Models
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First version of enzyme-constrained model (ecModel) for Escherichia coli
Creator: Cheewin Kittikunapong
Submitter: Cheewin Kittikunapong
Model type: Stoichiometric model
Model format: SBML
Environment: Matlab
Interactions of Nsp4 and Nsp6 proteins of SARS-CoV-2.
Creators: Arnau Montagud, Miguel Ponce-de-Leon
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Interactions of the SARS-CoV-2 Orf3a with human proteins, especially in the context of the HOPS Complex.
Creator: Muhammad Naveez
Submitter: Marek Ostaszewski
Model type: Not specified
Model format: Not specified
Environment: Not specified
A diagram of Nsp9 interactions.
Creators: Noriko Hiroi, Yusuke Hiki, Takahiro G. Yamada, Akira Funahashi
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Orf10 of SARS-CoV-2 and its interaction with the Cul2 pathway.
Creators: Jan Hasenauer, Leonard Schmiester, Paul Stapor
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Pyrimidine deprivation and immune response related to human coronavirus infection
Creators: Zsolt Bocskei, Franck Augé, Anna Niarakis
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The mechanisms of the Electron Transport Chain under COVID-19, including Nsp7, Nsp8 and Orf9c
Creator: Julia Scheel
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
SARS-CoV-2 impact on the ER stress
Creators: Cristobal Monraz, Inna Kuperstein, Barbara Brauner
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Model associated with the following:
Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim, An explanatory model of temperature influence on flowering through whole-plant accumulation of FLOWERING LOCUS T in Arabidopsis thaliana, in silico Plants, Volume 1, Issue 1, 2019, diz006, https://doi.org/10.1093/insilicoplants/diz006
Creator: Hannah Kinmonth-Schultz
Submitter: Hannah Kinmonth-Schultz
Model type: Not specified
Model format: Matlab package
Environment: Matlab
To obtain each of the figure 2A - 2E please download "Main Figure Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Not specified
Model format: SBML
Environment: Not specified
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Not specified
Model format: Not specified
Environment: Not specified
COVID-19 Causal Networks: The SIGNOR team has curated the causal relationships that, according to available evidence, are likely to be relevant for the COVID-19 pathology. The perturbations caused by viral infection are integrated into the cell networks. Evidence obtained using related human coronaviruses diseases such as SARS and MERS are also mapped to the networks. Most of these are indirect relationships as few mechanistic details are clarified to date. As new evidence will be published, it ...
Creators: Luana Licata, Marta Iannuccelli, University of Rome Tor Vergata, IT
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: Not specified
Environment: Not specified
Pathway: Assembly of the Replication Transcription Complex and Transcription
Creators: Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBGN-ML PD
Environment: Not specified
Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotinate and nicotinamide, and purine metabolism.
Creators: Alina Renz, Andreas Dräger
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Interactions of the SARS-CoV-2 E protein with human proteins in the context of histone acetylation.
Creator: Francesco Messina
Submitter: Marek Ostaszewski
Model type: Not specified
Model format: Not specified
Environment: Not specified
Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, entry, translation, transcription, replication, assembly and release.
Creators: Marcio Acencio, Alexander Mazein
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
A diagram of JNK pathway in COVID-19.
Creator: Daniela Börnigen
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
A diagram encoding PAMP signaling relevant to COVID-19/SARS-CoV-2
Creator: Matti Hoch
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
Mechanisms related to COVID-19 virus replication cycle, constructed using the mEPN graphical notation.
Creators: Liam Fergusson, Tom Freeman
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: Not specified
Environment: Not specified
The novel coronavirus (SARS-CoV-2) currently spreads worldwide, causing the disease COVID-19. The number of infections increases daily, without any approved antiviral therapy. The recently released viral nucleotide sequence enables the identification of therapeutic targets, e.g., by analyzing integrated human-virus metabolic models. Investigations of changed metabolic processes after virus infections and the effect of knock-outs on the host and the virus can reveal new potential targets. Results: ...
Creators: Alina Renz, Andreas Dräger
Submitter: Martin Golebiewski
Model type: Not specified
Model format: SBML
Environment: Not specified
RUN the model for steady state.
For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. Plot e.g. ATP.
For H2O2 experimental data validation for repeated treatment at 50uM, 150uM, and 300uM. To run the model with different dosing scenarios, one has to set both the H2O2 initial ...
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
This is a model about a ROS network that exhibits five design principles, and has been calibrated so as to predict quantitatively various steady state concentrations. 10191125.
Instructions RUN the model for steady state. For the Menadione experiment set the initial concentration of 'Menadione' species to experimental dosing i.e. 100 000 nM (0.1 mM) and make the simulation type "reaction" for both the species i.e. 'Menadione' and 'Menadione_internal'. Then run for 24 hr i.e. 1500 minutes approx. ...
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
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
Model type: Boolean network
Model format: SBML
Environment: Not specified
Model building:
The module was built using modular bottom-up approach where every module describes a certain process and then, when modules are connected together like domino tiles, we can reconstruct the emergent behavior of the whole system.
This is a blueprint model and might be used for various country/data. If one wans to use it for a particular country/data, we can recommend following steps:
- Adjust total population by changing initial condition of A-Initial_population_innocent_non-tested ...
Creators: Alexey Kolodkin, Hans V. Westerhoff
Submitter: Alexey Kolodkin
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
A collection of WikiPathways describing various COVID-19 mechanisms.
Creators: Alexander Pico, Chris Evelo, Rex D A B, Egon Willighagen, Lauren J. Dupuis, Matthew Conroy, Friederike Ehrhart, Kristina Hanspers, Amber Koning
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: Not specified
Environment: Not specified
Genome-scale metabolic model (GEM) for Streptomyces albus, maintained on https://github.com/SysBioChalmers/Salb-GEM.
Creator: Cheewin Kittikunapong
Submitter: Cheewin Kittikunapong
Model type: Metabolic network
Model format: SBML
Environment: Matlab
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica
Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Algebraic equations
Model format: Mathematica
Environment: Mathematica