Models

What is a Model?
418 Models visible to you, out of a total of 662

Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth and feed efficiency. Marine feed ingredients must be replaced to meet global demand, with challenges for fish health and sustainability. Metabolic models can address this by connecting genomes to metabolism, which converts nutrients in the feed to energy and biomass, but such models are currently not available for major aquaculture species ...

Originally submitted model file for PLaSMo accession ID PLM_74, version 1

Creators: BioData SynthSys, Yin Hoon Chew

Submitter: BioData SynthSys

Simplified model file for PLaSMo accession ID PLM_9, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_9, version 1

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Simplified model file for PLaSMo accession ID PLM_9, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Originally submitted model file for PLaSMo accession ID PLM_9, version 2

Creators: BioData SynthSys, Andrew Millar, Andrew Millar

Submitter: BioData SynthSys

Genome-scale metabolic model (GEM) for Streptomyces albus, maintained on https://github.com/SysBioChalmers/Salb-GEM.

Creator: Cheewin Kittikunapong

Submitter: Cheewin Kittikunapong

Thrombotic complications and coagulopathy in COVID-19

Creators: Goar Frischmann, Gisela Fobo, Corinna Montrone

Submitter: Marek Ostaszewski

SBML description of L. lactis glycolysis. Same as the uploaded Copasi file

Creator: Mark Musters

Submitter: Mark Musters

The model includes glycolysis, pentosephosphate pathway, purine salvage reactions, purine de novo synthesis, redox balance and biomass growth. The network balances adenylate pool as opened moiety.

Creator: Maksim Zakhartsev

Submitter: Maksim Zakhartsev

Executable versions of selected COVID-19 Disease Map diagrams, in SBML-Qual, converted using CaSQ: https://lifeware.inria.fr/~soliman/post/casq/

Creator: Anna Niarakis

Submitter: Marek Ostaszewski

No description specified

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

Submitter: Jay Moore

input: array of investigated quenching temperatures and volumetric flows output: quenching time and coil length as function of quenching temperature, and quenching time as function of temperature for varying coil lengths

Creator: Sebastian Curth

Submitter: Sebastian Curth

No description specified

Creator: Vincent Wagner

Submitter: Vincent Wagner

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

No description specified

Creator: Jacky Snoep

Submitter: Jacky Snoep

This model describes a core process during endocytosis. Intracellular vesicles called early endosomes contain the endocytosed cargo, e.g. signaling components like growth factors and RTKs, pathogens like viruses and nutrients like iron in transferrin. Early endosomes form an interacting pool of thousands of vesicles and jointly constitute the sorting and transport machinery in the endocytic pathway. Together with the cargo, membrane components travel to other compartments of the pathway which ...

Creator: Lutz Brusch

Submitter: Lutz Brusch

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

Particularly figure 2 of of Abudulikemu et al 2020 in press

Creator: Hans V. Westerhoff

Submitter: Hans V. Westerhoff

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

The zip-folder contains files for execution in matlab that allow for the simulation of stressosome dynamics and reproduction of published data on the stressosome. The important file for execution is 'liebal_stressosome-model_12_workflow-matlab.m'.

Creator: Ulf Liebal

Submitter: Ulf Liebal

Originally submitted model file for PLaSMo accession ID PLM_24, version 1

Creators: BioData SynthSys, Jonathan Massheder

Submitter: BioData SynthSys

No description specified

Creators: Dawie van Niekerk, Jacky Snoep

Submitter: Dawie van Niekerk

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson1) predicts the limit ...

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson2) predicts the damped ...

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson3) predicts the steady-state ...

Creators: Franco du Preez, Jacky Snoep, David D van Niekerk

Submitter: Franco du Preez

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson4) predicts the steady-state ...

Creators: Franco du Preez, Jacky Snoep, Dawie van Niekerk

Submitter: Franco du Preez

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