Studies
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This is the SimileXML for the Salazar model linked to the T6P/TPS pathway (Wahl et al. Science 2013). The Simile version of this model and the parameter file are also attached here. Time series data of T6P and FT mRNA for Col wild type and tps1 mutant from Fig. 1 in Wahl et al were used to re-optimise Bco, KCO, kT6P and vT6P (which replaces VCO). Note: This set of parameter values has only been optimised and tested for a 16:8 light:dark cycle, and the initial values in the Simile model are for ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Salazar Photoperiodism Model with T6P - PLM_82, version 1
This is the SimileXML for the Salazar2009_FloweringPhotoperiod model in PlaSMo. It corresponds to Model 3 in the publication of Salazar et al 2009. The Simile version of this model is also attached here. Instructions to run the Photoperiodism Model in Simile 1. Save all the files into the same folder. 2. Copy and paste the attached ‘lightfunction.pl’ file in the following folder: Program File > Simile6.0 (or other software version)> Functions 3. Download the ...
Submitter: BioData SynthSys
Investigation: Existing models that were re-factored and integ...
Assays: Salazar_et_al_2009_Photoperiodism_Model - PLM_74, version 1
The model shows how the CONSTANS gene and protein in Arabidopsis thaliana forms a day-length sensor. It corresponds to Model 3 in the publication of Salazar et al. 2009. Matlab versions of all the models in the paper are attached to this record as a ZIP archive, as are all the data waveforms curated from the literature to constrain the model. Further information may be available via links from the authors web site (www.amillar.org). Simulation notes for SBML version of Model3 from Salazar et al., ...
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Assays: Salazar2009_FloweringPhotoperiod - PLM_9, version 1, Salazar2009_FloweringPhotoperiod - PLM_9, version 2
Submitter: Jay Moore
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Assays: Metabolic pathway curation
This study briefly shows how a Selwyn test can be performed.
Submitter: Gudrun Gygli
Investigation: On the reproducibility of enzyme reactions and ...
Assays: Use a Jupyter Notebook to understand how the Selwyn test works
Sequence data for European Nucleotide Archive (ENA ) https://www.ebi.ac.uk/ena/
Submitter: Olga Krebs
Investigation: MESI-STRAT data for submission into public re...
Assays: Instructions for ENA submission
Determination of thermophysical properties (densities, diffusion coefficients, energy contributions) of different methanol-water mixtures using molecular dynamics simulations.
Submitter: Gudrun Gygli
Investigation: 1 hidden item
Assays: Analysis Version 1.5, Preparation, Results, Simulation Version 1.5
This study contains our single nuclei characterisation of whole hearts from Fzt.DU mice published in Cells.
Submitter: Markus Wolfien
Investigation: 1 hidden item
This study contains our snRNA-Seq based comparison of whole hearts from Fzt.DU and Bl6 mice published in Cardiovascular Research.
Submitter: Markus Wolfien
Investigation: 1 hidden item
Assays: Single nuclei RNA-Seq analysis of Fzt:DU and BL6 mice
This study contains the singele nuclei data analysis part of the Bl6 and Rag2del comparison. Here, we used Seurat, harmony, and monocle for an in-depth analysis.
Submitter: Markus Wolfien
Investigation: Disparate immune responses lead to varied outco...
An exploration on gene expression data was carried out on single-cell RNAseq analyses of bronchoalveolar lavages from nine COVID-19 patients, three moderate cases, one severe case and five critical cases (GSE145826) (doi: 10.1038/s41591-020-0901-9). To these data, single-cell RNA-sequencing from one COVID-19 lung biopsy, ~10 weeks after initial infection was added to represent persistent severe COVID19 patient group (3 weeks after symptom onset) (GSE163919). For this analysis, the epithelial cell ...
Detailed model of starch metabolism from Sorokina et al. BMC Sys Bio 2011. First upload is a draft.
Related Publications
Sorokina et al (2011). BMicroarray data can predict diurnal changes of starch content in the picoalga Ostreococcus.. BMC Systems Biology. Retrieved from: http://www.ncbi.nlm.nih.gov/pubmed/21352558
Originally submitted to PLaSMo on 2011-08-12 15:34:00
Submitter: BioData SynthSys
Investigation: Millar, Andrew (ex-PlaSMo models)
Measure Gre2p activity by following the change in NADPH absorbance at 340 nm for the conversion of different substrates.
Submitter: Gudrun Gygli
Investigation: Workflow for characterization of enzymes under ...
Assays: Kinetic parameters of Gre2p, Selwyn test of Gre2p, Specific activity of Gre2p
Steady state concentrations of metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1
Steady state fluxes in yeast Saccharomyces cerevisiae in anaerobic chemostat at D=0.1 h-1
Submitter: Maksim Zakhartsev
Investigation: Steady state metabolic fluxes and metabolite co...
Assays: Steady state extracellular fluxes in anaerobic yeast Saccharomyces cerev...
Lactic acid bacteria generally use homolactic fermentation for generation of ATP. Here we studied the role of the lactate dehydrogenase enzyme on the general physiology of the three lactic acid bacteria Lactococcus lactis, Enterococcus faecalis and Streptococcus pyogenes. Surprisingly deletion of the ldh genes hardly affected the growth rate in chemically defined medium, however growth rate was affected in rich medium. Furthermore, deletion of ldh affected the ability for utilization of various ...
We examined whether such a lockdown could be intermitted with periods with normal social contact, without endangering the success of the strategy.
Submitter: Alexey Kolodkin
Investigation: Construction of differential equation model to ...
The model is applied to spring wheat, with ample supply of nutrients and water, also without pests, diseases and weeds. Radiation and temperature, being the most important environmental factors, and crop characteristics determine growth and development. Crop growth and development are simulated based on underlying chemical, physiological and physical processes. Dry matter accumulation is calculated from daily crop CO2 assimilation based on leaf CO2 assimilation and taking into account the respiration ...
Supplemental files for the publication of the dataset collection.
Submitter: Malte Herold
Investigation: SysMetEx - Dataset collection
Proteomics and transcriptomics data tables, sample IDs and description, source code
Submitter: Malte Herold
Investigation: Reverse Engineering Directed Gene Regulatory Ne...
Assays: Proteome data, RNA data, Simulations for network engineering
Supplementary Information linked together
Submitter: Katy Wolstencroft
Investigation: Yeast Glycolytic Oscillations
Assays: Modelling sustained glycolytic oscillations in individual isolated yeast...
Submitter: Dawie van Niekerk
Investigation: Glycolytic oscillations in individual isolated ...
Assays: gustavsson1-4 models