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Counting_strategy_Ecoli_AKremling_June2021.zip (3.6 MB)
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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Counting_strategy_Ecoli_AKremling_June2021.zip | 2021-06-25 | 3.6 MB | |
| README.txt | 2021-06-25 | 1.4 kB | |
| resource_allocation_ecoli.zip | 2020-08-19 | 3.6 MB | |
| Totals: 3 Items | 7.2 MB | 0 |
Matlab Files for the publication:
A counting-strategy together with a spatial structured model describes RNA polymerase and ribosome availability in Escherichia coli
Accepted in Metabolic Engineering (June 2021)
by A. Kremling (a.kremling@tum.de)
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File structure
MAIN (runs 4 .m-files and produces figures)
data_integration: reads xls files with data sets SC and ES and provides the basic data structure
k_tl_calculation: in a first step translation initiation is calculated for individual genes, COG
groups (20 groups) and COG classes (4 classes)
calculation: main file to calculate the number of active ribos and RNA poly in the C and in the N compartment
rule_thumb: explores a simple heuristic equation
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aux. matlab-files
cell_mass & cell_mass_2: determines the cell mass according to the 2 possibilities described in the main file
comparison_MH_Li: reads data set from Li for absolute protein synthesis rate and provides data set
data_Dai_grab.mat: data from Dai paper for active ribos
data_ES_function: reads data for data set ES
data_Esquerre.mat: stores data set ES
data_MH_2_function: reads data for data set SC
data_mheineman2.mat: stores data set SC