Centre for Engineering Biology (prev. SynthSys)

Experiment data previously hosted on the original version of BioDare (biodare.ed.ac.uk).

Andrew Millar's research group, University of Edinburgh

What is PlaSMo? PlaSMo stands for Plant Systems-biology Modelling Ensuring the achievements of yesterday's Mathematical Modellers will be available for the Systems Biologists of tomorrow.

Our aims

To identify plant mathematical models useful to the UK plant systems biology community, which are currently in a variety of legacy formats and in danger of being lost To represent these models in a declarative XML-based format, which is closer to the systems biology standard SBML To evaluate the behaviour ...

Research programme in the Takato Imaizumi lab, with multiple collaborators. Published in Song et al. Nature Plants 2018; Kinmonth-Schultz et al., in silico Plant 2019.

For plants, light is a signal that carries information about the environment, and a source of energy for photosynthesis. PHYTOCAL focuses on the interaction between phytochrome signalling and photosynthesis, and seeks to understand fundamental processes that make carbon (C) and nitrogen (N) resources available for plant growth. These unexplored connections underlie biomass production and plasticity, which contribute significantly to yield variability in the field.

EPSRC project with Exeter, SynthSys and EPCC

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."

Collection of experiments created by Hibberd Victoria on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Kim, W.Y. on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Sawa, M. on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Ito, S. on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Niwa Y. on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Ven Tee Wei on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Carrington Jamie on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Hodge Sarah on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Nakamichi Norihito on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Somers DE on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Matsushika A on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Kim JY on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Song, Y.H. on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Hall A on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Tsuyoshi Mizoguchi on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Helfer A on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Gould Peter on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Kozma-Bognar Laszlo on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Thomson Adrian on the original BioDare and automatically transferred to FAIRDOM Hub.

Collection of experiments created by Munoz Felipe on the original BioDare and automatically transferred to FAIRDOM Hub.

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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.

Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods

Seedling hypocotyl data from literature for prr7 prr9 and Col wild-type plants under various photoperiods

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

effects of 1% increase in each parameter, more detailed analysis of water content

correlations of starch mobilisation and fresh weight under single parameter changes

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.

Biomass, leaf number and metabolites in Col0 (WT), prr7, prr7prr9, and lsf1. Metabolite data from plants after 28 days of growth were analysed most (27 days 'end of night', 28 days 'end of day' and 'end of night'). The data file also includes data from 21 days of growth ('end of day' and 'end of night'), which is useful for comparison to early-flowering plants not tested here, such as the lhycca1 double mutant, that flower before 28 days, altering their physiology.

Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and lsf1 (presented in the preprint/paper) and pgm (not analysed further).

Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and pgm at days 29 and 35, presented in the preprint/publication, with most data also for Col and lhycca1 at days 21/22/23, not analysed further.

We suggest that the lower carbon assimilation rate measured in lhycca1 (see gas exchange data) might allow a calibirated simulation in the FMv2 model in future to incorporate the indirect effects of nightly carbon starvation in this genotype ...

Simulation data from FMv2 calibrated for experiment L&H2, an experiment run at 18.5C instead of the 20.5C of the replicate and related studies. The Excel file includes the mean and SD of the relevant experimental data, and the figure panels.

Transcript profiling by microarray in 4, 6, 8, 12 and 18 h photoperiods, originally published in Flis et al, 2016, Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. doi: 10.1111/pce.12754.

Plant material The same plant material used for transcriptome analysis in (Flis et al., 2016) was the basis of our proteome study. Briefly, Arabidopsis thaliana Col-0 plants were grown on GS 90 soil mixed in a ratio 2:1 (v/v) with vermiculite. Plants were grown for 1 week in a 16 h light (250 μmol m−2 s−1, 20 °C)/8 h dark (6 °C) regime followed by an 8 h light (160 μmol m−2 s−1, 20 °C)/16 h dark (16 °C) regime for one week. Plants were then replanted with five seedlings per pot, transferred for ...

These Python scripts define and simulate the translational coincidence model. This model takes measured transcript dynamics (Blasing et al, 2005) in 12L:12D, measured synthesis rates of protein in light compared to dark (Pal et al, 2013), and outputs predicted changes in protein abundance between short (6h) and long (18h) photoperiods. These are compared to the photoperiod proteomics dataset we generated.

RNA timeseries data for Arabidopsis Col wild-type plants and clock mutants, as separate mean and SD files. The raw data is available on BioDare.ed.ac.uk, and is linked as 'Attribution' from elsewhere on FAIRDOMHub.

The starting models are included here in their original forms, the P2011 model as an SBML L3V1 model file, and the KF2014 model of Fogelmark et al. shared as SBML; both prepared by Uriel Urquiza.

Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.

Plate1118 #1-CCR2 for BioDare (from BioDare)

List of samples used in the assay (extracted from original BioDare metadata and converted to csv)

Original BioDare metadata, converted to json format

Readme file

Plate1117 #1-CAB2 for BioDare (from BioDare)

List of samples used in the assay (extracted from original BioDare metadata and converted to csv)

Original BioDare metadata, converted to json format

Readme file

Plate1116 #1-CCA1 for BioDare.1 (from BioDare)

List of samples used in the assay (extracted from original BioDare metadata and converted to csv)

Original BioDare metadata, converted to json format

Readme file

Kim_Nature07_suppl_tex (from BioDare)

Kim_Nature07 (from BioDare)

STANDARD_DATAFILE (from BioDare)

STANDARD_RAWDATAFILE (from BioDare)

Kim2007_wt_LD_TOC1_GI_ZTL_proteins (from BioDare)

List of samples used in the assay (extracted from original BioDare metadata and converted to csv)

Original BioDare metadata, converted to json format

Readme file

Parameters rescaled and scaling factors set to 1

This is the scaled version of U2020.4 in sbml file. It already contains the scaling factors

Paramters rescaled and scaling factors set to 1

Paramteres rescaled and scaling factors set to 1

Parameters rescaled and scaling factors set to 1

Derived from U2019.3 from Testing the inferred rate of dynamic, gene regulatory network in absolute units

Sbml version of U2019.4 with reacaling factors values already incoporated in the model. This was generated autmatically using tellurium python package

This file was derived from U2020.3 by introducing the scalig factors in the required locations in the model. This files is used then for numerically rescaling the model for matching synthetic protein data.

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. ...

Originally submitted model file for PLaSMo accession ID PLM_1030, version 1

Model derived from U2019.2, fitted to TiMet data mutants data set. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rated were obtained by taking the product of scaling factor and either transcription or translation, the latter required for ...

Model derived from U2019.1 in which the transcription rates were rescaled to match the scale of TiMet data set for absolute units of RNA concentration. The gmX scaling parameters in the model were fitted numerically. This model has equivalent dynamics to P2011.1.2.

Model derived from U2020.2, fitted to the TiMet RNA data for wild-type and clock mutants. Fixed parameters are scaling factors, COP1 and cP parameters. The rest of the parameters were left optimisable. The networks used in the fitting include WT, lhycca1, prr79, toc1, gi and ztl. The ztl network was only used for fixing the period in this mutant. Then final parameter values for transcription rates were obtained by taking the product of scaling factor and either transcription or translation, the ...

Model derived from U2020.1 by fitting the scaling factors for matching TiMet data set for wild-type and clock mutants, in absolute units.

Model derived from U2019.1, in which the way the PRR genes are regulated is modified. Repression mechanism introduced Instead of activation between the PRRs for producing the wave of expression. This is inspired in the result of three models P2012, F2014 and F2016. P2012 introduced TOC1 repression in earlier genes relative to its expression. F2014 introduced also the backward repression of PRR9 |-- PRR7 |--- PRR5, TOC1. However little attention was given to why there is a sharper expression ...

Model written in Antimony human-readable language and then translate into SBML using Tellurium

Model written in Antimony human-readable language, Model used in Pokhilko et al 2012

autogenerated equation listing from the SBML of U2020.3, as a .PDF file

autogenerated equation listing from the SBML of U2019.3, as a .PDF file