Related External Links to:
Kinetic simulation tools
• CellDesigner - Modeling tool for biochemical networks
• PottersWhell - Mathematical modeling of dynamical systems
Parameter estimation tools
• SBML-PET-MPI - Parameter estimation tool for SBML based models
• Copasi - Biochemical network simulator
• SBTOOLBOX2 - Systems Biology toolbox for MATLAB
Standards and exchange formats
• SBML - Systems Biology Markup Language
• MIRIAM - Minimum Information Requested in the Annotation of Models
• MIASE - Minimum Information About a Simulation Experiment
• SBGN - Systems Biology Graphical Notation
• SED-ML - Simulation Experiment Description Markup Language
• BioPAX - Biological Pathways Exchange
Databases
Pathways
• KEGG - Kyoto Encyclopedia of Genes and Genomes
• WikiPathways - Biological pathways for the scientific community
• Reactome - Manually curated pathway database
Kinetic information
• BRENDA - Kinetic parameters for several organisms
• Sabio-RK - Biochemical reactions and their kinetic properties
• BioNumbers - Key numbers in molecular biology
• TECR - Thermodynamics of Enzyme-Catalyzed Reactions
Metabolic reconstructions
Other data resources
• Stranford Microarray database - Database of microarray experiments reconstructions
• Gene Expression Omnibus - Gene expression data from microarray and high throughput sequencing studies