Assays
What is an Assay?Filters
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
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
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
Biological problem addressed: Gene Regulatory Network
Investigation: Existing models that were re-factored and integ...
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
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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
Biological problem addressed: Gene Regulatory Network
Investigation: Millar, Andrew (ex-PlaSMo models)
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 ...
Submitter: BioData SynthSys
Biological problem addressed: Gene Regulatory Network
Investigation: Massheder, Jonathan
Study: SUCROS1 - PLM_24