Models
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The pathway of heme metabolism under COVID-19, involving Orf3a and Orf9c
Creators: Julia Somers, Emek Demir
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
The impact of SARS-CoV-2 on the apoptosis pathway
Creators: Anna Niarakis, Vidisha Singh, Sara Sadat AGHAMIRI
Submitter: Marek Ostaszewski
Model type: Graphical model
Model format: SBML
Environment: Not specified
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
Model type: Not specified
Model format: Not specified
Environment: Not specified
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
Model type: Not specified
Model format: Not specified
Environment: Not specified
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
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
U2019.3 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
U2020.2 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
U2019.1 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
U2019.3 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
U2019.2 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
U2019.1 that simulates light condition with ISSF
Creators: Uriel Urquiza Garcia, Andrew Millar
Submitter: Uriel Urquiza Garcia
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
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
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
First version of enzyme-constrained model (ecModel) for Streptomyces albus J1074
Creator: Cheewin Kittikunapong
Submitter: Cheewin Kittikunapong
Model type: Stoichiometric model
Model format: SBML
Environment: Matlab
First version of enzyme-constrained model (ecModel) for Pseudomonas putida KT2440
Creator: Cheewin Kittikunapong
Submitter: Cheewin Kittikunapong
Model type: Stoichiometric model
Model format: SBML
Environment: Matlab
Creator: Saptarshi Bej
Submitter: Markus Wolfien
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Saptarshi Bej
Submitter: Saptarshi Bej
Model type: Not specified
Model format: Not specified
Environment: Not specified
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
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
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
Model type: Partial differential equations (PDE)
Model format: Not specified
Environment: Not specified
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
Model type: Graphical model
Model format: SBGN-ML PD
Environment: Not specified
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
Model type: Metabolic network
Model format: SBML
Environment: Matlab
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
Model type: Metabolic network
Model format: SBML
Environment: Matlab
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
Model type: Metabolic network
Model format: SBML
Environment: Matlab
NetLogo desktop version of Breast cancer development agent based model
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
Model type: Agent based modelling
Model format: Not specified
Environment: Not specified
Creator: Maria Krantz
Submitter: Maria Krantz
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified