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Version 1.6
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@mephenor mephenor released this 07 Apr 06:24
· 440 commits to master since this release
1.6
3dd08c0

Features and enhancements:

  • Added support for SQLite via sqlite-jdbc:
    The jar now contains a ready to use SQLite version of BiGGDB, so no locally running PostgreSQL BiGGDB is required to use the annotation functionality of ModelPolisher. To run ModelPolisher with the in-jar DB, use the "annotate-with-bigg=true" option and omit the additional arguments you would provide when connecting to PostgreSQL. This should in general be faster than annotation with the PSQL version.

  • We now use the MIRIAM registry-lib to check all resources against the identifiers.org regexes and provide simple correction mechanisms for KEGG collections, EC-codes, NCBIGI and GO IDs. If a resource does not match and cannot be corrected, it will not be added to model and will be logged instead.

  • COBRAparser is now able to parse multimodel mat files. Each model after the initial one will get an incrementing integer as suffix. Matlab fields are now matched in a case insensitive way, if no exact match can be obtained or are assigned, if the field name is a substring of a variant.

  • Basic unit definitions will now be added to models when missing.

  • Added a method to check for wrong html tags in a SBML model and replace them.

Bugfixes:

  • Added a few null checks to COBRAparser and improved its ability to recognize resource IDs (mainly PUBMED and DOI).

  • Fixed a bug in COBRAparser cutting of the last character of a Miriam ID

  • Added a check to assure output files for batch process always have the correct filetype ending.

  • Made the SQL-Query that retrieves resources from BiGGDB a bit more specific. This should prevent annotating reaction-specific resources to metabolites and vice versa.

Miscellaneous:

  • Refactoring removed some redundant assignments. This may result in a slight speedup when running ModelPolisher on a folder of models.

  • If you use runModelPolisher.sh, a copy of the call to ModelPolisher.sh with your provided arguments is now saved in ModelPolisherTemplate.sh, overwriting the default template - a simple backup of your previous call can be found in ModelPolisherTemplate.bckp.

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