update readme & model

MetaSys-LISBP · Oct 27, 2023 · 6cceec3 · 6cceec3
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 # GL_GNT_bypass
 
 This repository contains the model and data used for 13C metabolic flux analysis of the extracellular GL-GNT by-pass of E. coli, as detailed in <REF>. Details on the model structure and on the experiments can be found in the publication.
+
+## Quick-start
+
+The dynamic 13C-flux model can be used to simulate the dynamics of intracellular and extracellular metabolite concentrations. The model is provided in COPASI (`.cps`) and SBML (`.xml`) formats in the folder `model` and is also available in [Biomodels database](https://www.ebi.ac.uk/biomodels/) under identifier [MODEL2310250001](https://www.ebi.ac.uk/biomodels/MODEL2310250001).
+
+This model can also be used to calculate fluxes by fitting time-course measurements of the concentration of
+cells and extracellular (unlabeled and labeled) substrates and products, as detailed in the publication. The data used to calculate fluxes in each 
+biological replicate are provided in the folder `data`.
+
+## How to cite
+Publication in preparation.
+
+## Authors
+Pierre Millard
+
+## Contact
+:email: [email protected]
diff --git a/model/model_flux_13C_rep1.cps → data/model_flux_13C_rep1.cps b/model/model_flux_13C_rep1.cps → data/model_flux_13C_rep1.cps
diff --git a/model/model_flux_13C_rep2.cps → data/model_flux_13C_rep2.cps b/model/model_flux_13C_rep2.cps → data/model_flux_13C_rep2.cps
diff --git a/model/model_flux_13C_rep3.cps → data/model_flux_13C_rep3.cps b/model/model_flux_13C_rep3.cps → data/model_flux_13C_rep3.cps
diff --git a/model/pulse_glc_pgl_rep1.txt → data/pulse_glc_pgl_rep1.txt b/model/pulse_glc_pgl_rep1.txt → data/pulse_glc_pgl_rep1.txt
diff --git a/model/pulse_glc_pgl_rep2.txt → data/pulse_glc_pgl_rep2.txt b/model/pulse_glc_pgl_rep2.txt → data/pulse_glc_pgl_rep2.txt
diff --git a/model/pulse_glc_pgl_rep3.txt → data/pulse_glc_pgl_rep3.txt b/model/pulse_glc_pgl_rep3.txt → data/pulse_glc_pgl_rep3.txt
diff --git a/model/model_flux_13C.cps b/model/model_flux_13C.cps
diff --git a/model/model_flux_13C.xml b/model/model_flux_13C.xml