Tags: lobolab/mergem

Fixed problems merging community models with multiple compartments. C…

…ompartment ids are concatenated. Simplified localization dictionaries.

Simplified localization dictionary.

Community models improvements: compartment names are copied from orig…

…inals plus a number when compartmentalized, reaction ids are renamed with their compartments to avoid conflicts with metabolite ids, objective reaction is the combination of all other reactions with an intermediate metabolite for each model.

Updated version to 2.0.0. Added function to compartmentalize models a…

…llowing for community-based modeling. Added function to split metabolite IDs into the parts ID name, localization, and compartment, as well as functions to handle unique ID formats from MetaNetX or models whose IDs contain brackets. Updated command-line to reflect new community modeling feature. README updated to change outdated command formats as well as reflect community modeling.

Compartment names are included in the merged model.

Paper published.

Reaction IDs based on metabolite IDs (e.g., exchange reactions) are a…

…lso translated.

Updated documentation.

The metabolite and reaction source dictionaries now also include the …

…IDs of the mapped metabolites and reactions from the input models.

Fixed bugs, refactored code, and added documentation for translation,…

… protonation, and annotation extension options.