Assays

What is an Assay?

1319 Assays visible to you, out of a total of 2303

Supplemental Files

SysMetEx

Supplemental files for the publication

Submitter: Malte Herold

Biological problem addressed: Model Analysis Type

Investigation: SysMetEx - Dataset collection

Study: Supplemental Files

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: Supplemental File 1 - maxquant parameters, Supplemental File 2 - qc raw reads, Supplemental File 4 - mapping statistics, Supplemental Table 1 - omics samples, Supplemental file 3 - qc processed reads

Snapshots: No snapshots

Created: 23rd Jan 2020 at 11:03, Last updated: 23rd Jan 2020 at 12:14

Links to code repositories

SysMetEx

Links to additional gitlab repositories

Submitter: Malte Herold

Biological problem addressed: Model Analysis Type

Investigation: SysMetEx - Dataset collection

Study: Supplemental Files

Organisms: No organisms

Models: No Models

SOPs: No SOPs

Data files: Repository for data analysis, Repository for reference genomes

Snapshots: No snapshots

Created: 23rd Jan 2020 at 11:13, Last updated: 23rd Jan 2020 at 12:14

RNAseq rawdata

SysMetEx

Rawdata for RNAseq derived from biofilms on chalcopyrite grains

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: SysMetEx - Dataset collection

Study: Biofilms on chalcopyrite grains

Organisms: Acidithiobacillus caldus : Acidithiobacillus caldus ATCC 51756 (wild-type / wild-type), Leptospirillum ferriphilum : Leptospirillum ferriphilum DSM 14647 (wild-type / wild-type), Sulfobacillus thermosulfidooxidans : Sulfobacillus thermosulfidooxidans DSM_9293 (wild-type / wild-type)

SOPs: DNA, RNA, Protein extraction from mineral samples, SOP - RNA-Prot sampling for bioleaching, Sample Identification Code

Data files: Rawdata RNAseq

Snapshots: No snapshots

Created: 6th May 2019 at 15:10, Last updated: 23rd Jan 2020 at 12:14

RNAseq rawdata

SysMetEx

Link to RNAseq raw data

Submitter: Malte Herold

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: SysMetEx - Dataset collection

Study: Planktonic cells

SOPs: 003 Biomolecular Extractions from LAO (Qiagen A..., SOP - RNA-Prot sampling for bioleaching, Sample Identification Code

Data files: Rawdata RNAseq

Snapshots: No snapshots

Created: 6th May 2019 at 15:25, Last updated: 23rd Jan 2020 at 12:14

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

iRhythmics

(Show All)

No description specified

Submitter: Markus Wolfien

Biological problem addressed: Gene Expression

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...

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1227.1

Created: 16th Jan 2020 at 12:21, Last updated: 17th Jan 2020 at 10:12

Network reconstruction and comparison of BRAFi sensitive and resistant cells

Colosys

No description specified

Submitter: Evert Bosdriesz

Biological problem addressed: Model Analysis Type

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

Snapshots: No snapshots

Created: 9th Sep 2019 at 12:10, Last updated: 14th Jan 2020 at 15:03

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.995.2

Created: 11th Apr 2019 at 09:18, Last updated: 8th Jan 2020 at 15:12

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.994.2

Created: 11th Apr 2019 at 09:16, Last updated: 8th Jan 2020 at 15:11

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.993.2

Created: 11th Apr 2019 at 08:15, Last updated: 8th Jan 2020 at 15:10

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.991.2

Created: 10th Apr 2019 at 09:59, Last updated: 8th Jan 2020 at 15:10

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.989.2

Created: 9th Apr 2019 at 14:05, Last updated: 8th Jan 2020 at 15:09

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.988.2

Created: 9th Apr 2019 at 14:05, Last updated: 8th Jan 2020 at 15:09

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.987.2

Created: 9th Apr 2019 at 14:02, Last updated: 8th Jan 2020 at 15:09

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.986.2

Created: 9th Apr 2019 at 12:25, Last updated: 8th Jan 2020 at 15:08

Steady state cell free extract, with Mn and NAD recycling

Computational pathway design for biotechnological applications

No description specified

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

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

Snapshots: No snapshots

Created: 29th Nov 2019 at 16:49, Last updated: 6th Jan 2020 at 15:17

XDH

Computational pathway design for biotechnological applications

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

Organisms: No organisms

Models: XDH model

SOPs: No SOPs

Data files: XDH-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.968.1

Created: 26th Mar 2019 at 14:37, Last updated: 6th Jan 2020 at 15:17

XLA

Computational pathway design for biotechnological applications

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

Organisms: No organisms

Models: XLA model

SOPs: No SOPs

Data files: XLA-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.969.1

Created: 26th Mar 2019 at 14:41, Last updated: 6th Jan 2020 at 15:17

XAD

Computational pathway design for biotechnological applications

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

Organisms: No organisms

Models: XAD model

SOPs: No SOPs

Data files: XAD-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.970.1

Created: 26th Mar 2019 at 14:41, Last updated: 6th Jan 2020 at 15:17

KDXD

Computational pathway design for biotechnological applications

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

Organisms: No organisms

Models: KDXD model

SOPs: No SOPs

Data files: KDXD-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.971.1

Created: 26th Mar 2019 at 14:42, Last updated: 6th Jan 2020 at 15:17

KGSADH

Computational pathway design for biotechnological applications

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

Organisms: No organisms

Models: KGSADH model

SOPs: No SOPs

Data files: KGSADH-initial rate kinetics data

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.972.1

Created: 26th Mar 2019 at 14:42, Last updated: 6th Jan 2020 at 15:17

Progress curve XDH

Computational pathway design for biotechnological applications

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

Organisms: No organisms

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

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.978.2

Created: 30th Mar 2019 at 11:34, Last updated: 6th Jan 2020 at 15:17

Progress curve XLA

Computational pathway design for biotechnological applications

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

Organisms: No organisms

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

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.979.2

Created: 30th Mar 2019 at 18:41, Last updated: 6th Jan 2020 at 15:17

Progress curve XAD

Computational pathway design for biotechnological applications

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

Organisms: No organisms

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

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.980.2

Created: 30th Mar 2019 at 18:42, Last updated: 6th Jan 2020 at 15:17

Progress curve KDXD

Computational pathway design for biotechnological applications

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

Organisms: No organisms

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

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.981.2

Created: 30th Mar 2019 at 18:43, Last updated: 6th Jan 2020 at 15:17

Progress curve KGSADH

Computational pathway design for biotechnological applications

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

Organisms: No organisms

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

SOPs: No SOPs

Data files: Progress curve analysis data

Snapshots: Snapshot 1, Snapshot 2

DOI: 10.15490/fairdomhub.1.assay.982.2

Created: 30th Mar 2019 at 18:44, Last updated: 6th Jan 2020 at 15:17

F2014.1 - PLM_1030, version 1

PlaSMo model repository

(Show All)

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

Organisms: No organisms

Models: F2014 all parameters in SBML, F2014.1 - PLM_1030, version 1, SUBMITTED, F2014.1.2 Copasi, F2014.1.2 with stepfunction and 1 hidden item

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:40, Last updated: 20th Dec 2019 at 13:56

PLM_67v3withTempPulse - PLM_81, version 1

PlaSMo model repository

(Show All)

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

Study: PLM_67v3withTempPulse - PLM_81

Organisms: No organisms

Models: 2 hidden items

SOPs: No SOPs

Data files: No Data files

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:41, Last updated: 20th Dec 2019 at 13:38

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 ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

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

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:39, Last updated: 20th Dec 2019 at 11:10

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

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

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

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:39, Last updated: 20th Dec 2019 at 11:07

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 ...

Submitter: BioData SynthSys

Biological problem addressed: Gene Regulatory Network

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

Snapshots: No snapshots

Created: 10th Jan 2019 at 16:39, Last updated: 20th Dec 2019 at 10:58

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