Studies
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This section contains all the raw data and files required for each figures.
Submitter: Dorothee Houry
Investigation: 1 hidden item
Assays: FIGURE 2: Crystal structures of human NAMPT in complex with NA and PRPP,..., FIGURE 3: ATP is essential for NAMN formation by NAMPT, FIGURE 4: ATP indirectly stabilizes PRPP via pHis247., FIGURE 5: The deletion of the β1-β2 loop does not alter the geometry of ..., FIGURE 6: SAXS analysis of WT and Δ42-51 NAMPT.
Test by Martin for simileXML
Originally submitted to PLaSMo on 2012-03-08 11:39:23
Submitter: BioData SynthSys
Investigation: Beaton, Martin
Assays: Martin test - PLM_65, version 1, Martin test - PLM_65, version 2
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
Investigation: Muetzelfeldt, Robert
Assays: McMurtrie vegetation model - PLM_11, version 1, McMurtrie vegetation model - PLM_11, version 2
Submitter: Jurgen Haanstra
Investigation: Metabolism of HepG2 liver cancer cells
A meta-analysis of the impact of water content and temperature on the viscosities of four deep eutectic solvents (glyceline, reline, DEAG, DEACG), their components (choline chloride, urea, glycerol, ethylene glycol), methanol, and pure water was performed. We analyzed the viscosity data by an automated workflow, using Arrhenius and Vogel–Fulcher–Tammann-Hesse models.
Submitter: Meina Neumann-Schaal
Investigation: Salmonella enterica relies on carbon metabolism...
Flux will be measured using the metabolomics platforms based on absolute quantification method (isotope ratio based MS technique) by LC-MS, using heavy-isotope labelled precursors of the metabolites of interest. For example, 15N labelled cysteine, glycine and glutamate will be used to determine rates of synthesis of glutathione. 15N-labelled methionine to measure S-adenosyl methionine (and its decarboxylated form, as well as methionine cycle intermediates). 15N labelled arginine is used as precursor ...
Submitter: Meina Neumann-Schaal
Investigation: Systems biology investigation of aromatic compo...
Assays: Metabolic modeling of EbN1, Scenario files for Metano metabolic modeling
The steady state anaerobic culture (D = 0.1 h-1) was pertrubed by sudden increase of the extracellular glucose up to 1 g/L and both extra- and intracellular transient metabolite concentrations were measured
Submitter: Maksim Zakhartsev
Investigation: Kinetic analysis of metabolic system using tran...
Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during glucose pulse, Dynamics of intracellular metabolites during glucose pulse, Dynamics of macromolecules during glucose pulse, MOSES: dynamic model of glucose pulse
Metabolomics data a for Metabolight DB
Submitter: Olga Krebs
Investigation: MESI-STRAT data for submission into public re...
Assays: No Assays
Internal metabolites concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations External metabolite concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations Mutant (OE, KO, perturbation) metabolite measurements
Concrete is the second most consumed product by humans, after water. However, the production of cement, which is used as a binding material in concrete, causes more than 5% of anthropogenic CO2 emissions and has therefore a significant contribution to climate change and global warming. Due to increasing environmental awareness and international climate goals, there is a need for emission-reduced materials, that can replace conventional concrete in certain applications. One path to produce a solid, ...
Submitter: Jennifer Zehner
Investigation: 1 hidden item
Assays: Global pH monitoring_precipitation, Local pH monitoring Precipitation, Local pH monitoring dissolution, Optical microscopy for precipitation, Raman microspectroscopy
A minimal metadata template for high content screening experiments in microscopy. The template is compliant with REMBI (Recommended Metadata for Biological Images) and the ISA framework (Investigations, Studies and Assays).
Here you will find guidelines for filling in MIHCSME metadata templates, as well as examples of published HCS studies that use MIHCSME.
Submitter: Rohola Hosseini
Investigation: Minimal Information for High Content Screening ...
Assays: General MIHCSME template, MIHCSME template example for "Integration of biological data by kernels ..., MIHCSME template example for "Uncovering the signaling landscape control..., MIHCSME template example for compound screen on HepG2 CHOP-GFP reporter ..., MIHCSME template example for “Temporal single cell cellular stress respo...
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 ...
Symptoms obsevation, photosynthetic, pathogen (qPCR), transcriptomics (qPCR, microarrays, Degradome-Seq) and proteomics (MS) measurements.
Submitter: Ziva Ramsak
Investigation: MOA - Multiomics analysis of potato response to...
Assays: Degradomics, Disease symptoms, Pathogen abundance, Photosynthetic activity, Proteomics, Transcriptomics (microarrays), Transcriptomics (qPCR), sRNAomics (bioinformatics), sRNAomics (qPCR), sRNAomics (sRNA-Seq)
Hormonomics measurements.
Submitter: Ziva Ramsak
Investigation: MOA - Multiomics analysis of potato response to...
Assays: Hormone concentrations
Submitter: Dawie van Niekerk
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Assays: Inhibition of glucose transport, Inhibition of lactate flux, Supply-demand analysis
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: Comparing acyl-CoA dehydrogenase deficiencies, MCADD patient personalised modelling, MCADD rescue titration, Metabolic control analysis, Predicting urinary acylcarnitines under metabolic decompensation.
This study includes all the experimental data, SOPs and modelling files for the individual reactions used for the model construction.
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: Kinetics Minireviews, Models
Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus
Submitter: Jacky Snoep
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Assays: FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates
This study includes the experimental data for model validation and the model predictions of that data set.
Submitter: Dawie van Niekerk
Investigation: Glucose metabolism in Plasmodium falciparum tro...
Assays: GLC incubation, Steady state
Submitter: Christoff Odendaal
Investigation: Mitochondrial fatty acid oxidation in human liver
Assays: ACAD activity partitioning, HepG2 oxygen consumption, Whole-body ketogenic flux
Data analysis and modelling scripts and results for the Seaton et al. 2017 study, from Daniel Seaton.
Submitter: Andrew Millar
Investigation: Photoperiodic control of the Arabidopsis proteo...
Assays: Translational coincidence model
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
Investigation: Seaton, Daniel
Assays: Modelling circadian regulation of flowering time and hypocotyl elongatio...
Our current gene-expression model (Haanstra et al. 2008 PMID: 19008351) will be parameterized for the different genes of interest. The framework of this gene expression model has been used to include mRNA half life data into the model of glycolysis For the enzymes of redox metabolism we will use newly measured rates of transcription, RNA precursor degradation, mRNA degradation, concentrations of mature mRNAs and proteins, enzyme turnover, Vmax values and metabolic fluxes (WP3&5). Regulation ...
Submitter: Jurgen Haanstra
Investigation: Dynamic modelling of redox metabolism and gene ...
Assays: No Assays
We are in the process of construct an ODE model of the trypanothione pathway. As input we will use newly determined and existing kinetic data and measured metabolite concentrations at the boundaries (from WP3&6). Recently the glycolysis model was extended with the pentose phosphate pathway. This pathway will yield the NAPDH that maintains trypanothione in a reduced state. For some complex enzymes (i.e trypanothione synthase) we are intensively discussing the kinetic data obtained on the ...
Submitter: Jurgen Haanstra
Investigation: Dynamic modelling of redox metabolism and gene ...
Assays: No Assays
To model the ENA1 transcriptional regulation a model has to be established. First this will be just a graphical representation, it shall then be extended to a boolean model and shall at one point be converted to a kinetic model.
Mathematical modelling of the dynamic shift experiments and the effect of pH upon gene regulation.
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
Investigation: Adams, Richard
Assays: Modified Locke Arabadopsis 3 loop Circadian Clock - PLM_66, version 1
Amanda L. Armijo, Pennapa Thongaram, Bogdan I. Fedeles, Judy Yau, Jennifer E Kay, Joshua J. Corrigan, Marisa Chancharoen, Supawadee Chawanthayatham, Leona D. Samson, Sebastian E. Carrasco, Bevin P. Engelward, James G. Fox, Robert G. Croy & John M. Essigmann
DNA-methylating environmental carcinogens such as N-nitrosodimethylamine (NDMA) and certain alkylators used in chemotherapy form O6-methylguanine (m6G) as a functionally critical intermediate. NDMA ...
Hannah P.Gideon, Travis K.Hughes, Constantine N.Tzouanas, Marc H.WadsworthII, Ang AndyTu, Todd M.Gierahn, Joshua M.Peters, Forrest F.Hopkins, Jun-RongWei, Conner Kummerlowe, Nicole L.Grant, Kievershen Nargan, Jia YaoPhuah, H. JacobBorish, Pauline Maiello, Alexander G.White, Caylin G.Winchell, Sarah K.Nyquist, Sharie Keanne C.Ganchua, Amy Myers, Kush V.Patel, Cassaundra L.Ameel, Catherine T.Cochran, Samira Ibrahim, Jaime A.Tomko, Lonnie JamesFrye, Jacob ...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: Immunohistochemistry – Data Linked, Library Creation – Metadata, NHP Necropsy – Metadata, PET-CT Scan Analysis – Data Linked, PET-CT Scan – Data Linked, Patient Visit – Metadata, Single Cell Clustering Analysis – Data Linked, Single Cell Expression Matrix Analysis – Data Linked, Single Cell Sequencing – Data Linked
Leela RL Davies, Chuangqi Wang, Pia Steigler, Kathryn A Bowman, Stephanie Fischinger, Mark Hatherill, Michelle Fisher, Staney Kimbung Mbandi, Miguel Rodo, Tom HM Ottenhoff, Hazel M Dockrell, Jayne S Sutherland, Harriet Mayanja-Kizza, W Henry Boom, Gerhard Walzl, Stefan H.E. Kaufmann, Elisa Nemes, Thomas J Scriba, Douglas Lauffenburger, Galit Alter, Sarah M. Fortune.
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, FC Receptor Binding Assay - Data Linked, Linear Mixed Model - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata, Titer Assay - Data Linked