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



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

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

GSMNDB - Genome-scale metabolic networks

Other data resources

Stranford Microarray database - Database of microarray experiments reconstructions

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