Abstract
BackgroundThere 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.ResultsWe 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.ConclusionsModel 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.
Highlights
There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used
Towards fulfilling the above-mentioned needs, we have developed an all-in-one web interface to compose new models from models defined in SBML format as a tool within PathCase-SB [10,11]
Implementation we describe the details of the model composition interface, the merge algorithm and the model simulation interface
Summary
There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. Systems biology researchers have built, over the years, a large number of computational biological models, and, these models are recently becoming available in webbased data repositories such as the BioModels Database [1] and CellML Model Repository [2] These web-based data repositories store hundreds of computational models, and provide manual curations of some of the models submitted by researchers. Creating more complete or larger models of biological networks and Randhawa, R et al [3] proposed windows-based modeling tools to develop new models from the combination of multiple models They define three different operators to combine SBML models, namely, Fusion, Composition, Aggregation and Flattening [4]. Partial implementations of these approaches can be found at JigCell’s web site [5]
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