Bio Simulators: a web UI for biological simulation

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Abstract

Summary:

A host of formal, textual languages for modeling cellular processes have recently emerged, but their simulation tools often require an installation process which can pose a barrier for use. Bio Simulators is a framework for easy online deployment of simulators, providing a uniform web-based user interface to a diverse pool of tools. The framework is demonstrated through two plugins based on the KaSim Kappa simulator, one running directly in the browser and another running in the cloud.

Availability:

Web tool: bsims.azurewebsites.net. KaSim client side simulator: github.com/NicolasOury/KaSimJS. KaSim cloud simulator: github.com/mdpedersen/KaSimCloud.

Contact:

michael.d.pedersen@gmail.com or Andrew.Phillips@microsoft.com

Supplementary information:

Supplementary data are available at Bioinformatics online.

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