Models

What is a Model?
Created At
Go
Updated At
Go
395 Models visible to you, out of a total of 637

Kynurenine synthesis pathway

Creators: Julia Somers, Gökçe Yağmur Summak, Ebru Kocakaya

Submitter: Marek Ostaszewski

TGF beta signalling

Creator: Francesco Messina

Submitter: Marek Ostaszewski

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

Creators: Andreas Ruepp, Corinna Montrone, Gisela Fobo, Enrico Glaab

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

Creators: Anna Niarakis, Vidisha Singh, Sara Sadat AGHAMIRI

Submitter: Marek Ostaszewski

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

Creators: Emek Demir, Julia Somers

Submitter: Marek Ostaszewski

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

Creators: Anna Niarakis, Vidisha Singh, Sara Sadat AGHAMIRI

Submitter: Marek Ostaszewski

Here, we describe the index file generation of the mm10 genome, the genome alignment with kallisto, and quantification with bustools to obtain the used spliced / unspliced transcript input.

Creator: Markus Wolfien

Submitter: Markus Wolfien

Here is the detailed R script to generate the input needed by scSynO for synthetic cell generation and classification model training.

The code that can be embedded into any other Seurat data processing workflow is:

cell_expression_target_cluster <- as.matrix(GetAssayData(seuratobject, slot = "data")[, WhichCells(seuratobject, ident = "target_cluster_number")]) cell_expression_all_other_clusters <- as.matrix(GetAssayData(seuratobject, slot = "data")[, WhichCells(seuratobject, ident = ...

Creator: Markus Wolfien

Submitter: Markus Wolfien

Single nuclei transcriptomics data as .csv files from the Allen Brain atlas data set of mus musculus (https://celltypes.brain-map.org/) have been utilized as an input for scSynO. The underlying analysis is part of the manuscript entitled "Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling". Data anaylsis and visalizations were mainly generated with the Seurat R package (https://satijalab.org/seurat/archive/v3.2/spatial_vignette.html)

Creator: Markus Wolfien

Submitter: Markus Wolfien

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

No description specified

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2019.3 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2020.2 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2019.1 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2019.3 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2019.2 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

U2019.1 that simulates light condition with ISSF

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from P2011.1.2 in which the steady state assumptions for the Evening complex in P2011 were eliminated. After eliminating these assumptions the model was fitted to the original dynamics of P2011.1.2 for the networks WT, lhycca1, prr79, toc1, gi, ztl. In particular for the lhycca1 double mutant only the repressive "arms" (edges) for cL were set to zero. The parameter values or cP and for COP1 variables were fixed as these have been fitted before in Pokhilko et al 2012 Mol Sys Bio.

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

First version of enzyme-constrained model (ecModel) for Streptomyces albus J1074

Creator: Cheewin Kittikunapong

Submitter: Cheewin Kittikunapong

First version of enzyme-constrained model (ecModel) for Pseudomonas putida KT2440

Creator: Cheewin Kittikunapong

Submitter: Cheewin Kittikunapong

No description specified

Creator: Saptarshi Bej

Submitter: Markus Wolfien

No description specified

Creator: Saptarshi Bej

Submitter: Saptarshi Bej

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 ...

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, ...

Creators: Lutz Brusch, Jörn Starruß, Michael Kücken

Submitter: Lutz Brusch

Powered by
(v.1.13.0)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH