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Welcome

Installation instructions

Features

  • Selection, integration and storage of metabolic information using an Ontology-Based Mediator of KEGG, CHEBI, SABIORK and BRENDA.
  • SBML compatible (import and export).
  • Use SBGN and yFiles layouts for metabolic networks visualization.
  • Automatic annotation following MIRIAM specifications (only for integrated databases).
  • Design of metabolic networks from KEGG pathway, SBML file or list of EC numbers.
  • Friendly assistant to define kinetic properties of biochemical reactions.
Screenshots


kinetic panel general panel ec list

Publications

Reyes-Palomares A., Montañez R., Real-Chicharro A., Chniber O., Kerzazi A., Navas-Delgado I., Medina MA., Aldana-Montes J.F.  and Sánchez-Jiménez F. Systems Biology Metabolic Modeling Assistant (SBMM): An ontology-based tool for the integration of metabolic data in kinetic modeling. Bioinformatics, doi:10.1093/bioinformatics/btp061.

Systems Biology Metabolic Modeling assistant (SBMM assistant) is a web application to consult basic metabolic information, to build metabolic models, and to annotate them in SBML files with external resource annotations suggested by MIRIAM. SBMM assistant integrates the information data from KEGG, CHEBI, BRENDA and SABIORK based on an ontology-based mediator that takes advantage of semantic web technologies. The main objective of SBMM assistant is to enhance the interoperability between the kinetic modeling programs and the kinetic parameters databases (BRENDA and SABIORK) to perform simulations and analyses. This interoperability is possible due to the compatibility generated in the SBML community.

Supported by CIBER-ER (The "CIBER de Enfermedades Raras" is an initiative of the ISCIII), Spanish MCIN (Ministerio de Ciencia e Innoavación) (SAF2008-02522 and TIN2008-04844), Fundación Ramón Areces and "Plan Andaluz de Investigación" (BIO-267, P07-CVI-02999, CVI-657 and P07-TIC-02978).

Tutorial

Contact

sbmm@uma.es

Department of Molecular Biology and Biochemistry
Faculty of Sciences
Campus Teatinos
University of Malaga, 29071 Malaga, Spain
(+34) 952132025

© 2008 ASP, UMA Creative Commons License