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 ...
Set of pathways encompassing the replication cycle of SARS-CoV-2: attachment, entry, translation, transcription, replication, assembly and release.
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: ...
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 ...
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. ...
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 ...
A collection of WikiPathways describing various COVID-19 mechanisms.