This is a repository for models I use in my research and teaching. Many have been used in COPASI tutorials, others are used as benchmarks, while others are historical models, published decades ago and which I have encoded in a format that can be used by modern simulators.
Most models here are in COPASI's own format *.cps. Some may be also encoded in SBML, a widely used standard for systems biology models. Others can also be part of an OMEX format file, also known as COMBINE archive (which are zip files containing several model and simulation files). All of these files can be loaded into COPASI and from there they can be exported to several standards (including SBML and OMEX). Other packages are able to read SBML and OMEX, so these models are not restricted to COPASI.
Most models contain metadata that links them to their original publications and identifies their components, etc. Some may lack such metadata but I strive to include it (in the spirit of MIRIAM). All models also include comments that identify their origin, purpose, etc. (though, to read these comments they have to be loaded into COPASI).
| File / Folder | Description |
|---|---|
| Neuron | folder with electrophysiological models of neurons |
| optimization_benchmarks | folder with models encoding optimization function benchmarks, useful to test COPASI's optimization algorithms |
| vonDassow2000 | folder with a model and code for a segment polarity network model of von Dassow et al. (2000) as published in Mendes (2023) |
| 100GeneNetwork.cps | an artificial 100-gene network from the AGN suite (pubmed) |
| AllostericKinetics.cps | simulates a typical enzyme kinetics experiment of an allosteric enzyme |
| ChI_DePitta2009.cps | core model of IP3-dependent calcium oscillations by De Pittà et al. (2009) |
| CICR_Li-Rinzel1994.cps | core model of calcium-induded calcium release by Li and Rinzel |
| Frank1953homochirality.cps | Frank's model of homochirality (1953) |
| Goodwin1963.cps | the Goodwin oscillator, from Temporal organization in cells (1963) |
| IrreversibleReactionChain.cps | model of a simple irreversible linear chain of reactions |
| Lotka.cps | the Lotka-Volterra model of oscillating reactions and population dynamics |
| Mendes97TiBS_SignalCascade.cps | model of signalling enzyme cascade controlling metabolism, from Biochemistry by numbers |
| MichaelisMenten.cps | simulates a typical enzyme kinetics experiment of a classic Michaelis-Menten enzyme |
| NeurosporaCircadian-Leloup1999.cps | minimal model of Neurospora circadian clock by Leloup et al (1999) |
| PulsedDrug.cps | model with a drug added in pulses (example with discrete events) |
| PulsedDrugLadder.cps | model with a drug added in pulses at increasing concentrations (example with discrete events) |
| ReversibleMM.cps | reversible Michaelis-Menten enzyme mechanism (from Haldane's 1930 book) |
| Selkov-Wolf-Heinrich.cps | Wolf-Heinrich version of the Sel'kov (1968) model of glycolytic oscillations |
| SEQFB.cps | model of a branched pathway with sequential feedback by Hofmeyr (1986) |
| VariableVolume.cps | model with a compartment that changes volume as a function of time (assignment) |
Models included here are licensed with CC-Zero license unless they were derived from sources that imposed other restrictions. Most were either created by me, some were edited based on other public sources (such as Biomodels)