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Releases: draeger-lab/ModelPolisher

Version 1.1

24 Jan 09:27
@draeger draeger
1.1
51d39d5
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Version 1.1 Pre-release
Pre-release

This version of ModelPolisher is not fully functional. We strongly recommend waiting for version 1.2. The package ModelFix.jar solves some major issues.

ModelPolisher has been adapted to the latest version of BiGG Models knowledgebase and brings several new features with it:

  • Instead of only posting a severe message when an undeclared gene product is used in a gene-product association with in a reaction, ModelPolisher now generates the missing gene product on the fly and only displays a warning.
  • ModelPolisher now comes with a first version of a *.mat file parser for MATLAB COBRA files that directly converts those files into SBML L3V1 with FBC V2, and Groups. A few features of some MATLAB model files are not yet supported.
  • It is now possible to pass alternative XHTML templates for model or document notes to the application as command-line arguments.
  • Several external databases were added to the list of MIRIAM resources: UPA, Inchi, DOI, Pubmed, and EC code.

Bug fixes:

  • When writing subsystem information as groups of reactions, the mandatory kind attribute of the groups was forgotten. Since all reactions are part of the respective subsystem, ModelPolisher uses the group kind 'partonomy'.
  • Forgotten gene prefix ‘G’ is now also allowed within BiGG ids.
  • Refined the id patterns for reaction types (demand, ATP maintennance, Biomass, demand, and exchange.

Currently not supported are the following third-party databases:

  • EnsemblGenomes
  • EnsemblGenomes-Gn
  • EnsemblGenomes-Tr
  • IMGT/GENE-DB
  • PSEUDO
  • REBASE
  • refseq_name
  • refseq_locus_tag
  • refseq_old_locus_tag
  • refseq_orf_id
  • refseq_synonym
Assets 6
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Version 1.0

19 Oct 09:24
@draeger draeger
1.0
00c64db
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Version 1.0

This release supports BiGG Models database from October 17th 2015, including the following features:

  • Writes notes into SBML document and Model for informative display of SBML files in a web browser.
  • Subsystems using the groups extension for SBML
  • FBC version 2 with check if all criteria for strict FBC are satisfied
  • Atom balance check
  • Optional SBML validation (through web service at sbml.org)
  • Output compression
  • Error logging
  • Compartment assignment checking and correction
  • Pseudoreaction annotation and update of reaction ids from *_sink_* to *_SK_*
  • Annotation of each SBML component with third-party resources
  • Determination of component roles and SBO term assignment
  • and many more...

Currently not supported are the following annotations of gene products:

  • refseq_name
  • refseq_old_locus_tag
  • refseq_orf_id
  • refseq_synonym
Assets 5
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