Models

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379 Models visible to you, out of a total of 609

Originally submitted model file for PLaSMo accession ID PLM_1030, version 1

Model derived from U2019.2, fitted to TiMet data mutants data set. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rated were obtained by taking the product of scaling factor and either transcription or translation, the latter required for ...

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from U2019.1 in which the transcription rates were rescaled to match the scale of TiMet data set for absolute units of RNA concentration. The gmX scaling parameters in the model were fitted numerically. This model has equivalent dynamics to P2011.1.2.

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from U2020.2, fitted to the TiMet RNA data for wild-type and clock mutants. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rates were obtained by taking the product of scaling factor and either transcription or translation, the ...

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from U2020.1 by fitting the scaling factors for matching TiMet data set for wild-type and clock mutants, in absolute units.

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model derived from U2019.1, in which the way the PRR genes are regulated is modified. Repression mechanism introduced Instead of activation between the PRRs for producing the wave of expression. This is inspired in the result of three models P2012, F2014 and F2016. P2012 introduced TOC1 repression in earlier genes relative to its expression. F2014 introduced also the backward repression of PRR9 |-- PRR7 |--- PRR5, TOC1. However little attention was given to why there is a sharper expression ...

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model written in Antimony human-readable language and then translate into SBML using Tellurium

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

Model written in Antimony human-readable language, Model used in Pokhilko et al 2012

Creators: Uriel Urquiza Garcia, Andrew Millar

Submitter: Uriel Urquiza Garcia

autogenerated equation listing from the SBML of U2020.3, as a .PDF file

Creators: Andrew Millar, Uriel Urquiza Garcia

Submitter: Andrew Millar

autogenerated equation listing from the SBML of U2019.3, as a .PDF file

Creators: Andrew Millar, Uriel Urquiza Garcia

Submitter: Andrew Millar

NLRP3 inflammasome activation

Creators: Julia Somers, Gökçe Yağmur Summak, Ebru Kocakaya

Submitter: Marek Ostaszewski

Thrombotic complications and coagulopathy in COVID-19

Creators: Goar Frischmann, Gisela Fobo, Corinna Montrone

Submitter: Marek Ostaszewski

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

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: Julia Somers, Emek Demir

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:

cellexpressiontarget_cluster

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: Vincent Wagner

Submitter: Vincent Wagner

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

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