Tag: kinetic model

The Kinetic Simulation Algorithm Ontology aims at providing support in unambiguously referring to simulation algorithms when describing a simulation experiment. It describes and classifies existing algorithms and their inter-relationships through the ...

The Ontology of Physics for Biology is a reference of classical physics as applied to the dynamics of biological systems. This resource provides a reference ontology of physical properties (e.g., pressure, chemical concentration) and principles (e.g. ...

JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.

The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. ...

BioSimulators is a registry of containerized biosimulation tools that provide consistent command-line interfaces. The BioSimulations web application helps investigators browse this registry to find simulation tools that have the capabilities (support ...

KIDA (KInetic Database for Astrochemistry) is a database of kinetic data of interest for astrochemical (interstellar medium and planetary atmospheres) studies. KIDA is a project initiated by different communities in order to 1) improve the interactio ...

The Numerical Markup Language (NuML) (pronounce "neumeul" and not "new em el", that sounds like NewML) is a simple XML format to exchange multidimensional arrays of numbers to be used with model and simulation descriptions. NuML was initially develop ...

BioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model ...

EnzymeML is a free and open standard XML-based interchange format for data on enzyme-catalyzed reactions. The purpose of EnzymeML is to store and exchange enzyme kinetics data between instruments, software tools, and databases. EnzymeML will allow sc ...

The BioSimulators conventions encompass several conventions for biosimulation tools (see below). In combination with modeling languages such as Cell-ML and SBML, SED-ML, KISAO, and COMBINE/OMEX, the BioSimulators standards enable investigators to use ...