Assays
What is an Assay?Filters
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
To obtain each of the figure 2A - 2E please download "Main Figure Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
To obtain each of the figure 4A - 4D please download "Main Figure 4 Copasi" and open the sub-directory with the name of the sub-figure, run the Copasi files and the time dependence simulation. This will reproduce the figure in this paper.
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
Determinations of parasite volumes in a well-synchronised, infected culture treated with a cytosolic stain, using fluorescence microscopy. Diameters used to calculate parasite volume, assuming a spherical parasite cell.
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Glucose metabolism in Plasmodium falciparum inf...
Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.
Submitter: Daniel Seaton
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: Photoperiodic control of the Arabidopsis proteo...
Test by Martin for simileXML
Originally submitted to PLaSMo on 2012-03-08 11:39:23
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Beaton, Martin
Study: Martin test - PLM_65
Test by Martin for simileXML
Version Comments
Version 2, the product of many seconds of research..
Originally submitted to PLaSMo on 2012-03-08 11:39:23
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Beaton, Martin
Study: Martin test - PLM_65
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
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: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Adlung et al (2017) Molecular Systems Biology
L. lactis, E. faecalis and S. pyogenes are referred to as LAB because of the fact that in the presence of glucose lactate is produced as the main fermentation product . This metabolic pathway is relatively inefficient, since only 2 ATP are generated from one glucose molecule. All three LAB possess the genetic make up for mixed acid fermentation, a more effective way of fermentation generating 3 ATP per molecule of glucose. All three genomes reveal (at least) two genes encoding a lactate dehydrogenase ...
Submitter: Martijn Bekker
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
Creation of personalised models of control, symptomatic MCADD, asymptomatic MCADD, and early diagnosis MCADD individuals using fibroblast proteomics to adjust model Vmaxes. Generates Fig. 7 and S7.
Download and unzip "Model_notebooks.rar" and run "13, Fig7-personalised-models-[needs-(1-and-12)]-20221109.nb" after running "1, generate-model-20221109.nb" and "12, Fig7-S7-preprocessing-[needs-(1)-]-20221109.nb".
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model analysis
Incrementally increase the activity of some target rescue enzymes from 20% of default expression to 200% of default expression in a control and MCADD model to see if flux and CoASH concentration are rescued. Generates Fig. 6, S5, and S6.
Download "Model_notebooks.rar", unzip, and run "11, Fig6+S5-rescues-[needs-(1-and-10)]-20221109.nb", "10, Fig6B-inset-rescues-(low-acetylCoA)-[needs-(1)]-20221109.nb", and "16, FigS6-rescues-20221109-fixed-[needs-(1)]-CoASH.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
This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration. In the original paper, the model is used twice, once for the trees and once for the grass under the trees, with the grass receiving light not intercepted by the trees. The model provided here is just for a single vegetation component.Related PublicationsMcMurtrie RE, Wolf L (1983). A model of competition between trees and grass for radiation, water and ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Muetzelfeldt, Robert
This is a very simple generic vegetation model, with just one state variable (plant biomass), and two processes: assimilation and respiration. In the original paper, the model is used twice, once for the trees and once for the grass under the trees, with the grass receiving light not intercepted by the trees. The model provided here is just for a single vegetation component.Related PublicationsMcMurtrie RE, Wolf L (1983). A model of competition between trees and grass for radiation, water and ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Muetzelfeldt, Robert
This .csv file shows the numbers of different cytochrome molecules per cell from steady-state continuously-grown cultures at various aerobiosis levels (0%, 31%, 56%, 85% and 115% AAU).
Submitter: Alison Graham
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
To estimate the relative level of plasma-membrane potential in the wild type, single trk1 and trk2 or double trk1 trk2 mutants, the diSC3(3) fluorescent probe was added to cells grown under various conditions and the levels of cell fluorescence were monitored.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
To estimate the relative level of plasma-membrane potential in the wild type, single trk1 and trk2 or double trk1 trk2 mutants, the diSC3(3) fluorescent probe was added to cells grown under various conditions and the levels of cell fluorescence were monitored.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Calculation of control and response coefficients. Generates Fig. 5, Fig. S4, and Table S2 in the associated publication.
Download "Model_notebooks.rar", unzip, and run: "8, Fig5-control-coefficients-[needs-(1)]-20221109.nb", "9, TableS2-response-coefficients-[needs-(1)]-20230302.nb", and "15, FigS4-control-coefficients-low-AcetylCoA-[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
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glucose metabolism in Plasmodium falciparum inf...
Metabolic control analysis: Local control coefficients for 40 independent samples based on 100x sampling from the measurement distribution Global control analysis based on 100.000 Latin Hypercube sampling from the parameter search range (0.01-100 for Km values and 0.001-1000 for Vmax values)
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Core Model predictions
Genome scale metabolic model of Sulfolobus solfataricus specific scenario: modelling of L-fucose degradation pathways
Submitter: Jacqueline Wolf
Biological problem addressed: Metabolic Network
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
All flux balance analyses of the stoichiometric model
Submitter: Julia Koblitz
Biological problem addressed: Modelling analysis
Investigation: Systems biology investigation of aromatic compo...
Study: Metabolic Modelling
Growth on D-glucose served as reference scenario
Submitter: Jacqueline Wolf
Biological problem addressed: Genome Scale
Investigation: Amino acid degradation in Sulfolobus solfataric...
Submitter: Jay Moore
Biological problem addressed: Metabolic Network
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Submitter: Lars Wöhlbrand
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Heat stress response of Prorcentrum cordatum
Concentration of glycolytic intermediates over time
Submitter: Katy Wolstencroft
Assay type: Discontinuous Enzymatic
Technology type: Enzymatic Activity Measurements
Investigation: Yeast Glycolytic Oscillations
Metabolite profiling on T. brucei exposed to methylene blue has been carried out using LC-MS to investigate metabolic changes caused by oxidative stress
Submitter: Dong-Hyun Kim
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
Intracellular and extracellular metabolome analysis
Submitter: Jacqueline Wolf
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Amino acid degradation in Sulfolobus solfataric...
Submitter: Jacqueline Wolf
Assay type: Experimental Assay Type
Technology type: Gas Chromatography
Investigation: Phenol degradation in Saccharolobus solfataricu...
Submitter: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Investigation on the effect of pulsed metabolit...
Submitter: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Investigation on the effect of pulsed metabolit...
Measurement of intra- and extra-cellular metabolome.
Submitter: Ulf Liebal
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: The transition from growing to non-growing Baci...
Submitter: Jay Moore
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Study: Timeseries 1
NB! The files here are the old version for the files in Lipidomics (Experimental Assay)
Lipidomic analysis by LC-MS of tissue samples from the GSF1 feed-switch experiment. Samples were analyzed at NTNU by Zdenka Bartosova and Per Bruheim.
There are two separate data files of lipid analysis in muscle and liver samples. Excel sheets contains both raw and normalised data of compounds abundance. Normalization to all compounds was used as a normalization method.
We have also performed a "normalization ...
Submitter: Jon Olav Vik
Assay type: Experimental Assay Type
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Omega-3 metabolism of salmon in relation to die...
Global metabolomics screening of 36 liver samples from Atlantic cod exposed to chlorpyrifos-methyl for 30 days.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Measurements of external metabolites based on growth curve data. Flux estimates for uptake of external metabolites such as glucose and production rates for external metabolites lactate and acetate
Submitter: Niels Zondervan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Metabolomics measurements
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
This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.
Submitter: Katy Wolstencroft
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Creating data sheet template for 'omics data
Curation guidelines for molecular interaction causal statements
Submitter: Vasundra Toure
Assay type: Instructions
Technology type: Technology Type
Investigation: WP1: Creation of an integrated and curated canc...
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MetNet
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Microscopy
Investigation: SysMetEx - Dataset collection
RNAi Screen of 100 candidate genes predicted to be involved in mitotic chromosome condensation. MIHCSME template example for IDR0002 dataset.
Submitter: Rohola Hosseini
Assay type: high content screen of cells treated with library of siRNAs
Technology type: fluorescence microscopy
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
MIHCSME template example for IDR0022 dataset. Primary and validation RNAi screen using smartpool and single siRNAs to identify cell migratory regulators in Hs578T and MDA-MB-231 triple-negative breast cancer cells.
Submitter: Rohola Hosseini
Assay type: high content screen of cells treated with library of siRNAs
Technology type: bright-field microscopy
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Compound screen on 13 HepG2 -GFP reporter lines, to measure GFP protein induction, and cell death induction. Template and associated files describe High Content Screening experimental data that conform to the MIHCSME specification.
Submitter: Rohola Hosseini
Assay type: high content screening
Technology type: Confocal Laser Scanning Microscopy (CLSM)
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Compound screen on HepG2 CHOP-GFP reporter, to measure CHOP-GFP protein induction upon treatment with compounds. Template and associated files describe High Content Screening experimental data that conform to the MIHCSME specification.
Submitter: Rohola Hosseini
Assay type: high content screen of cells in treated with a compound library
Technology type: Confocal microscopy
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Validation: Validated against the original running in Excel. Each calculation in the model was individually validated as well. Comments on numerical integration: Euler integration with time steps of 1. In Simile the "time units" were set to "day" and execution was for 364 days as the simulation starts at time 0 (not time 1 as in the Excel model). Comments on running Simile model: Users must specify the temperature controlled growing season themselves. To do this use the following steps which take ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Davey, Chris
Study: Miscanmod - PLM_3
Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Seedling hypocotyl data from literature for prr7 prr9 and Col wild-type plants under various photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Model simulations for 24h incubations with different ratios of HSD11B1 andd AKR1C3 transfected HEK293 cells are given in Mathematica notebook format.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Effect of 11BHSD inhibition on 11-ketotestoster...
A mathematica notebook that simulates the combined effect of HSD11B1/AKR1C3 ratio variation and HSD11B1 inhibition.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Effect of 11BHSD inhibition on 11-ketotestoster...
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Bachmann et al (2011) Molecular Systems Biology...
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/bachmann2011/simulate
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Kolodkin et al (2010) Molecular Systems Biology...
Lumped kinetic model of L. lactis glycolysis, formulated with ordinary differential equations. Simulations are in line with experimental data
Submitter: Mark Musters
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
HSD11B1 was inhibitied by CBX and the effect of the inhibition on cortisone and 11KA4 conversion was simulated. The model was coded in Mathematica and the f=manuscript figures 3 A,B,C,D,E anbd F are presented in the notebook.
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Effect of 11BHSD inhibition on 11-ketotestoster...
Model prediction of the conversion of 3PG to fructose-6-phosphate and the gluconeogenic pathway intermediates. https://jjj.bio.vu.nl/models/experiments/kouril3_experiment-user/simulate
Submitter: Jacky Snoep
Biological problem addressed: Metabolic Network
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Model files accompanying Seaton et al., Molecular Systems Biology, 2015 Abstract: Clock?regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best?understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN?BINDING, KELCH REPEAT, F?BOX 1 (FKF1) transcription. ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Seaton, Daniel
Modelling the degradation of BPG, GAP and DHAP at high temperature
Submitter: Jacky Snoep
Biological problem addressed: Metabolism
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Based on a kinetic model a description of the potassium current is achieved. Its properties with respect to changes in membrane potential and potassium concentrations are derived.
Submitter: Falko Krause
Biological problem addressed: Model Analysis Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Study: Kinetic properties of Trk
Submitter: Katy Wolstencroft
Biological problem addressed: Model Analysis Type
Investigation: Yeast Glycolytic Oscillations
The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length
Submitter: Jurgen Haanstra
Biological problem addressed: Model Analysis Type
Investigation: Gene expression in Trypanosoma brucei
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model construction
This is a modified version of Biomodels89, containing a light-forcing function. This variant is configured to run cycles of LD8:16Related Publicationsocke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ. (2006). Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. . Mol Syst Biol . Originally submitted to PLaSMo on 2012-03-29 10:24:44
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Adams, Richard
Submitter: Pasquale Linciano
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phenotypic and machine learning approaches for ...
Submitter: Pasquale Linciano
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phenotypic and machine learning approaches for ...
The dynamic model describes response of yeast metabolic network on metabolic perturbation (i.e. glucose-pulse). One compartmental ODE-based model of yeast anaerobic metabolism includes: glycolysis, pentose phosphate reactions, purine de novo synthesis pathway, purine salvage reactions, redox reactions and biomass growth. The model describes metabolic perturbation of steady state growing cells in chemostat.
Submitter: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Investigation: Kinetic analysis of metabolic system using tran...
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
This assay is designed to measure the decay kinetics of mRNA in T. brucei blood forms. T. brucei lacks the canonical transcriptional regulation employed by other eukaryotes through transcription factors, and relies almost entirely on regulation of mRNA decay and further downstream steps in order to control gene expression. 3 replicates of 8 time points were taken to measure mRNA abundance in the cell using RNA-seq. The first time point was fot WT, untreated cells; the second was 5 min after the ...
Submitter: Abeer Fadda
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: Gene expression in Trypanosoma brucei
Alignments of various alpha-tubulin and beta-tubulin sequences from dinitroaniline-sensitive and dinitroaniline-resistant species. Sequences were retrieved from UniProt with the identifiers listed below and subjected to a multiple sequence alignment using ClustalOmega (ebi.ac.uk/Tools/msa/clustalo/; ClustalOmega webserver, last accessed 16-02-23):
alpha-tubulin:
- [dinitroaniline sensitive] T. cruzi - Q27352; T. brucei brucei - Q4GYY5; L. infantum - ...
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
Submitter: Arnau Montagud
Biological problem addressed: Gene Regulatory Network
Investigation: PhysiBoSS-COVID: the Boolean modelling of COVID...
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP