• CellDesigner - Modeling tool for biochemical networks

• PottersWhell - Mathematical modeling of dynamical systems

• SBML-PET-MPI - Parameter estimation tool for SBML based models

• Copasi - Biochemical network simulator

• SBTOOLBOX2 - Systems Biology toolbox for MATLAB

• 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

• KEGG - Kyoto Encyclopedia of Genes and Genomes

• WikiPathways - Biological pathways for the scientific community

• Reactome - Manually curated pathway database

• 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

• BIGG - Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

• GSMNDB - Genome-scale metabolic networks

• Stranford Microarray database - Database of microarray experiments reconstructions

• Gene Expression Omnibus - Gene expression data from microarray and high throughput sequencing studies