Models

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344 Models visible to you, out of a total of 584
No description specified

Creator: Saptarshi Bej

Submitter: Markus Wolfien

No description specified

Creator: Saptarshi Bej

Submitter: Saptarshi Bej

This is not my model

Creator: Alan Williams

Submitter: Alan Williams

First draft of Genome-scale metabolic model (GEM) for reconstraction of flavonoids biosynthetic pathways. This model includes as a chassis , the Pseudomonas Putida GEM (iJN1411) .

Creators: David San León Granado, Juan Nogales, Álvaro Gargantilla Becerra

Submitter: David San León Granado

For the spatio-temporal dynamics of bile transport, bile canalicular dilation, mechanical stimulation and transduction of YAP signaling during liver regeneration see the open access publication and its appendix:
Meyer et al. (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985. https://doi.org/10.15252/msb.20198985

The model format is MorpheusML that can readily be loaded and run in the free and open source software
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Creator: Lutz Brusch

Submitter: Lutz Brusch

Spatio-temporal liver zonation in mouse and human with Wnt-Hh crosstalk and transport are modeled using coupled partial differential equations. The model file is in MorpheusML format and can be opened in the free, open-source multicellular modeling software Morpheus (https://morpheus.gitlab.io). In Morpheus, the model will simulate the time course (movie) of dynamic liver zonation for a 2D cross-section of several liver lobules, showing the patterns of Wnt ligands, intracellular Wnt signaling,
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Creators: Lutz Brusch, Jörn Starruß, Michael Kücken

Submitter: Lutz Brusch

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

Creators: Marc Gillespie, Robin Haw, Peter D'Eustachio

Submitter: Marek Ostaszewski

This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090003.

[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415

Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski

Submitter: Xiaokang Zhang

This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090002.

[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415

Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski

Submitter: Xiaokang Zhang

This is an auto-generated model with COBRA Matlab toolbox. This model was deposited in BioModels [1] and assigned the identifier MODEL2010090001.

[1] Malik-Sheriff et al. BioModels — 15 years of sharing computational models in life science. Nucleic Acids Research. 2020 Jan, 48(D1):D407–415

Creators: Xiaokang Zhang, Eileen Marie Hanna, Marta Eide, Shirin Fallahi, Fekadu Yadetie, Anders Goksøyr, Inge Jonassen, Tomasz Furmanek; Daniel Craig Zielinski

Submitter: Xiaokang Zhang

NetLogo desktop version of Breast cancer development agent based model

Creator: Hannah O'Keefe

Submitter: Hannah O'Keefe

No description specified

Creator: Maria Krantz

Submitter: Maria Krantz

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

Creator: Cheewin Kittikunapong

Submitter: Cheewin Kittikunapong

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

Creators: Arnau Montagud, Miguel Ponce-de-Leon

Submitter: Marek Ostaszewski

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

Creator: Muhammad Naveez

Submitter: Marek Ostaszewski

A diagram of Nsp9 interactions.

Creators: Noriko Hiroi, Yusuke Hiki, Takahiro G. Yamada, Akira Funahashi

Submitter: Marek Ostaszewski

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

Creators: Jan Hasenauer, Leonard Schmiester, Paul Stapor

Submitter: Marek Ostaszewski

Pyrimidine deprivation and immune response related to human coronavirus infection

Creators: Zsolt Bocskei, Franck Augé, Anna Niarakis

Submitter: Marek Ostaszewski

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

Creators: Anna Niarakis, Vidisha Singh, Sara AGHAMIRI

Submitter: Marek Ostaszewski

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

Creators: Marius Rameil, Vanessa Nakonecnij, Marta Conti

Submitter: Marek Ostaszewski

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

Creators: Julia Somers, Emek Demir

Submitter: Marek Ostaszewski

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

Creator: Julia Scheel

Submitter: Marek Ostaszewski

SARS-CoV-2 impact on the ER stress

Creators: Cristobal Monraz, Inna Kuperstein, Barbara Brauner

Submitter: Marek Ostaszewski

Thrombotic complications and coagulopathy in COVID-19

Creators: Marek Ostaszewski, Goar Frischmann, Gisela Fobo, Corinna Montrone

Submitter: Marek Ostaszewski

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

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 Westerhoff, Raju Prasad Sharma

Submitter: Alexey Kolodkin

No description specified

Creators: Alexey Kolodkin, Hans Westerhoff, Raju Prasad Sharma

Submitter: Alexey Kolodkin

No description specified

Creators: Alexey Kolodkin, Hans Westerhoff, Raju Prasad Sharma

Submitter: Alexey Kolodkin

No description specified

Creators: Alexey Kolodkin, Hans Westerhoff, Raju Prasad Sharma

Submitter: Alexey Kolodkin

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

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