What is a Model?
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401 Models visible to you, out of a total of 654

Fixed parameter model, where the glycolysis model of bloodstream form T. brucei is extended with the pentose phosphate pathway and an ATP:ADP antiporter over the glycosomal membrane. Non-final version.

Creators: Eduard Kerkhoven, Fiona Achcar

Submitter: Eduard Kerkhoven

SBML file supplementary material of the publication.

Creators: Fiona Achcar, Barbara Bakker, Mike Barrett, Rainer Breitling, Eduard Kerkhoven

Submitter: Fiona Achcar

The model describes the electron transport chain (ETC) of Escherichia coli by ordinary differential equations. Also a simplified growth model based on an abstract reducing potential describing the balance of electron donor (glucose) and electron acceptors is coupled to the ETC. The model should reproduce and predict the regulation of the described system for different oxygen availability within the aerobiosis scale (glucose limited continuous culture<=>chemostat). Therefore oxygen is changed ...

Creator: Sebastian Henkel

Submitter: Sebastian Henkel

A model of E. coli central carbon core metabolism, used as starting point for B. subtilis modelling. It is developed by Chassagnole et al. doi:10.1002/bit.10288.

Creators: Ulf Liebal, Fei He

Submitter: Ulf Liebal

Simplified model of the electron-transport chain(s) (ETC) of Escherichia coli and its regulation by ArcA and FNR. The goal is to demonstrate a hypothetical design principle in the regulatory structure (->partly qualitative parameter values). Oxygen is changed slowly (100% aerobiosis at 1000000 time units) thus the basis variable is not the time but the oxygen flux voxi.

Creator: Sebastian Henkel

Submitter: Sebastian Henkel

An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum, incorporating the effect of pH upon gene regulation and subsequent end-product levels.

The zip file containes 4 models (in SBML), each representing slightly different experimental conditions.

Creators: Sara Jabbari, Sylvia Haus

Submitter: The JERM Harvester

No description specified

Creators: Jay Moore, David Hodgson, Veronica Armendarez, Emma Laing , Govind Chandra, Mervyn Bibb

Submitter: Jay Moore

No description specified

Creator: Paul Heusden

Submitter: The JERM Harvester

The model can simulate the the dynamics of sigB dependent transcription at the transition to starvation. It is was developed along the comic in 'sigB-activation-comic_vol1'. Parameters were partly taken from Delumeau et al., 2002, J. Bact. and Igoshin et al., 2007, JMB. Parameter estimation was performed using experimental data from '0804_shake-flask'. Use the .m-file with matlab as: % reading initial conditions from the file: inic = sigb_model_liebal;

% performing the simulation: [t,y] = ...

Creator: Ulf Liebal

Submitter: Ulf Liebal

The model describes the Entner-Doudoroff pathway in Sulfolobus solfataricus under temperature variation. The package contains source code written in FORTRAN as well as binaries for Mac OSX, Linux, and Windows. If compiling from source code, a FORTRAN compiler is required. On-line versions of the model are also available at:

Creator: Peter Ruoff

Submitter: Peter Ruoff

The agent-based model involves the representation of each individual molecule of interest as an autonomous agent that exists within the cellular environment and interacts with other molecules according to the biochemical situation. FLAME environmet has beem used for agent-based development. The FLAME framework is an enabling tool to create agent-based models that can be run on high performance computers (HPCs). Models are created based upon extended finite state machines that include message input ...

Creator: Afsaneh Maleki-Dizaji

Submitter: Afsaneh Maleki-Dizaji

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