Models

Mathematica notebook with model simulation of metabolite profiles after 24h incubation with different ratios of HSD11B1 and AKR1C3 transfected HEK293 cells.

Adjusted model to test the model's ability to oxygen consumption rate by permeabilised HepG2 cells in an Oroboros oxygraph. Data from Fletcher et al. (2019).

Adjusted model to test the model's ability to predict palmitoyl-CoA and octanoyl-CoA dehydrogenation in human liver lysate, with and without anti-MCAD and anti-VLCAD antibodies. Data from Aoyama et al. (1995).

Unzip model notebooks and keep in the same folder. Notebook names state which notebooks need to be run before them in order for them to word, e.g. "[needs-(1)]" indicates that the notebook numbered 1 must be run and its exported output generated before the given notebook can work. This has to do with the model being generated in only one notebook to avoid duplication.

NLRP3 inflammasome activation

Thrombotic complications and coagulopathy in COVID-19

Kynurenine synthesis pathway

TGF beta signalling

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

The Interferon-lambda (IFNL) map describes the action of the drug candidate IFNL on intra- and intercellular signal transduction under SARS-CoV-2.

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

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

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

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

A diagram of Nsp9 interactions.

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

Pyrimidine deprivation and immune response related to human coronavirus infection

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

SARS-CoV-2 impact on the ER stress

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 ...

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

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

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

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 ...

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 ...

A collection of WikiPathways describing various COVID-19 mechanisms.