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Title:
SBML support in the Newt pathway editor

Authors:
Umut Utku Ersahince, Ugur Dogrusoz, and Hasan Balci

Abstract:
The availability of standardized, machine-readable formats such as SBGN and SBML has facilitated the generation of an increasing volume of pathway data. Effective visualization of this information is essential for biological data analysis, particularly in the context of -omics research. As data analysis tools transition to web-based platforms, there is a growing demand for advanced, web-based pathway visualization tools that accommodate diverse use cases.

To address this need, we developed Newt, a web-based pathway editing tool that supports both SBGN and a simplified notation. Newt enables hierarchical pathway representation with arbitrary depth, allowing users to model molecular complexes and cellular compartments with collapsible structures. It features automatic layout, editing, and highlighting functionalities, enabling users to efficiently navigate large pathway maps and inspect pathway components in detail. Newt runs directly in a web browser without requiring installation and can be seamlessly embedded into web applications.

The latest version of Newt now supports not only building maps interactively in a notation compatible with SBML but also allows running simulations given the availability of kinetic data. In this talk, we will cover the general features of Newt followed by the new SBML support.