Models

First version of enzyme-constrained model (ecModel) for Escherichia coli

NetLogo desktop version of Breast cancer development agent based model

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

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

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

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

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

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

SARS-CoV-2 impact on the ER stress

Thrombotic complications and coagulopathy in COVID-19

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

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.

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

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

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

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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