py` directory with these commands in the Escher root:



```

npm install

npm run build

npm run copy

```



Then in the `py` directory, install the Python package:



```

cd py

pip install -e . # installs escher in develop mode and dependencies

```



For Python testing, run this in the `py` directory:



```

cd py

pytest

```



To develop the Jupyter notebook and Jupyter Lab extensions, you will need

install them with symlinks.



First, install the Python package for development as described above.



For the Jupyter notebooks, run:



```

cd py

jupyter nbextension install --py --symlink escher

jupyter nbextension enable --py escher

```



If you are using virtualenv or conda, you can add the `--sys-prefix` flag to

those commands to keep your environment isolated and reproducible.



When you make changes, you will need to `yarn build && yarn copy` and refresh

notebook browser tab.



For Jupyter Lab, run (in the root directory):



```

yarn watch # keep this running as a separate process

jupyter labextension install @jupyter-widgets/jupyterlab-manager

jupyter labextension link

jupyter lab --watch

```



If you don't see changes when you edit the code, try refreshing or restarting

`jupyter lab --watch`.



## Docs



Build and run the docs::



```

cd docs

./build_docs

cd _build/html

python -m SimpleHTTPServer # python 2

python -m http.server # python 3

```