Faculty Collaboration Database

An online model composition tool for system biology models. BMC Syst Biol 2013 Sep 05;7:88

Date

09/07/2013

Pubmed ID

24006914

Pubmed Central ID

PMC3846440

DOI

10.1186/1752-0509-7-88

Scopus ID

2-s2.0-84883453083 (requires institutional sign-in at Scopus site)   7 Citations

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.

Author List

Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G

Author

Ranjan K. Dash PhD Professor in the Biomedical Engineering department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Algorithms
Computer Simulation
Energy Metabolism
Enzymes
Humans
Internet
Kinetics
Online Systems
Software
Systems Biology
User-Computer Interface