ModelDB: Models that contain SBML

Simulation Environment: SBML

Note: this list includes both models hosted here at ModelDB and models where have metadata and link to the sourcecode somewhere else. These may also be viewed separately; see the browse by simulator page.

A multiscale approach to analyze circadian rhythms (Vasalou & Henson, 2010) (SBML)
A nicotinic acetylcholine receptor kinetic model (Edelstein et al. 1996)
Squid axon (Hodgkin, Huxley 1952) (SBML, XPP, other)
Circadian clock model based on protein sequestration (simple version) (Kim & Forger 2012)
Response of AMPA receptor kinetic model to glutamate release distance (Allam et al., 2015)

http://sbml.org/Main_Page
"The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes. It's applicable to simulations of metabolism, cell-signaling, and many other topics. SBML has been evolving since mid-2000 thanks to an international community of software developers and users. ..."

Top authors for SBML:

Vasalou C (1)
Henson MA (1)
Edelstein SJ (1)
Schaad O (1)
Henry E (1)
Bertrand D (1)
Changeux JP (1)
HODGKIN AL (1)
HUXLEY AF (1)
Kim JK (1)

Top concepts studied with SBML:

Oscillations (2)
Action Potentials (2)
Circadian Rhythms (2)
Activity Patterns (1)
Temporal Pattern Generation (1)
Signaling pathways (1)
Calcium dynamics (1)
Reaction-diffusion (1)
Ion Channel Kinetics (1)
Invertebrate (1)

Top neurons studied with SBML:

Suprachiasmatic nucleus (SCN) neuron (2)
Abstract rate-based neuron (1)
Squid axon (1)

Top currents studied with SBML:

I K,Ca (1)
I Sodium (1)
I Calcium (1)
I Potassium (1)
I Na,t (1)
I K (1)

Top references cited by these models:

Leloup JC, Goldbeter A. (2003). Toward a detailed computational model for the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 100 (2)
HODGKIN AL, HUXLEY AF. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. The Journal of physiology. 117 (1)
Goldbeter A, Dupont G, Berridge MJ. (1990). Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation. Proceedings of the National Academy of Sciences of the United States of America. 87 (1)
Ikeda M, Sugiyama T, Wallace CS, Gompf HS, Yoshioka T, Miyawaki A, Allen CN. (2003). Circadian dynamics of cytosolic and nuclear Ca2+ in single suprachiasmatic nucleus neurons. Neuron. 38 (1)
Jackson AC, Yao GL, Bean BP. (2004). Mechanism of spontaneous firing in dorsomedial suprachiasmatic nucleus neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 24 (1)