Arabidopsis Framework Model v2

Yin-Hoon Chew, Daniel Seaton, with help from Argyris Zardilis (University of Edinburgh)


Model category FSPM
Plant part Shoot
Scale Organs, Whole_plant
Licence open_source
Operating system Any
Programming language Matlab
Format of model inputs and outputs Text files
Species studied Arabidopsis
Execution environment Console
Modelling environment FAIRDOMHub

Scientific article

The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation
Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Gavin M. George, Michael Moulin, Alastair Hume, Samuel C. Zeeman, Teresa B. Fitzpatrick, Alison M. Smith, Mark Stitt, Andrew J. Millar
, 2017 View paper

Model description

Model of Arabidopsis rosette growth that is focussed on the contribution of the 24-hour, circadian clock. Detailed gene circuit model of the clock with TF outputs to hypocotyl elongation and flowering time. Simple C metabolism with clock-regulated starch degradation, controls growth, with individual leaf areas. Simple root as C sink.

Some case studies

Chew et al. 2017 preprint compares biomass growth of well-watered, nutrient-replete but light-limited WT and slow-clock mutant Arabidopsis (prr7prr9 double mutant).