Models

Originally submitted model file for PLaSMo accession ID PLM_77, version 1

Originally submitted model file for PLaSMo accession ID PLM_41, version 1

Originally submitted model file for PLaSMo accession ID PLM_32, version 1

Originally submitted model file for PLaSMo accession ID PLM_40, version 1

Originally submitted model file for PLaSMo accession ID PLM_38, version 1

Originally submitted model file for PLaSMo accession ID PLM_39, version 1

Originally submitted model file for PLaSMo accession ID PLM_36, version 1

Originally submitted model file for PLaSMo accession ID PLM_37, version 1

Originally submitted model file for PLaSMo accession ID PLM_34, version 1

Originally submitted model file for PLaSMo accession ID PLM_35, version 1

Originally submitted model file for PLaSMo accession ID PLM_12, version 1

Originally submitted model file for PLaSMo accession ID PLM_33, version 1

Here is a kinetic model (in COPASI format) of L. lactis glycolysis.

Butanol producing iNS142, redesigned using RobOKoD.

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 ...

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 ...

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

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

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

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

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.

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

PGK-GAPDH model Sulfolobus kouril8

PGK-GAPDH model yeast kouril7

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

PGK 70C SBML