TY - GEN
T1 - PathCase-MAW
T2 - 2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
AU - Cicek, A. Ercument
AU - Qi, Xinjian
AU - Cakmak, Ali
AU - Johnson, Stephen R.
AU - Han, Xu
AU - Alshalwi, Sami
AU - Ozsoyoglu, Gultekin
PY - 2013
Y1 - 2013
N2 - 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 running 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 sub-systems. It is easy to work with by design, and is a promising tool for metabolomics research and for educational purposes.
AB - 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 running 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 sub-systems. It is easy to work with by design, and is a promising tool for metabolomics research and for educational purposes.
KW - Metabolic network database
KW - SBML
KW - SMDA
UR - http://www.scopus.com/inward/record.url?scp=84888143522&partnerID=8YFLogxK
U2 - 10.1145/2506583.2506621
DO - 10.1145/2506583.2506621
M3 - Conference contribution
AN - SCOPUS:84888143522
SN - 9781450324342
T3 - 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
SP - 219
EP - 228
BT - 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Y2 - 22 September 2013 through 25 September 2013
ER -