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Cicek AE, Qi X, Cakmak A, Johnson SR, Han X, Alshalwi S, Ozsoyoglu ZM, Ozsoyoglu G. An online system for metabolic network analysis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau091. [PMID: 25267793 PMCID: PMC4178370 DOI: 10.1093/database/bau091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Metabolic networks have become one of the centers of attention in life sciences research with the advancements in the metabolomics field. A vast array of studies analyzes metabolites and their interrelations to seek explanations for various biological questions, and numerous genome-scale metabolic networks have been assembled to serve for this purpose. The increasing focus on this topic comes with the need for software systems that store, query, browse, analyze and visualize metabolic networks. PathCase Metabolomics Analysis Workbench (PathCaseMAW) is built, released and runs on a manually created generic mammalian metabolic network. The PathCaseMAW system provides a database-enabled framework and Web-based computational tools for browsing, querying, analyzing and visualizing stored metabolic networks. PathCaseMAW editor, with its user-friendly interface, can be used to create a new metabolic network and/or update an existing metabolic network. The network can also be created from an existing genome-scale reconstructed network using the PathCaseMAW SBML parser. The metabolic network can be accessed through a Web interface or an iPad application. For metabolomics analysis, steady-state metabolic network dynamics analysis (SMDA) algorithm is implemented and integrated with the system. SMDA tool is accessible through both the Web-based interface and the iPad application for metabolomics analysis based on a metabolic profile. PathCaseMAW is a comprehensive system with various data input and data access subsystems. It is easy to work with by design, and is a promising tool for metabolomics research and for educational purposes. Database URL: http://nashua.case.edu/PathwaysMAW/Web
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Affiliation(s)
- Abdullah Ercument Cicek
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15222, USA, Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Computer Science, Istanbul Sehir University, Istanbul 34662, Turkey
| | - Xinjian Qi
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15222, USA, Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Computer Science, Istanbul Sehir University, Istanbul 34662, Turkey
| | - Ali Cakmak
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15222, USA, Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Computer Science, Istanbul Sehir University, Istanbul 34662, Turkey
| | - Stephen R Johnson
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15222, USA, Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Computer Science, Istanbul Sehir University, Istanbul 34662, Turkey
| | - Xu Han
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15222, USA, Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Computer Science, Istanbul Sehir University, Istanbul 34662, Turkey
| | - Sami Alshalwi
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15222, USA, Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Computer Science, Istanbul Sehir University, Istanbul 34662, Turkey
| | - Zehra Meral Ozsoyoglu
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15222, USA, Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Computer Science, Istanbul Sehir University, Istanbul 34662, Turkey
| | - Gultekin Ozsoyoglu
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15222, USA, Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Computer Science, Istanbul Sehir University, Istanbul 34662, Turkey
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Coskun SA, Qi X, Cakmak A, Cheng E, Cicek AE, Yang L, Jadeja R, Dash RK, Lai N, Ozsoyoglu G, Ozsoyoglu ZM. PathCase-SB: integrating data sources and providing tools for systems biology research. BMC SYSTEMS BIOLOGY 2012; 6:67. [PMID: 22697505 PMCID: PMC3410775 DOI: 10.1186/1752-0509-6-67] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 06/14/2012] [Indexed: 11/10/2022]
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.
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Affiliation(s)
- Sarp A Coskun
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
| | - Xinjian Qi
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
| | - Ali Cakmak
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
| | - En Cheng
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
| | - A Ercument Cicek
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
| | - Lei Yang
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
| | - Rishiraj Jadeja
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
| | - Ranjan K Dash
- Department of Physiology, Medical College of Wisconsin, Milwaukee, USA
| | - Nicola Lai
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, USA
- Department of Pediatrics, Case Western Reserve University, Cleveland, USA
| | - Gultekin Ozsoyoglu
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
| | - Zehra Meral Ozsoyoglu
- Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
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