Assays
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P2011.1.2 written in Antimony and converted in SBML using python package Tellurium. Parameters values correspond to P2011.1.2
Submitter: Uriel Urquiza Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units in Arabidopsis clock models up t...
Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS do not use lightly. Derived from PLM_49, after removing ABA regulation and tidying up the SBML in COPASI. Please see version comments for IMPORTANT notes.Comments No parameters constrained in version 1 file. 2013-02-26 17:31:26 3 amillar2 andrew.millar@ed.ac.uk Compiled successfully in SBSI for optimisation. 2013-02-26 17:28:18 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Version 1 is file P2012_NoSinkNoABAParamsNom38_freshCopasi.xml ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: P2012_AJMv2_NoABA - PLM_69
Andrew's work-in-progress P2012 version. NB KNOWN PROBLEMS do not use lightly. Derived from PLM_49, after removing ABA regulation and tidying up the SBML in COPASI. Please see version comments for IMPORTANT notes.Comments No parameters constrained in version 1 file. 2013-02-26 17:31:26 3 amillar2 andrew.millar@ed.ac.uk Compiled successfully in SBSI for optimisation. 2013-02-26 17:28:18 3 amillar2 andrew.millar@ed.ac.ukVersion Comments Version 2 is file P2012_fin_NoABAv4.xml of 6th March.
It ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
Study: P2012_AJMv2_NoABA - PLM_69
In silico check and filtering for potential Pan-assay interference compounds.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Cells were grown to mid-exponential phase (OD600nm ~0.2) in GM17 medium at 37°C (with 0.15 mM ZnSO4 where relevant) and 84 ml of culture was mixed by inverting with 8.4 ml of fixing solution (50 mM Tris pH 8.0, 100 mM NaCl, 0.5 mM EGTA, 1 mM EDTA, 30% (v/v) formaldehyde) and incubated at room temperature for 30 min. Cells were disrupted and crosslinked DNA was sheared by sonication. Antibodies coupled to magnetic beads were used to pull down cross-linked complexes. DNA was purified, amplified, ...
Submitter: Jan-Willem Veening
Assay type: Transcriptomics
Technology type: ChIP-on-chip
Investigation: Wetlab approach to transcription fidelity
This is part of the GreenLab Functional-Structural Plant Model for Arabidopsis published in Christophe et al 2008. This model was re-factored, to facilitate the integration in the Chew et al Framework Model, and it cannot be run as a standalone model. Related PublicationsAngélique Christophe A E, Véronique Letort B, Irène Hummel A, Paul-Henry Cournède B, Philippe de Reffye C, Jérémie Lecœur (2008). A model-based analysis of the dynamics of carbon balance at the whole-plant level in Arabidopsis ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
Submitter: Ziva Ramsak
Assay type: Q_PCR
Technology type: qPCR
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Endometriosis
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Endometriosis
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MetNet
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Kinetic characterisation en mathematical modelling of PFK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation en mathematical modelling of PGI.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Kinetic characterisation of phosphoglycerate kinase
Submitter: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Kinetic characterisation en mathematical modelling of PGK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
PGK - GAPDH models
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
Experimental data for the yeast PGK incubations at 30C, with and without recycling of ATP.
Submitter: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-30C
A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-30C
Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: NMR
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-70C
PGK 70C model
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-70C
Mathematical model for PGK kinetics, saturation with ADP, ATP, 3PG and BPG.
Submitter: Jacky Snoep
Biological problem addressed: Enzymology
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
Submitter: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
Kinetic characterisation en mathematical modelling of PGM.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Plant material The same plant material used for transcriptome analysis in (Flis et al., 2016) was the basis of our proteome study. Briefly, Arabidopsis thaliana Col-0 plants were grown on GS 90 soil mixed in a ratio 2:1 (v/v) with vermiculite. Plants were grown for 1 week in a 16 h light (250 μmol m−2 s−1, 20 °C)/8 h dark (6 °C) regime followed by an 8 h light (160 μmol m−2 s−1, 20 °C)/16 h dark (16 °C) regime for one week. Plants were then replanted with five seedlings per pot, transferred for ...
Submitter: Daniel Seaton
Assay type: Protein Quantification
Technology type: Mass Spectrometry
Investigation: Photoperiodic control of the Arabidopsis proteo...
Submitter: Ziva Ramsak
Assay type: Phenotype observation
Technology type: Leaf Chamber Fluorometer
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
L. lactis, S. pyogenes and E. faecalis were grown in C-limited chemostat cultures at various pH's and dilution rates. General flux distribution, yields and other physiological factors were studied.
Submitter: Martijn Bekker
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
These files show physiological measurements from the Sheffield Infors chemostat which were made during acetate calibration and also when sampling for the steady-state transcriptional profiles.
Submitter: Matthew Rolfe
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
Kinetic characterisation en mathematical modelling of PK.
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Measurement of plasma parameters: activities of cholinesterase, alanine aminotransferase, aspartate aminotransferase + cortisol and total protein levels in cod exposed to chlorpyrifos-methyl
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
To check if all works fine after struts update. Checking editorial options
Additional Attributes
tested:
Yes, against schema
Originally submitted to PLaSMo on 2013-11-22 15:15:40
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: Plasmo test model1 - PLM_80
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 external potassium changes will be monitored by the MIFE and FLISE technique. This allows an estimation of internal potassium changes by determining an initial concentration.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Potassium uptake in Saccharomyces cerevisiae
Is internal potassium affected by mutations in the Trk1,2 system? Under which conditions? Potassium measurements in wild type and TRK mutants grown and/or incubated under several external conditions.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
The potassium fluxes will be estimated from the internal and external concentration changes.
How potassium starvation regulates the parameters of rubidium (potassium) transport. Analysis of transport characteristics during the starvation process. Kinetic characteristics of rubidium transport.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Ion Flux Changes
The potassium influx after the addition of a certain amount of KCl to a potassium free medium, followed by the injection of glucose will be measured by using the MIFE and FLISE technique. This reveals a time course of potassium. Also the external potassium concentrations will be measured.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Potassium uptake in Saccharomyces cerevisiae
Genes are transcribed in polysictronic messages (pre-mRNA) that are destined for either maturation into mRNAs, or degradation. Since transcription regulation is non-existent with few exceptions, the rate of pre-mRNA processing, together with mRNA decay and translation rates, are believed to control gene expression. In this assay, 2T1 blood form trypanosomes are subject to treatment by ActinomycinD for 5 minutes, inhibiting transcription. The cells are harvested, depleted for ribosomal RNA, and ...
Submitter: Abeer Fadda
Assay type: Transcriptomics
Technology type: Rna-seq
Investigation: Gene expression in Trypanosoma brucei
Prediction of patient urinary acylcarnitine under metabolic decompensation. Generates Fig. 3, Table 1, and Table S2 in the associated publication.
Download and unzip "Model_notebooks.rar" and run "7, Fig3+4+S1+S3-ACADDs-[needs-(1)]-20221109.nb" after running "1, generate-model-20221109.nb"
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model analysis
Preparation needed to use Simulation Foundry, Version 1.5.
Please read the manual before working with this Simulation Foundry.
Pay careful attention to the installation instructions.
Note the known issues.
Submitter: Gudrun Gygli
Assay type: Instructions
Technology type: Technical Computer Installation
Investigation: 1 hidden item
Prepared multimeric tubulin protein receptors for docking studies, generated by alignment of two identical models of alpha-tubulin on alpha-tubulin chains of two neighboring protofilaments.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
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
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 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 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: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Is protein content of trk1,2 mutants affected? Determination of proteins in wild type and TRK mutants
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
What are the main proteins identified? Spots sampling and identification by MS
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Proteomic Studies
Submitter: Jacqueline Wolf
Assay type: Proteomics
Technology type: Tandem Mass Spectrometry
Investigation: Amino acid degradation in Sulfolobus solfataric...
Submitter: Theresa Kouril
Assay type: Proteomics
Technology type: Tandem Mass Spectrometry
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Data derived from protein samples
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Reverse Engineering Directed Gene Regulatory Ne...
Study: Supplementary files
Submitter: Lars Wöhlbrand
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Heat stress response of Prorcentrum cordatum
Submitter: Lars Wöhlbrand
Assay type: Protein Identification
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
Submitter: Jay Moore
Assay type: Proteomics
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Study: Timeseries 1
Proteomics data for L.ferriphilum samples (continuous and with mineral)
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Submitter: Ziva Ramsak
Assay type: Protein Quantification
Technology type: Orbitrap Velos
Investigation: MOA - Multiomics analysis of potato response to...
Study: MOA2010-05
Some results from proteomics analyses of cod liver exposed to PAH and PFAS
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
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
The data is submitted to the PRIDE repository, and will be linked here.
Submitter: Marta Eide
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Submitter: Malte Herold
Assay type: Proteomics
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Raw proteomics data derived from planktonic cells in chalcopyrite leaching experiments
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Study: Planktonic cells
Proteomics data for samples derived from continuous cultures
Submitter: Malte Herold
Assay type: Proteomics
Technology type: Technology Type
Investigation: SysMetEx - Dataset collection
Study: Continuous cultures
Examples of proteomics templates for gele electrophoresis data that conform to the MIAPE-GE specification
Submitter: Katy Wolstencroft
Assay type: Proteomics
Technology type: Electrophoresis
Investigation: Creating data sheet template for 'omics data
Some examples of proteomics templates for Mass Spectrometry data that conform to the MIAPE specification
Submitter: Katy Wolstencroft
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: Creating data sheet template for 'omics data
The external pH changes will be monitored by the MIFE and FLISE technique. This allows an estimation of internal pH changes by determining an initial pH. pH changes will be also determined by using green fluorescent protein dyes. Relating the proton efflux and the change of internal pH allows an estimate of the proton buffering capacity.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Potassium uptake in Saccharomyces cerevisiae
Related to the internal pH changes the proton efflux will be estimated from the internal and external concentration changes.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Ion Flux Changes
In parallel with the potassium influx the efflux of protons is monitored by measuring the external proton concentration changes with MIFE or FLISE.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Potassium uptake in Saccharomyces cerevisiae
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
Pyruvate formate-lyase (PFL) is an important enzyme in the metabolic pathway of lactic acid bacteria (LAB) and is held responsible for the regulation of the shift between homolactic acid to mixed acid fermentation. PFL catalysis the reversible reaction of acetyl-CoA and formate into pyruvate and CoA. A glycyl radical, who is regenerated within the reaction, is involved; therefore, PFL works only under strictly anaerobic conditions. For its activation, the C-terminal domain has to bind to the ...
Submitter: Stefan Henrich
Biological problem addressed: Model Analysis Type
Investigation: The Attic
Study: Pyruvate formate-lyase (PFL)