Assays
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Validation Validated against original code running under GNU FORTRAN 95. Comments on numerical integration No integration needed. Comments on running the (Simile) model The variable "num errors" accumulates the number of times the ribulose bis-phosphate limited photosynthesis rate cannot be calculated. See the documentation dialogue for the Simile variable "jl_electron transport" for details.Additional AttributesOriginal Model: Language: FORTRAN 95 Author:Daniel P. Rasse File name of original ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Davey, Chris
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MetNet
Extraction of causalities from transcription and translation reactions from the Reactome pathway database.
Submitter: Vasundra Toure
Biological problem addressed: Biological Network Analysis
Investigation: WP1: Creation of an integrated and curated canc...
Submitter: Jurgen Haanstra
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Metabolism of HepG2 liver cancer cells
Submitter: Jurgen Haanstra
Assay type: Cell Count
Technology type: Technology Type
Investigation: Metabolism of HepG2 liver cancer cells
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: Jacqueline Wolf
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
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
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
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
Submitter: Lars Wöhlbrand
Assay type: Protein Expression Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: 1 hidden item
Submitter: Lars Wöhlbrand
Assay type: Protein Identification
Technology type: Ion Mobility Spectrometry Mass Spectrometry
Investigation: 1 hidden item
Cellular size and granularity (measured by FACS) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Submitter: Maksim Zakhartsev
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Kinetic analysis of metabolic system using tran...
This is the representation of major parts of the central metabolism in monocotyledon plants. The information has been derived from the MetaCrop [2] database, a manually curated repository of high quality information concerning the metabolism of crop plants. This includes pathways, reactions, locations, transport processes, and moreOriginally submitted to PLaSMo on 2012-03-05 11:52:18
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Beaton, Martin
"The CENTURY model is a general model of plant-soil nutrient cycling which is being used to simulate carbon and nutrient dynamics for different types of ecosystems including grasslands, agricultural lands, forests and savannas. CENTURY is composed of a soil organic matter/ decomposition submodel, a water budget model, a grassland/crop submodel, a forest production submodel, and management and events scheduling functions. It computes the flow of carbon, nitrogen, phosphorus, and sulfur through ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Muetzelfeldt, Robert
Study: CENTURY_Rowe_daily - PLM_22
E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant strains were characterized in batch growth curves aerobic and anaerobically. Optical density, glucose consumption and by-product accumulation were measured during growth.
Submitter: Sonja Steinsiek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
Enzymes involved in butanediol formation from pyruvate in L. Lactis and E. faecalis were characterized with respect to their Km's for their substrates and their Vmaxes
Submitter: Martijn Bekker
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Investigation: The Attic
S. pyogenes wildetype, an arcA- and a glnA-deletion mutants were grown in CDM-LAB cultures at pH 6.5 and 7.5 and at a growth rate of 0.05
Submitter: Antje Sieg
Assay type: Experimental Assay Type
Technology type: HPLC
Investigation: Amino acid metabolism of four LAB species: Stre...
Mutant strains which lack one or more of the glucose transport systems were analyzed in aerobic chemostat cultures and compared to batch cultures.
Submitter: Sonja Steinsiek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Analysis of the glucose transport in Escherichi...
Submitter: Theresa Bender
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Consortium for Clinical Characterization of COV...
Study: General Information
This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Study: 1 hidden item
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Version Comments
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Originally submitted to PLaSMo on 2015-09-02 18:27:55
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Zielinski, Tomasz
Chemical analyses in Kollevåg includes sediment contaminant concentrations, concentrations of various contaminants in cod liver and concentrations of PAH metabolites in cod bile.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Study: Caging study - Kollevåg
Concentrations of chlorpyrifos-methyl and its metabolite TCP in cod liver and bile quantified using gas chromatography
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Measurements of PAH metabolites in bile (1-OH-napthalene, 2-OH-naphthalene, 1-OH-phenanthrene, 1-OH-pyrene) and PFAS compounds in liver (PFOS, PFOA, PFNA, PFTrDa) in Atlantic cod exposed to mixtures of PAHs and PFASs.
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Build the chemical defensome gene list for 5 fish: Zebrafish (Danio rerio), Atlantic cod (Gadus morhua), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus) and stickleback (Gasterosteus aculeatus). Source code and relevant files can be found on GitHub: https://github.com/zhxiaokang/fishDefensome/tree/main/defensomeGenes
Submitter: Xiaokang Zhang
Biological problem addressed: Stress response/Adaptation
Investigation: 1 hidden item
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
This is a photothermal model for Arabidopsis that predicts flowering time, published in Chew et al (2012). It is an improved version of the model in Wilczek et al (Science 2009). A Simile version of the model is attached. Instructions to run the Photothermal Model in Simile 1. Download the Simile file attached or import the XML into Simile: a. File > Import > XML Model Description 2. To run the model: a. Model > Run or click on the ‘Play’ ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
This is the Framework Model (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111) that links the following: 1. Arabidopsis leaf carbohydrate model (Rasse and Tocquin) - Carbon Dynamic Model 2. Part of the Christophe et al 2008 Functional-Structural Plant Model 3. Chew et al 2012 Photothermal Model 4. Salazar et al 2009 Photoperiodism Model To run the model in Simile, please download the Evaluation Edition of the software from http://www.simulistics.com/products/simile.php ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model). Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: ChIP-on-chip
Investigation: Creating data sheet template for 'omics data
Luciferase reporter gene assay for circadian period of seedlings in constant light, for Col0 (WT) and prr7prr9, with and without exogenous gibberellins (GA). Supplementary Figure 11f in Chew et al., _in Silico _Plants.
Raw and processed data, together with circadian period analysis and summary statistics, are available from BioDare.ed.ac.uk: choose https://biodare.ed.ac.uk/experiment ("Browse Public Resources" on the Login screen), then you can link to https://biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=3838, ...
Submitter: Andrew Millar
Assay type: Transcriptional reporter gene
Technology type: Imaging
Investigation: Prediction and analysis of phenotypes in the Ar...
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MetNet
This is a collection of data that have been used to analyse data on deep eutectic solvent mixtures of choline chloride:glycerol:water.
Submitter: Gudrun Gygli
Biological problem addressed: Model Analysis Type
Investigation: Deep Eutectic Solvents
Submitter: Meina Neumann-Schaal
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
tbd
Submitter: Malte Herold
Biological problem addressed: Model Analysis Type
Investigation: Deep Neural Networks Outperform Human Expert’s ...
Measurement of DNA fragmentation using the Comet Assay, in white blood cells of Atlantic cod exposed to PAHs and PFASs
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Submitter: Charles Demurjian
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: MIT SRP
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Creation of homology models of various tubulins from dinitroaniline-sensitive and -resistant species, and a comparative analysis of their electrostatic potential grids overall and in putative binding site regions using PIPSA (Protein Interaction Property Similarity Analysis).
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
We will compare two different procedures to extract ATP from yeast cells: Standard kit procedure (hot Tris/EDTA) and Serrano procedure (cold perchloric acid). In addition we have tested different condition as it turned out that some are important.
Submitter: Walter Glaser
Assay type: Metabolomics
Technology type: Imaging
Investigation: Effect of Benzoic Acid on ATP Levels
Based on odendaal1, a control model is made and compared to model deficient for short-chain acyl-CoA dehydrogenase (SCADD, 0%), medium-chain acyl-CoA dehydrogenase (MCADD, 0%), and very long-chain acyl-CoA dehydrogenase (VLCADD, 10%). With and withou metabolite partitioning, and with a fixed mitohondrial free CoASH. Generates Figures 3, 4, S1, S2, and S3 in the related paper.
Download "Model_notebooks.rar", unzip, and run: "7, Fig3+4+S1+S3-ACADDs-[needs-(1)]-20221109.nb" and "14, ...
Submitter: Christoff Odendaal
Biological problem addressed: Model Analysis Type
Investigation: Mitochondrial fatty acid oxidation in human liver
Study: Model analysis
Here, we conduct a proof of principle by comparing a 2D and 3D fluorescent image analysis based approach on unlabeled cardiomyocytes. Based on the CellProfiler software, we extracted high-dimensional features of individual cells and nuclei, which are subsequently down-sampled and clustered. These clusters are furthermore benchmarked via different machine learning classifiers (e.g., AdaBoost, Gradient Boosting, Random Forest) as the ground truth for our proposed approach.
Submitter: Markus Wolfien
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: 1 hidden item
Comparison of Kcat values from the model and values from literature.
Submitter: Niels Zondervan
Assay type: Enzymatic Assay
Technology type: Technology Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Core Model training
Samples obtained form the central fermentation facility of Sulfosys have been compared using iTRAQ (isobaric tag for relative and absolute quantification). A pilot experiment resulted in creation of SOP and initial data on cells grown at 70 and 80C
Submitter: Pawel Sierocinski
Assay type: Protein Expression Profiling
Technology type: Isotope Ratio Mass Spectrometry
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Investigation of all steady state pH-values between pH 5.7 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7).
Submitter: Sara Jabbari
Assay type: Proteomics
Technology type: Technology Type
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH on the proteome
Comparison of the transcriptome at steady state in acidogenesis and at steady state in solventogenesis.
Submitter: Sara Jabbari
Assay type: Genomics
Technology type: Microarray
Investigation: The effect of pH upon the metabolic shift in Cl...
Investigation of the dynamic switch at pH values between 5.8 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7 and 4.5).
Submitter: Sara Jabbari
Assay type: Genomics
Technology type: Microarray
Investigation: The effect of pH upon the metabolic shift in Cl...
The pilot experiment was conducted in order to create SOPs and to gain insight in transcriptome of cells grown at 70 and 80C
Submitter: Pawel Sierocinski
Assay type: Transcriptional Profiling
Technology type: Microarray
Investigation: Analysis of Central Carbon Metabolism of Sulfol...
Combination of multiple sub-models to form Framework Model version 2
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Model files for FMv1.5. The model is based on FMv1 of Chew et al. PNAS 2014, which is also in FAIRDOMHub and linked to the Model record as an 'Attribution'. FMv1 was extended in this work by Hannah Kinmonth-Schultz and Daniel Seaton, in Matlab.
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Temperature effects on Arabidopsis floral induc...
Compound data, library construction schemes and preparation routine for small drug-like molecules as ligands in docking and for further analysis.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Submitter: Alexey Kolodkin
Biological problem addressed: Model Analysis Type
Investigation: ROS networks: designs, aging, Parkinson's disea...
Training of the model, parameter estimation using Evolutionary Programming using metabolomics, proteomics and some flux data.
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Investigation: Modelling of M. pneumoniae metabolism
Study: Core Model training
Construction and manual curated Genome Scale Metabolitic model of M. hyopneumoniae. Dynamic flux balance analysis was performed for glucose uptake
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Investigation: Modelling of M. pneumoniae metabolism
In order to construct an in vivo-like buffer for S. pyogenes, the intracellular concentrations of Fe, K, Mg, Mn Na, P and S elements were determined via ICP-AES (inductively coupled plasma atomic emissionspectroscopy) method at the Institute of Land Use, University of Rostock. The samples for the analysis were obtained from a steady state culture grown on CDM-LAB with glucose.
Submitter: Araz Zeyniyev
Assay type: Metabolite Profiling
Technology type: Inductively Coupled Plasma Mass Spectrometry
Investigation: Amino acid metabolism of four LAB species: Stre...
Assessment of possible linear correlations between predicted ADMET descriptors from QikProp (Schrödinger, LLC, New York, NY) runs and experimentally determined activities against T. brucei brucei bloodstream forms with the help of a Python script.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Assessment of the possible multiple correlation between experimentally determined TbPTR1 and TbDHFR inhibition values and corresponding anti-parasitic activities against T. brucei brucei bloodstream forms using a Python script.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Submitter: Harald Kusch
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Further information collections on COVID-19
We here create a kinetic model for a single enzyme within the T. brucei trypanothione synthesis pathway, the enzyme trypanothione synthetase based on the insights from the laboratory experiments
Submitter: Jurgen Haanstra
Biological problem addressed: Enzymology
Investigation: Kinetic understanding of the T. brucei trypanot...
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: MIT SRP
Harvest optical densites and methods of transcriptom, proteom and metabolom samples for all tested substrat conditions.
Submitter: Meina Neumann-Schaal
Assay type: Experimental Assay Type
Technology type: Cultivation experiment
Investigation: Systems biology investigation of aromatic compo...
Study: Experimental multi-OMICS
Submitter: Dawie van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Study: Model construction
The current-voltage relation for Trk1,2 will be determined according to the conditions of Kuroda et al.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Study: Current-voltage relation
The current-voltage relation for Trk1,2 will be determined for various external potassium concentrations.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: NHA1 Transport System in Saccharomyces cerevisiae
Study: Current-voltage relations
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: TRK1,2 Transport Systems of Saccharomyces cerev...
Study: Current-voltage relation
Current- voltage relations for will be determined for various internal potassium concentrations.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: NHA1 Transport System in Saccharomyces cerevisiae
Study: Current-voltage relations