Merge curateExchangeRxns branch into devel - #72
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Push to master for pre-release v0.6.1
- As discussed in #28, this script aims to address the attempted curations for exchange reactions, Sink and DM reactions.
- As discussed in #43, this new array struct works as an archive to store the nearly identical reactions that will be removed at a certain point.
haowang-bioinfo
approved these changes
Dec 15, 2018
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Main improvements in this PR:
Curations to the model exchange reactions (as well as sink and demand reactions) were implemented in the script
curateExchangeRxns.m, and address many of the points addressed in issue #28. Changes implemented by the curation script are summarized below.The current
humanGEMmodel has a mix of exchange reactions that are formulated such that negative flux corresponds to export, whereas others have positive flux corresponding to export. In order to standardize this, all exchange reactions will be converted to the second format (positive flux = export).In the model there are 7 exchange reactions that are duplicated but written in opposite directions. For each pair of duplicates, one reaction was deleted, and the second was made reversible. It was confirmed in advance that none of these reactions are associated with any genes. Before removal, these reactions were stored in a new array structure "redundantRxns" (as explained in Removal/Curation of nearly identical reactions #43) and saved as a plaintext JSON file, in order to migrate this repo to a binary-free mode (Migrating toward a binary-free repo #27).
All sink (
sink_) and demand (DM_) reactions were inactivated by constraining their upper and lower bounds to zero. These reactions will be considered for full deletion in future model versions.The upper and lower bounds of all exchange reactions are set to +/-1000, respectively. As a result, the model is by default completely "open", allowing free exchange of all metabolites.
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