Documents

The promoter regions for clock genes that present a ChIP-seq signal were extracted from TAIR10 using costume python scripts using the gene list for Kamioka et al CCA1 or Daphne Ezer et al for LUX. The promoter was considered from the TSS of the gene until the annotated end of the upstream gene. Then, this region was scanned using the Energy Matrix derived using EMA working as a classifier for bound or unbound. After classification the calibrated PBM data calibrated using in vitro data was used ...

This describes how models were linked to in vitro data and then from there also linked to in-vivo data by detrending and rescaling in vivo data to match in vitro data for CCA1 and TOC1. The detrending was also derived by performing a long LD experiemnt fro servarl days and using the expression peaks of TOC1 to extract the trend in NLUC decay and plant growth.

equations in PDF

U2020.5 equations in PDF

With this file the user can type

docker-compose up

and will be able to run the operating system were the modelling and analysis took place

The jupyter notebook contains the code that predicts the number of monomers of several clock proteins and rescales the U2019.4 model which was published https://doi.org/10.1093/insilicoplants/diab022

This file contains the scaling factors that can be used with U2019.4 that will match synthetic protein data generated with the simple translation model.

The jupyter notebook contains the code that predicts the number of monomers of several clock proteins and rescales the U2019.4 model which was published https://doi.org/10.1093/insilicoplants/diab022

PDF of U2019.4 equations

PDF of U2020.4 equations

Jupyter notebook file that describes how the models were finally linked to produce several plots were model predictions and data are compared

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_liq-GC-MS/

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_myc-GC-MS/

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_liq-GC-MS/

_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_myc-GC-MS/

_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/

_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/_A_TransientCompLPPSCPPS-GCMS/

_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/_A_TransientCompLPPSCPPS-GCMS/

_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_GC-MS-EAD-EAG/

_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_GC-MS-EAD-EAG/

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr20-GC-MS/

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr80-GC-MS/

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr80-GC-MS/

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fresh-GC-MS/

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhEmissionPlants/_A_emission_nontruncated-GC-MS/

_p_SUSPHIRE/_I_T24_phero/_S_P5_PhEmissionPlants/_A_emission_truncated-GC-MS/

_p_SUSPHIRE/_I_T24_phero/