Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Aug 23, 2026

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Escher is a web application designed to visualize data on biological pathways, addressing challenges in interpreting large, multi-omics datasets. The software enables rapid construction of new pathway maps with semi-automated pathway suggestions derived from user data and genome-scale models. It supports gene- and protein-associated visualization on reactions and pathways through enzyme-catalysis rules, helping reveal trends across common genomic data types alongside metabolite- and reaction-oriented measurements. Built on web technologies, Escher facilitates rapid adaptation, extension, sharing, and embedding of visualizations while providing examples of these capabilities.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages13

Reading Time33 min

AccessFree to download

Abstract

Author Summary

Introduction

Data visualization needs in systems biology

Escher’s role in pathway-based analysis

OPEN ACCESS Citation: King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO (2015) Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol 11(8): e1004321 . doi:10.1371/journal.pcbi.1004321 Editor: Paul P Gardner, University of Canterbury, NEW ZEALAND Received: March 18, 2015 Accepted: May 5, 2015 Published: August 27, 2015 Copyright: © 2015 King et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: Funding for this work was provided by: ZK: The National Science Foundation Graduate Research Fellowship ([https://www.nsfgrfp.org/](https://www.nsfgrfp.org/)) under Grant no. DGE-1144086 AD: 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://](http://)[ ](http://)[ec.europa.eu/research/mariecurieactions/about-mca/](ec.europa.eu/research/mariecurieactions/about-mca/)[ ](ec.europa.eu/research/mariecurieactions/about-mca/)[actions/iof/index_en.htm](actions/iof/index_en.htm)) AE, NS, BOP: A grant from RESEARCH ARTICLE Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways Zachary A. King1, Andreas Dräger1,2, Ali Ebrahim1, Nikolaus Sonnenschein3, Nathan E. Lewis4, Bernhard O. Palsson1,4 * 1 Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America, USA, 2 Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany, 3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark, 4 Department of Pediatrics, University of California, San Diego, La Jolla, California, United States of America * [palsson@ucsd.edu](palsson@ucsd.edu) Abstract Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite-and reaction-oriented data types (e.g. metabolomics, fluxomics) . Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools. Author Summary We are now in the age of big data. More than ever before, biological discoveries require powerful and flexible tools for managing large datasets, including both visual and statistical tools. Pathway-based visualization is particularly powerful since it enables one to analyze complex datasets within the context of actual biological processes and to elucidate how each change in a cell effects related processes. To facilitate such approaches, we present Escher, a web application that can be used to rapidly build pathway maps. On Escher maps, diverse datasets related to genes, reactions, and metabolites can be quickly contextualized within metabolism and, increasingly, beyond metabolism. Escher is available now for free use (under

FAQs

What is Escher used for?

Escher is a web application for visualizing data on biological pathways, helping contextualize diverse datasets within biological processes.

How does Escher help users create new pathway maps?

Users can rapidly design new pathway maps, with suggestions derived from user data and genome-scale models to enable semi-automated drawing.

How does Escher connect genes or proteins to pathway reactions?

Escher visualizes gene- and protein-related data on associated reactions and pathways using rules that define which enzymes catalyze each reaction.

Aug 23, 2026

Upload by Jacob