Assays
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Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, using old enzymes with optimal protein distribution, with NAD recycling, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: One pot cascade
Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, with NAD recycling, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: One pot cascade
Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, omitting XLA, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: One pot cascade
Conversion of XYL to KG in one pot cascade of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: One pot cascade
Conversion of XYL to KG by sequential addition of Weimberg pathway enzymes of Caulobacter crescentus, measured in NMR. https://jjj.bio.vu.nl/models/experiments/shen2020_fig2c/simulate
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Cell free extract
Kinetic characterisation and mathematical modelling of XDH.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Kinetic characterisation and mathematical modelling of XLA.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Kinetic characterisation and mathematical modelling of XAD.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Kinetic characterisation and mathematical modelling of KDXD.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Kinetic characterisation and mathematical modelling of KGSADH.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Initial rate kinetics
Conversion of Xyl to XLAC by Caulobacter crescentus XDH, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Conversion of XLAC to XA by Caulobacter crescentus XLA, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Conversion of XA to KDX by Caulobacter crescentus XAD, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Conversion of KDX to KGSA by Caulobacter crescentus KDXD, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Conversion of KGSA to KG by Caulobacter crescentus KGSADH, measured in NMR.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Caulobacter crescentus Weimberg pathway
Study: Progress curves
Model that eliminates several light inputs. RVE8, NOX are incorporated. Individual representation of CCA1 and LHY. Several changes in conections and light inputs. Fogelmark reports eight parameter sets. This SBML file contains the first parameter set Related PublicationsFogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003705Originally ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Urquiza Garcia, Uriel
Study: F2014.1 - PLM_1030
The model is an extensio of PLM_67v3 with an additional an additional variable Temp in ODE 25. This change allows to simulated warm pulses that affect EC stability using COPASI.
Originally submitted to PLaSMo on 2014-03-10 13:16:25
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Urquiza Garcia, Uriel
The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper.
Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6
Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412 Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
The models in this record were published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper.
Original model: Arabidopsis clock model P2011.1.1 from Pokhilko et al. Mol Syst. Biol. 2012, http://dx.doi.org/10.1038/msb.2012.6
Published version is Biomodels ID 00412, http://www.ebi.ac.uk/compneur-srv/biomodels-main/BIOMD0000000412 Also public in Plasmo as PLM_64, with several versions, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_64 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.6.1 is public model ID PLM_1044, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
This model is one of five new parameter sets for P2011, published in Flis et al. Royal Society Open Biology 2015. They will be submitted to Biomodels when we have a PubMed ID for the paper. Derived from Original model: P2011.1.2 is public model ID PLM_71 version 1, http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1 This model P2011.3.1 is public model ID PLM_1041, with parameters optimised by Kevin Stratford using SBSInumerics software on the UK national ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
Submitter: Fekadu Yadetie
Assay type: RNA-seq
Technology type: Next generation sequencing
Investigation: 1 hidden item
RNA-seq data for In vivo 7 samples. Only 32 RNA samples from liver of male fish sequenced. Illumina poly(A)-RNA sequencing at UiB GCF, as in Yadetie et al., 2018.
Submitter: Fekadu Yadetie
Assay type: RNA-seq
Technology type: Next generation sequencing
Investigation: 1 hidden item
Study: 1 hidden item
Simulation of OE mutants targetting enzymes in the model, combined with metabolite concentrations and enzyme fold change of from the 40 samples. For each second mutant the enzyme concentrations in case of OE and KO mutants in updated and the metabolite concentrations of the second sample are loaded in the model. Using this approach the model approximately predicts combinatorial effects of OE mutations with other mutations, perturbations and time series concentrations.
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Investigation: Modelling of M. pneumoniae metabolism
The associated zip files contains all input files and a Jupyter notebook to rerun sampled simmulations, combined simmulations, parameter scan for the model with addition of an oxygin inhibiton of LDH, local- and global-sensitivity analysis and plot simmulation output in various formats. In addition the zip file contains the py36.yaml file that can be used to recreate the model simmulation environment using Anaconda making all simmulations completely reproducable. All information on how to use ...
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Core Model predictions
Training of the model, parameter estimation using Evolutionary Programming using metabolomics, proteomics and some flux data.
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Core Model training
Validation by simulating independent OE, KO mutant and perturbation samples, using sampling of the gausian distribution based on the mean and SD of measurements per sample. A 1000 samples of the gausian distribution of the mean and SD was performed per sample to show error in the measurements and how it propegates in predicted metabolite concentration in SS
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Core Model predictions
Protein copy number at 6h, 12h, 24h, 48h, 72h, 96h, average values and SD for the measurements
Submitter: Niels Zondervan
Assay type: Proteomics
Technology type: Technology Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Proteomics analysis
Metabolomics time series measurements for internal metabolites for 6h, 24h and 48h for multiple experiments. Largely based on MAss spectrometry, bioluminescence kits to measure NAD, NADH at 24h, other time points are infered from relative measurements times the absolute measurements at 24h.
Submitter: Niels Zondervan
Assay type: Experimental Assay Type
Technology type: Mass Spectrometry
Investigation: Modelling of M. pneumoniae metabolism
Study: Metabolomics measurements