Assays

519 Assays visible to you, out of a total of 993

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Single nuclei RNA-Seq analysis of Fzt:DU and BL6 mice

iRhythmics

(Show All)

No description specified

Contributor: Markus Wolfien

Biological problem addressed: Gene Expression

Snapshots: No snapshots

Investigation: 1 hidden item

Study: Single nuclei comparison

Organisms: No organisms

Models: No Models

SOPs: R script for single nuclei analysis, UNIX script for snRNA-Seq processing

Data files: Marker genes for single nuclei clusters, Nuclei characteristics for the single nuclei an...

Created: 16th Jan 2020 at 13:21, Last updated: 17th Jan 2020 at 11:12

Network reconstruction and comparison of BRAFi sensitive and resistant cells

Colosys

No description specified

Contributor: Evert Bosdriesz

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Investigation: 1 hidden item

Study: 1 hidden item

Organisms: No organisms

Models: 1 hidden item

SOPs: No SOPs

Data files: VACO PTPN11 KO perturbations, VACO PTPN11 KO/BRAFi resistant perturbations, VACO parental perturbations

Created: 9th Sep 2019 at 14:10, Last updated: 14th Jan 2020 at 16:03

Cell free extract, without added Mn, with NAD recycling

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Organisms: No organisms

Models: CFE analysis (shen2), CFE no Mn, with NADrec

SOPs: No SOPs

Data files: CFE no-Mn but with NADrec data

Created: 11th Apr 2019 at 11:18, Last updated: 8th Jan 2020 at 16:12

Cell free extract, with Mn, no NAD recycling

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Organisms: No organisms

Models: CFE Mn noNADrec, CFE analysis (shen2)

SOPs: No SOPs

Data files: CFE Mn no-NADrec data

Created: 11th Apr 2019 at 11:16, Last updated: 8th Jan 2020 at 16:11

Cell free extract, with Mn and NAD recycling

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Organisms: No organisms

Models: CFE Mn NADrec, CFE analysis (shen2)

SOPs: No SOPs

Data files: CFE Mn NADrec data

Created: 11th Apr 2019 at 10:15, Last updated: 8th Jan 2020 at 16:10

One pot cascade 16

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: One pot cascade

Organisms: No organisms

Models: Cascade analysis (shen2), One pot cascade 16

SOPs: No SOPs

Data files: One-Pot-Cascade 16 data

Created: 10th Apr 2019 at 11:59, Last updated: 8th Jan 2020 at 16:10

One pot cascade 13

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: One pot cascade

Organisms: No organisms

Models: Cascade analysis (shen2), One-Pot-Cascade 13

SOPs: No SOPs

Data files: One-Pot-Cascade 13 data

Created: 9th Apr 2019 at 16:05, Last updated: 8th Jan 2020 at 16:09

One pot cascade 12

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: One pot cascade

Organisms: No organisms

Models: Cascade analysis (shen2), One pot cascade 12

SOPs: No SOPs

Data files: One-Pot-Cascade 12 data

Created: 9th Apr 2019 at 16:05, Last updated: 8th Jan 2020 at 16:09

One pot cascade 10

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: One pot cascade

Organisms: No organisms

Models: Cascade analysis (shen2), One-Pot-Cascade 10

SOPs: No SOPs

Data files: One-Pot-Cascade 10 data

Created: 9th Apr 2019 at 16:02, Last updated: 8th Jan 2020 at 16:09

Progress curves combined

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis combined

SOPs: No SOPs

Data files: Progress curve analysis data

Created: 9th Apr 2019 at 14:25, Last updated: 8th Jan 2020 at 16:08

Steady state cell free extract, with Mn and NAD recycling

Computational pathway design for biotechnological applications

No description specified

Contributor: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Investigation: Caulobacter crescentus Weimberg pathway

Study: Cell free extract

Organisms: No organisms

Models: CFE steady state analysis (shen3)

SOPs: No SOPs

Data files: No Data files

Created: 29th Nov 2019 at 17:49, Last updated: 6th Jan 2020 at 16:17

Progress curve KGSADH

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis KGSADH

SOPs: No SOPs

Data files: Progress curve analysis data

Created: 30th Mar 2019 at 19:44, Last updated: 6th Jan 2020 at 16:17

Progress curve KDXD

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis KDXD

SOPs: No SOPs

Data files: Progress curve analysis data

Created: 30th Mar 2019 at 19:43, Last updated: 6th Jan 2020 at 16:17

Progress curve XAD

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis XAD

SOPs: No SOPs

Data files: Progress curve analysis data

Created: 30th Mar 2019 at 19:42, Last updated: 6th Jan 2020 at 16:17

Progress curve XLA

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis XLA

SOPs: No SOPs

Data files: Progress curve analysis data

Created: 30th Mar 2019 at 19:41, Last updated: 6th Jan 2020 at 16:17

Progress curve XDH

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Progress curves

Organisms: No organisms

Models: Progress curve analysis (shen1), Progress curve analysis XDH

SOPs: No SOPs

Data files: Progress curve analysis data

Created: 30th Mar 2019 at 12:34, Last updated: 6th Jan 2020 at 16:17

KGSADH

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: KGSADH model

SOPs: No SOPs

Data files: KGSADH-initial rate kinetics data

Created: 26th Mar 2019 at 15:42, Last updated: 6th Jan 2020 at 16:17

KDXD

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: KDXD model

SOPs: No SOPs

Data files: KDXD-initial rate kinetics data

Created: 26th Mar 2019 at 15:42, Last updated: 6th Jan 2020 at 16:17

XAD

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: XAD model

SOPs: No SOPs

Data files: XAD-initial rate kinetics data

Created: 26th Mar 2019 at 15:41, Last updated: 6th Jan 2020 at 16:17

XLA

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: XLA model

SOPs: No SOPs

Data files: XLA-initial rate kinetics data

Created: 26th Mar 2019 at 15:41, Last updated: 6th Jan 2020 at 16:17

XDH

Computational pathway design for biotechnological applications

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

Investigation: Caulobacter crescentus Weimberg pathway

Study: Initial rate kinetics

Organisms: No organisms

Models: XDH model

SOPs: No SOPs

Data files: XDH-initial rate kinetics data

Created: 26th Mar 2019 at 15:37, Last updated: 6th Jan 2020 at 16:17

F2014.1 - PLM_1030, version 1

PlaSMo model repository

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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
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Investigation: Urquiza Garcia, Uriel

Study: F2014.1 - PLM_1030

Organisms: No organisms

Models: 5 hidden items

SOPs: No SOPs

Data files: No Data files

Created: 10th Jan 2019 at 17:40, Last updated: 20th Dec 2019 at 14:56

PLM_67v3withTempPulse - PLM_81, version 1

PlaSMo model repository

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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

Investigation: Urquiza Garcia, Uriel

Study: PLM_67v3withTempPulse - PLM_81

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: No Data files

Created: 10th Jan 2019 at 17:41, Last updated: 20th Dec 2019 at 14:38

Arabidopsis clock model P2011.2.1 - PLM_71, version 2

Millar group, PlaSMo model repository

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
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis clock models P2011.1.2 and P2011.2....

Organisms: Arabidopsis thaliana

Models: Arabidopsis clock model P2011.2.1 - PLM_71, ver..., Arabidopsis clock model P2011.2.1 - PLM_71, ver...

SOPs: No SOPs

Data files: SBSI output from optimisation 26-30 July 2013, ..., Unpacked SBSI optimisation results, PLM_71_ 2

Created: 10th Jan 2019 at 17:39, Last updated: 20th Dec 2019 at 12:10

Arabidopsis clock model P2011.1.2 - PLM_71, version 1

Millar group, PlaSMo model repository

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

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis clock models P2011.1.2 and P2011.2....

Organisms: Arabidopsis thaliana

Models: Arabidopsis clock model P2011.1.2 - PLM_71, ver..., Arabidopsis clock model P2011.1.2 - PLM_71, ver...

SOPs: No SOPs

Data files: No Data files

Created: 10th Jan 2019 at 17:39, Last updated: 20th Dec 2019 at 12:07

Arabidopsis clock model P2011.6.1 - PLM_1044, version 1

Millar group, PlaSMo model repository

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
...

Contributor: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

Snapshots: No snapshots

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis clock model P2011.6.1 - PLM_1044

Organisms: No organisms

Models: Arabidopsis clock model P2011.6.1 - PLM_1044, v..., Arabidopsis clock model P2011.6.1 - PLM_1044, v..., P2011.6.1 Copasi

SOPs: No SOPs

Data files: No Data files

Created: 10th Jan 2019 at 17:39, Last updated: 20th Dec 2019 at 11:58

Arabidopsis clock model P2011.3.1 - PLM_1041, version 1

Millar group, PlaSMo model repository

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

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis clock model P2011.3.1 - PLM_1041

Organisms: No organisms

Models: Arabidopsis clock model P2011.3.1 - PLM_1041, v..., Arabidopsis clock model P2011.3.1 - PLM_1041, v..., P2011.3.1 Copasi

SOPs: No SOPs

Data files: No Data files

Created: 10th Jan 2019 at 17:39, Last updated: 20th Dec 2019 at 11:55

RNA-seq data for BaP and EE2 treated PCLS

Systems toxicology of Atlantic cod

No description specified

Contributor: Fekadu Yadetie

Assay type: RNA-seq

Technology type: Next generation sequencing

Snapshots: No snapshots

Investigation: 1 hidden item

Study: Effects of BaP and EE2 treatments on transcript...

Organisms: Gadus morhua

SOPs: No SOPs

Data files: PCLS_BaP-EE2_RNAseq - analysis, PCLS_BaP-EE2_RNAseq - reads, RNA-seq metadata for BaP and EE2 treated PCLS s...

Created: 6th Dec 2019 at 14:15, Last updated: 10th Dec 2019 at 23:06

Liver RNA-seq data for in vivo VII

Systems toxicology of Atlantic cod

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

Investigation: 1 hidden item

Study: 1 hidden item

Organisms: Gadus morhua

SOPs: No SOPs

Data files: 3 hidden items

Created: 5th Dec 2019 at 21:34, Last updated: 6th Dec 2019 at 13:25

Dynamic model simmulation pipeline

MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine

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
...

Contributor: Niels Zondervan

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Investigation: Modelling of M. pneumoniae metabolism

Study: Core Model predictions

Organisms: No organisms

Models: Dynamic model of glycolysis, pyruvate metabolis...

SOPs: No SOPs

Data files: Dynamic modelling pipeline

Created: 10th Jan 2019 at 13:44, Last updated: 20th Nov 2019 at 00:19

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