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. 2020 Aug 26;16(8):e9235. doi: 10.15252/msb.20199235
Reconstruction
Availability:

  • Is the reconstruction publicly available?

    • o

      On BioModels?

    • o

      Elsewhere? (optional)

  • Is the reconstruction shared on an accessible database?

Formatting:

  • Is the model saved in a language‐independent format (i.e., SBML)?

  • Optional: additional formats (e.g., XLS, JSON)

Nomenclature:

  • Does the reconstruction's name indicate a version?

  • Does the reconstruction's name indicate an organism?

  • Are identifiers (genes, metabolites, reactions) consistently from one namespace?

Optimization:

  • Have Memote (preprint: Lieven et al, 2020) tests been run?

  • Is the objective reaction indicated?

  • Is evidence (i.e., references) provided for use of the objective function(s)?

  • Are exchange, sink, and demand reactions and all necessary constraints included as defaults or in code?

  • Can the reconstruction be instantiated without error with COBRA software?

Simulations:

  • Are simulation parameters (objective reaction, constraints, etc.) provided in any of the following formats (include at least one):

    • o

      README.md file?

    • o

      COMBINE repository?

    • o

      full analytic code? e.g., iPython notebook or equivalent

  • Is the COBRA software version documented?

  • Are the solvers documented?

Manuscript:

  • Are COBRA software efforts appropriately credited?

  • Are previous iterations and/or other versions of the reconstruction appropriately credited?

  • Is the model clearly referenced (i.e., with a resolvable link and identifier) in Materials & Method or in the Data Availability Statement?