Welcome to the documentation for Escher¶
Escher is a web-based tool for building, viewing, and sharing visualizations of biological pathways. These ‘pathway maps’ are a great way to contextualize biological datasets. The easiest way to use Escher is to browse and build maps on the Escher website. New users may be interested in the Getting started guide.
Escher in 3 minutes¶
Help! I just upgraded to v1.2 and my map and model caches are empty!¶
Starting with Escher v1.2, the maps and models available from the Escher website are versioned. Each time you upgrade Escher, you will have access to the new versions of the Escher maps and models. Any maps and models you were using before are still saved in the Escher cache in case you need them. For more details on finding, managing, and clearing the cache, see the Python cache functions.
Also starting with Escher v1.2, the maps and models in Escher are the same as those in the BiGG Database.
- View pathway maps in any modern web browser
- Build maps using the content of genome-scale metabolic models
- Visualize data on reactions, genes, and metabolites
- Full text search
- Detailed options for changing colors, sizes, and more, all from the web browser
- View maps inside the IPython Notebook
- Embed maps within any website, with minimal dependencies (escher.js, d3.js, and optionally Twitter Bootstrap)
We recommend using Google Chrome for optimal performance, but Escher will also run in the latest versions of Firefox, Internet Explorer, and Safari (including mobile Safari).
Escher can be used without any installation by visiting the Escher website. However, you can install escher if you would like to (1) run Escher offline, (2) include your own maps and models in the launch page, (3) view Escher maps in an IPython Notebook, or (4) modify the source code.
To install the latest stable version of Escher, run:
pip install escher
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
- 1. Getting started
- 2. Escher, COBRA, and COBRApy
- 3. Run Escher locally and in IPython
- 4. Validate and convert maps
- 5. Building and contributing maps
- 6. Developing with Escher
- 7. EscherConverter
- 9. Python API
- 10. License