An online model composition tool for system biology models

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 PathCaseSB (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

Metadata-based modeling of information resources on the web

This paper deals with the problem of modeling Web information resources using expert knowledge and personalized user information for improved Web searching capabilities. We propose a "Web information space" model, which is composed of Web-based information resources (HTML/XML [Hypertext Markup Language/Extensible Markup Language] documents on the Web), expert advice repositories (domain-expert-specified meta-data for information resources), and personalized information about users (captured as user profiles that indicate users' preferences about experts as well as users' knowledge about topics)

Topic-centric querying of web information resources

This paper deals with the problem of modeling web information resources using expert knowledge and personalized user information, and querying them in terms of topics and topic relationships. We propose a model for web information resources, and a query language SQL-TC (Topic-Centric SQL) to query the model. The model is composed of web-based information resources (XML or HTML documents on the web), expert advice repositories (domain-expert-specified metadata for information resources), and personalized information about users (captured as user profiles, that indicate users' preferences as to which expert advice they would like to follow, and which to ignore, etc)

Querying Web Metadata: Native score management and text support in databases

In this article, we discuss the issues involved in adding a native score management system to object-relational databases; to be used in querying Web metadata (that describes the semantic content of Web resources). The Web metadata model is based on topics (representing entities), relationships among topics (called metalinks), and importance scores (sideway values) of topic and metalinks. We extend database relations with scoring functions and importance scores. We add to SQL score-management clauses with well-defined semantic, and propose the sideway-value algebra (SVA), to evaluate the extended SQL queries. SQL extensions and the SVA algebra are illustrated through two Web resources, namely, the DBLP Bibliography and the SIGMOD Anthology

PathCase-SB: integrating data sources and providing tools for systems biology research

<p>Abstract</p> <p>Background</p> <p>Integration of metabolic pathways resources and metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation of metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks.</p> <p>Results</p> <p>PathCase Systems Biology (PathCase-SB) is built and released. This paper describes PathCase-SB user interfaces developed to date. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate systems biology models data and metabolic network data of selected biological data sources on the web (currently, BioModels Database and KEGG, respectively), and to provide more powerful and/or new capabilities via the new web-based integrative framework.</p> <p>Conclusions</p> <p>Each of the <b>c</b>urrent four PathCase-SB interfaces, namely, Browser, Visualization, Querying, and Simulation interfaces, have expanded and new capabilities as compared with the original data sources. PathCase-SB is already available on the web and being used by researchers across the globe.</p