Models

140 Models visible to you, out of a total of 248

Butanol producing iNS142, redesigned using RobOKoD.

Creator: Natalie Stanford

Contributor: Natalie Stanford

This record includes Matlab and Simile format versions of the Arabidopsis Framework Model version 1, FMv1 (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111), copied from the PlaSMo resource (www.plasmo.ed.ac.uk), PLM_ID=76. The model description is in the Supplementary Materials of the publication, which should be uploaded somewhere here also but I don't see how to do it.

The FMv1 links the following sub-models:
1. Arabidopsis leaf carbohydrate model (Rasse and
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Creators: Andrew Millar, Yin Hoon Chew

Contributor: Andrew Millar

No description specified

Creator: Jacky Snoep

Contributor: Jacky Snoep

No description specified

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

No description specified

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).

The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model:
Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was
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Creators: Daniel Seaton, Yin Hoon Chew, Andrew Millar

Contributor: Daniel Seaton

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
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Creator: Lutz Brusch

Contributor: Lutz Brusch

The model is adapted from A.P. Kupinski, I. Raabe, M. Michel, D. Ail, L. Brusch, T. Weidemann, C. Bökel (2013) Phosphorylation of the Smo tail is controlled by membrane localization and is dispensable for clustering, J. Cell Sci., 126, 20, 4684-4697 doi: 10.1242/​jcs.128926

The model format is MorpheusML that can readily be loaded and run in Morpheus: https://imc.zih.tu-dresden.de//wiki/morpheus

Creator: Lutz Brusch

Contributor: Lutz Brusch

Morpheus is the modelling and simulation framework for multicellular systems biology developed at Technische Universität Dresden.
Manual, examples and binaries for Windows, Linux, MacOS at: https://imc.zih.tu-dresden.de/wiki/morpheus
Open source code at: https://gitlab.com/morpheus.lab/morpheus

Creators: Lutz Brusch, Jörn Starruß, Walter de Back, Andreas Deutsch

Contributor: Lutz Brusch

Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.

Creator: Andrew Millar

Contributor: Andrew Millar

This version is P2011.1.2, model ID PLM_71 version 1. Dynamics identical to P2011.1.1 of the Pokhilko et al. 2012 publication.

http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1

Creator: Andrew Millar

Contributor: Andrew Millar

Python scripts to run the analysis estimating rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.

Creators: Daniel Seaton, Andrew Millar

Contributor: Daniel Seaton

No description specified

Creator: Daniel Seaton

Contributor: Daniel Seaton

This mechanistic ODE model describes the growth dynamics of P. aeruginosa, including an antibiotic-induced morphological transition to a fragile spherical form.

Creators: Chloe Spalding, Sara Jabbari

Contributor: Chloe Spalding

PGK-GAPDH model Sulfolobus kouril8

Creator: Jacky Snoep

Contributor: Jacky Snoep

PGK-GAPDH model yeast kouril7

Creator: Jacky Snoep

Contributor: Jacky Snoep

PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript

Creator: Jacky Snoep

Contributor: Jacky Snoep

PGK 70C model, Fig 3 in manuscript

Creator: Jacky Snoep

Contributor: Jacky Snoep

PGK 70C SBML

Creator: Jacky Snoep

Contributor: Jacky Snoep

BPG stability notebook

Creator: Jacky Snoep

Contributor: Jacky Snoep

PGK yeast Fig1a

Creator: Jacky Snoep

Contributor: Jacky Snoep

PGK yeast with/without recycling

Creator: Jacky Snoep

Contributor: Jacky Snoep

No description specified

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

No description specified

Creator: Robert Muetzelfeldt

Contributor: Robert Muetzelfeldt

No description specified

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

No description specified

Creators: Dawie Van Niekerk, Jacky Snoep

Contributor: Dawie Van Niekerk

Metabolic model of Sulfolobus solfataricus P2 in the SBML (xml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or L-fucose as sole carbon source. Different theoretical routes of L-fucose degradation were modeled (E. coli-like, Xanthomonas-like and lactaldehyde-forming). Highest overall agreement between the model and experimental data was observed for the lactaldehyde-forming route.

Creators: Jacqueline Wolf, Helge Stark, Dietmar Schomburg

Contributor: Jacqueline Wolf

This is BIOMD0000000005.

Creators: Ron Henkel, Dagmar Waltemath

Contributor: Ron Henkel

No description specified

Creator: Matthias König

Contributor: Matthias König

The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that
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Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov

Contributor: Maksim Zakhartsev

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