Assays

519 Assays visible to you, out of a total of 993
No description specified

Contributor: Markus Wolfien

Biological problem addressed: Gene Expression

Snapshots: No snapshots

No description specified

Contributor: Evert Bosdriesz

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, without Mn2+ added, but with NAD recycling, metabolites measured enzymatically.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig4d/simulate

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.995.2

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, but no NAD recycling, metabolites measured enzymatically.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig4c/simulate

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.994.2

Conversion of XYL to KG in a cell free extract of Caulobacter crescentus, with 0.15 mM Mn2+ added, and with NAD recycling, metabolites measured enzymatically.
https://jjj.bio.vu.nl/models/experiments/shen2020_fig4b/simulate

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.993.2

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

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.991.1

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

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.989.1

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

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.988.1

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

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.987.1

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

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.986.2

No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Conversion of KGSA to KG by Caulobacter crescentus KGSADH, measured in NMR.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.982.2

Conversion of KDX to KGSA by Caulobacter crescentus KDXD, measured in NMR.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.981.2

Conversion of XA to KDX by Caulobacter crescentus XAD, measured in NMR.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.980.2

Conversion of XLAC to XA by Caulobacter crescentus XLA, measured in NMR.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.979.2

Conversion of Xyl to XLAC by Caulobacter crescentus XDH, measured in NMR.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.978.2

Kinetic characterisation and mathematical modelling of KGSADH.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.972.1

Kinetic characterisation and mathematical modelling of KDXD.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.971.1

Kinetic characterisation and mathematical modelling of XAD.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.970.1

Kinetic characterisation and mathematical modelling of XLA.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.969.1

Kinetic characterisation and mathematical modelling of XDH.

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.968.1

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
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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
...

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
...

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
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Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

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
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

No description specified

Contributor: Fekadu Yadetie

Assay type: RNA-seq

Technology type: Next generation sequencing

Snapshots: No snapshots

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.

Contributor: Fekadu Yadetie

Assay type: RNA-seq

Technology type: Next generation sequencing

Snapshots: No snapshots

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
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Contributor: Niels Zondervan

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

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