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  BioUML module: sbml

SBML Model Repository module

Download (52 kb).

The module contains an number of SBML models published at http://www.sbw-sbml.org/ModelsWebPages/ModelRepository.htm.

SBML models have not information about species layout, thus some very simple layout algorithm is used by SBML plug-in for initial species and reactions layout. Further we plan to provide models with hand made layout and optimize them for BioUML workbench.

Further reading:

module import - describes how the module can be imported into BioUML workbench
SBML plug-in - describes how SBML format is supported by BioUML workbench
model list - list of SBML models in the current module version.

 


Model list

Current module version contains 18 models that were downloaded from SBML model Repository at May 27, 2003.

Code

Model Description

CellCycle-1991Gol

Minimal Mitotic Oscillator

(Goldbeter, 1991)

CellCycle-1991Tys

Cell Cycle Model - 6 variables

(Tyson, 1991)

CellCycle-1991Tys-2

Cell Cycle Model - 2 variables

(Tyson, 1991)

CellCycle-1997Nov

Cell Cycle Model, 13 variables

(Novak & Tyson, 1997)

CellCycle-1998Gar

Minimal Mitotic Oscillator with Inhibitor

(Gardner et al., 1998)

CircClock-1999Lel

Circadian Oscillator involving PER and TIM

(Leloup & Goldbeter, 1999)

CircClock-2002Vil

Minimal Model for Circadian Oscillations

(Vilar et al, 2002)

Genetic-2000Elo

Repressilator: A synthetic oscillatory network of transcriptional regulators (Elowitz & Leibler, 2000)

MAPKcasc-2000Lev

MAPK cascade in solution (no scaffold)

(Levchenko et al, 2000)

MAPKcasc-2000Lev-2

MAPK cascade on a scaffold

(Levchenko et al, 2000)

MAPKcasc-2000Kho

MAPK cascade with negative feedback

(Kholodenko, 2000)

Metabolism-2000Teu

Glycolysis in Saccharomyces cerevisiae

(Teusink et al, 2000)

Metabolism-2001Hel

Glycolysis in Trypanosoma brucei

(Helfert et al, 2001)

Metabolism-2002Hoe

Pyruvate branches in Lactococcus lactis

(Hoefnagel et al., 2002)

Metabolism-2002Lam

Glycogenolysis in skeletal muscle

(Lambeth & Kushmeric, 2002)

Miscellaneous-1963Lor

Lorenz equations: Deterministic nonperiodic flow

(Lorenz, 1963)

Miscellaneous-1974Fie

Oregonator: Field-Koros-Noyes model of the Belasov-Zhabotinskii reaction (Field & Noyes, 1974)

Receptor-2000DeY

IP3 dependent Calcium Channel

(DeYoung & Keizer, 2000)

 



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