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

Sarp A. Coskun; Xinjian Qi; Ali Cakmak; En Cheng; A. E. Cicek; Lei Yang; Rishiraj Jadeja; Ranjan K. Dash; Nicola Lai; Gultekin Ozsoyoglu; Zehra M. Ozsoyoglu

doi:10.1186/1752-0509-6-67

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

Sarp A. Coskun, Xinjian Qi, Ali Cakmak, En Cheng, A. E. Cicek, Lei Yang, Rishiraj Jadeja, Ranjan K. Dash, Nicola Lai, Gultekin Ozsoyoglu^*, Zehra M. Ozsoyoglu

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

Abstract

Background: 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.Results: 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.Conclusions: Each of the current 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.

Original language	English
Article number	67
Journal	BMC Systems Biology
Volume	6
DOIs	https://doi.org/10.1186/1752-0509-6-67
Publication status	Published - 16 Jun 2012
Externally published	Yes

Funding

Authors acknowledge the contributions of (late) Marco Cabrera for his early contributions to PathCase-SB, and Herbert Sauro for his critical comments, which forced us to reevaluate the contributions of Pathcase-SB. We acknowledge PathCase-SB design and coding contributions of many graduate and undergraduate students. PathCase-SB derives from PathCase, and the authors acknowledge the PathCase design and development contributions of many (more than 30) graduate students, including Mustafa Kirac (original designer and coder of Graph Viewer), Brendan Elliott (all parts of PathCase, from which PathCase-SB has evolved) and many others. This research has been supported by the National Science Foundation grants DBI 0743705, DBI 0849956, CRI 0551603 and by the National Institute of Health grant GM088823.

Funders	Funder number
National Science Foundation	DBI 0849956, DBI 0743705, CRI 0551603
National Institutes of Health
National Institute of General Medical Sciences	R01GM088823

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title = "PathCase-SB: Integrating data sources and providing tools for systems biology research",

abstract = "Background: 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.Results: 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.Conclusions: Each of the current 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.",

author = "Coskun, {Sarp A.} and Xinjian Qi and Ali Cakmak and En Cheng and Cicek, {A. E.} and Lei Yang and Rishiraj Jadeja and Dash, {Ranjan K.} and Nicola Lai and Gultekin Ozsoyoglu and Ozsoyoglu, {Zehra M.}",

year = "2012",

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doi = "10.1186/1752-0509-6-67",

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AU - Coskun, Sarp A.

AU - Qi, Xinjian

AU - Cakmak, Ali

AU - Cheng, En

AU - Cicek, A. E.

AU - Yang, Lei

AU - Jadeja, Rishiraj

AU - Dash, Ranjan K.

AU - Lai, Nicola

AU - Ozsoyoglu, Gultekin

AU - Ozsoyoglu, Zehra M.

PY - 2012/6/16

Y1 - 2012/6/16

N2 - Background: 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.Results: 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.Conclusions: Each of the current 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.

AB - Background: 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.Results: 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.Conclusions: Each of the current 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.

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

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