Models

What is a Model?
20 Models visible to you, out of a total of 40

The FEM models how metabolic slowdown will induce the age-related changes of weight gain, insulin resistance, basal inflammation, mitochondrial dysfunction, as well as the age-related disease of atherosclerosis, via a series of unavoidable homeostatic shifts.

Creators: James Wordsworth, Pernille Yde Nielsen

Submitter: James Wordsworth

Underlying R script for the investigation of immune cells. Script contains basic data processing, as well as a DE and monocle analysis.

Creator: Markus Wolfien

Submitter: Markus Wolfien

Stoichiometric model in SBML format using the acetate-aerobic standard scenario.

Please note that SBML was exported using the sbmlwriter class of Metano. This file was not used for the actual analyses.

Creator: Julia Koblitz

Submitter: Julia Koblitz

This stoichiometric model of Aromatoleum aromaticum EbN1 is a genome-scale model and comprises 655 enzyme-catalyzed reactions and 731 distinct metabolites.

The model is in the plain-text reaction format of Metano that is human-readable and can be opened with every text editor. To run this version of the model, please use the Metano Modeling Toolbox (mmtb.brenda-enzymes.org) and the associated scenario files.

Creators: Julia Koblitz, Dietmar Schomburg, Meina Neumann-Schaal

Submitter: Julia Koblitz

A population of turtles have between 1 and 3 genes contributing to the strength of selective destruction, which can either cause ageing or allow for negligible senescence.

Creator: James Wordsworth

Submitter: James Wordsworth

Model of selective destruction in a single population of cells with differing sensitivities for growth. Fast growing cells can be epigenetically converted to slower cells rather than simple cell death as in previous models.

Creator: James Wordsworth

Submitter: James Wordsworth

Model of unselective destruction in a single population of cells with differing sensitivities for growth

Creator: James Wordsworth

Submitter: James Wordsworth

Model of selective destruction in a single population of cells with differing sensitivities for growth

Creators: James Wordsworth, Daryl Shanley, Hannah O'Keefe

Submitter: James Wordsworth

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

Creator: Saptarshi Bej

Submitter: Markus Wolfien

No description specified

Creator: Saptarshi Bej

Submitter: Saptarshi Bej

Dynamic model of glycolysis, pyruvate metabolism and NoxE. The model is parameterized by selecting the best out of 100 parameter set using Copasi's Genetic algorithm with 1000 itterations and 500 simmulatanious models.

The new GEM of S. coelicolor developed by Tjasa Kumelj, Snorre Sulheim, Alexander Wentzel and Eivind Almaas in 2017/2018

Creators: Snorre Sulheim, Tjasa Kumelj

Submitter: Snorre Sulheim

No description specified

Creator: Niels Zondervan

Submitter: Niels Zondervan

Core model with the addition of a NoxE reaction to regenerate NAD using O2. COPASI’s build in Evolutionary programming algorithm was used to estimate parameters using a maximum of 2000 generations with a population size of 100 models with value scaling as weights to train the 5 parameters of the NoxE reaction.

Creator: Niels Zondervan

Submitter: Niels Zondervan

Butanol producing iNS142, redesigned using RobOKoD.

Creator: Natalie Stanford

Submitter: Natalie Stanford

No description specified

Creator: Robert Muetzelfeldt

Submitter: Robert Muetzelfeldt

E.coli Core model, with additional reactions added to generate the beta-oxadation cycle. This is the basic model used in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).

Creator: Natalie Stanford

Submitter: Natalie Stanford

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