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An online model composition tool for system biology models

Sarp A Coskun1, A Ercument Cicek2, Nicola Lai3, Ranjan K Dash4, Z Meral Ozsoyoglu1 and Gultekin Ozsoyoglu1*

Author Affiliations

1 Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA

2 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA

3 Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA

4 Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA

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BMC Systems Biology 2013, 7:88  doi:10.1186/1752-0509-7-88

Published: 5 September 2013

Abstract

Background

There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models.

Results

We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user’s input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models.

Conclusions

Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.

Keywords:
System biology models; Simulation; Composition; ODE solver