Models

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
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The role of the interaction between the SARS-CoV-2 Spike protein and the renin-angiotensin pathway, in particular human ACE2 in pulmonary blood pressure regulation

Pathway: Assembly of the Replication Transcription Complex and Transcription

Interactions of Nsp4 and Nsp6 proteins of SARS-CoV-2.

Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotinate and nicotinamide, and purine metabolism.

The impact of SARS-CoV-2 on the apoptosis pathway

The pathway of heme metabolism under COVID-19, involving Orf3a and Orf9c

Interactions of the SARS-CoV-2 Orf3a with human proteins, especially in the context of the HOPS Complex.

Interactions of the SARS-CoV-2 E protein with human proteins in the context of histone acetylation.

Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, entry, translation, transcription, replication, assembly and release.

A diagram of JNK pathway in COVID-19.

A diagram of Nsp9 interactions.

The mechanisms of the Electron Transport Chain under COVID-19, including Nsp7, Nsp8 and Orf9c

The relation of the interferon 2 pathway and SARS-CoV-2.

SARS-CoV-2 impact on the ER stress

Orf10 of SARS-CoV-2 and its interaction with the Cul2 pathway.

A diagram encoding PAMP signaling relevant to COVID-19/SARS-CoV-2

The pathways focused on SARS-CoV infections curated in Reactome.
These pathways are work-in-progress.

Mechanisms related to COVID-19 virus replication cycle, constructed using the mEPN graphical notation.

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

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:

1. Adjust total population by changing initial condition of
A-Initial_population_innocent_non-tested
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A collection of WikiPathways describing various COVID-19 mechanisms.

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

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.

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.

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.

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.