This is a repository for supplementary scripts and notebooks of publications.
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0. 0_ecoli_models

The directory contains E. coli genome-scale metabolic model: the core model and the most updated model iML1515, and some notes on the models.

1. 2020_formaldehyde condensation

The directory contains Jupyter notebooks of modelling in vivo formaldehyde-THF condensation (He et al., Metabolites 2020).

The formaldehyde-THF spontaneous condensation reaction was added to the adjusted E. coli genome-scale metabolic model iML1515. Flux balance analysis and phenotypic phase plane calculations were conducted using COBRApy.

2. 2020_Promiscuous aldolases

The directory contains Jupyter notebooks of MDF and FBA modeling of the newly designed formaldehyde assimilation pathway, the homoserine cycle (He et al., Metabolic Engineering 2020).

3. 2020_GED

The directory contains Jupyter notebook of FBA modeling of bioproduction via the newly identified GED (Gnd-Entner-Doudoroff) cycle from CO₂ (Satanowski & Dronsella et al., Nature Communications 2020).

4. 2020_Energy_Auxotroph

The directory contains Jupyter notebook of FBA modeling of different NADH producing routes within a “energy-auxotroph” strain, Δlpd strain (Wenk & Schann et al., Biotechnology & Bioengineering 2020).

5. 2020_TaCo

The directory contains Jupyter notebooks of FBA and MDF modeling of the tartronyl-CoA (TaCo) pathway, a new-to-nature carboxylation pathway (Scheffen et al., Nature Catalysis 2021).

6. 2022_STC

The directory contains Jupyter notebook of FBA modeling of the serine threonine cycle (STC), an autocatalytic C1 assimilation pathway (Wenk et al., bioRxiv 2022).

7. 2022_formate_reduction

The directory contains scripts and models for MDF and FBA modeling of different formate reduction routes (Nattermann et al., Nature Communications 2023). The freezed version for the publication was also deposited on Zenodo

8. 2023_THETA

The directory contains scripts and models for MDF analysis of the THETA cycle (Luo et al., Nature Catalysis 2023).

9. 2023_FALD_sensors

The directory contains scripts and models for estimation of formaldehyde dependencies of formaldehyde metabolic sensors (Schann et al., bioRxiv 2023).

10. 2022_EuMP

The directory contains Jupyter notebooks of FBA and MDF modeling of the Erythrulose MonoPhosphate (EuMP) cycle, a new-to-nature C1/formaldehyde assimilation pathway (Wu et al., Nature Communications 2023). The freezed version for the publication was also deposited on Zenodo.