title: An online system for metabolic network analysis.
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.
authors.affiliation: 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 cicek@cs.cmu.edu.
authors.forename: Abdullah Ercument
authors.initials: AE
authors.lastname: Cicek
authors.affiliation: 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.
authors.forename: Xinjian
authors.initials: X
authors.lastname: Qi
authors.affiliation: 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.
authors.forename: Ali
authors.initials: A
authors.lastname: Cakmak
authors.affiliation: 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.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Johnson
authors.affiliation: 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.
authors.forename: Xu
authors.initials: X
authors.lastname: Han
authors.affiliation: 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.
authors.forename: Sami
authors.initials: S
authors.lastname: Alshalwi
authors.affiliation: 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.
authors.forename: Zehra Meral
authors.initials: ZM
authors.lastname: Ozsoyoglu
authors.affiliation: 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.
authors.forename: Gultekin
authors.initials: G
authors.lastname: Ozsoyoglu
mesh_terms: D030541:Databases, Genetic; D020407:Internet; D053858:Metabolic Networks and Pathways; D055432:Metabolomics / Q000379:methods*; D012984:Software; D014584:User-Computer Interface