Comparison of pathway analysis and constraint-based methods for cell factory design

Minimal cut set enumeration library

Link to GitHub repository

Supplementary material

Access files

About this:
This website contains the datasets generated using the mcslibrary package along with some useful R scripts to analyse the data and generate plots.

Where are the datasets stored?
- iAF1260_ethanol: Anaerobic ethanol production on Escherichia coli
- iMM904_succinate: Aerobic succinic acid production on Saccharomyces cerevisiae.
- ecoli_core_itacon: Itaconic acid production on Escherichia coli (core model)

What files can be found in each folder?
-*MetricsOverview*.csv - Dataframe with useful productivity metrics
-*pFBA*.csv - Matrix with the pFBA flux distributions (maximizing biomass)
-*[lowerLim/upperLim]* - Flux ranges (upper or lower) for each mutant
-RxFrequency/SubsetRxFrequency - Reaction/subset counts within the knockouts

These files contain prefixes to identify the algorithm/environmental conditions to which they belong.
Additionally, these folders will contain plain .txt files with the solutions themselves.

How to visualise this data using R?
The R scripts should work with any machine, given the packages used are installed and the cloudPath variable is pointing toward the root folder containing this file.
These can be located in the ASAP/Scripts folder

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