Construction of Framework Model version 2 (FMv2)

SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).

Andrew Millar's research group, University of Edinburgh

EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015. "TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."

Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated in 2022, mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants. This is one of the outputs from the EU FP7 TiMet project, https://fairdomhub.org/projects/92.

This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and a Snapshot was published. The updates are not changing the core data or the FMv2 model that has been ...

Metabolite analysis in clock mutants: Col-0 parent and mutants gi-201, toc1-101 and prr7prr9; WS parent and lhy/cca1 double mutant. Plants grown in Golm and harvested at End of Day and End of Night, , assays 22 major metabolites. More detail on TiMet wiki if required. Heteroscedastic t-tests to highlight most significant changes, without multiple-testing correction.

RNA timeseries data from TiMet for clock genes in prr7 prr9 and Col wild-type plants under 12L:12D cycle and LL

Combination of multiple sub-models to form Framework Model version 2

Comparison of simulated wild-type and prr7prr9 double mutant under 12L:12D cycles. Simulation with CVODE simulator via SBSI v1.5 framework.

Analysis of carbon metabolites in clock mutants by Anna Flis and Ronan Sulpice, Mark Stitt lab

For Chew, Seaton et al. Figure 1

RNA levels for control amplicons and multiple clock genes in 2 WT (Col, Ws) and 5 clock mutants of Arabidopsis, in biological duplicates, from three conditions: Diurnal cycle (12L/12D), Extended night (DD), Extended light (LL), harvested every 2 hours. Numbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells. Comments: Data from LD are concateneted with DD and LL for better visualization. Toc1-101 (col-0) gi-201 (col-0) prr7-3 prr9-1 (col-0) , lhy cca1 (ws) elf3-4 ...

for Chew, Seaton et al. paper Figure 1

For Chew, Seaton et al. Figure 1

A model of the circadian regulation of starch turnover, as published in Seaton, Ebenhoeh, Millar, Pokhilko, "Regulatory principles and experimental approaches to the circadian control of starch turnover", J. Roy. Soc. Interface, 2013. This model is referred to as "Model Variant 2". The other model variants are all available from www.plasmo.ed.ac.uk as stated in the publication. Note that the 'P2011' circadian clock model was modified for this publication (as described), in order to replicate the ...

Matlab model (could not be represented in SBML) from publication with 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. ...

Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).

The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model: Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was ...

This record includes Matlab and Simile format versions of the Arabidopsis Framework Model version 1, FMv1 (Chew et al, PNAS 2014; http://www.pnas.org/content/early/2014/08/27/1410238111), copied from the PlaSMo resource (www.plasmo.ed.ac.uk), PLM_ID=76. The model description is in the Supplementary Materials of the publication, which should be uploaded somewhere here also but I don't see how to do it.

The FMv1 links the following sub-models:

1. Arabidopsis leaf carbohydrate model (Rasse and ...

Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.

This version is P2011.1.2, model ID PLM_71 version 1. Dynamics identical to P2011.1.1 of the Pokhilko et al. 2012 publication.

http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1