Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
Abstract
Several studies have shown that neither the formal representation nor the functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability of models across groups and software tools cannot be guaranteed.
Here, we present memote (https://github.com/opencobra/memote) an open-source software containing a community-maintained, standardized set of metabolic model tests. The tests cover a range of aspects from annotations to conceptual integrity and can be extended to include experimental datasets for automatic model validation. In addition to testing a model once, memote can be configured to do so automatically, i.e., while building a GEM. A comprehensive report displays the model’s performance parameters, which supports informed model development and facilitates error detection.
Memote provides a measure for model quality that is consistent across reconstruction platforms and analysis software and simplifies collaboration within the community by establishing workflows for publicly hosted and version controlled models.
- Biochemistry (11773)
- Bioengineering (8764)
- Bioinformatics (29239)
- Biophysics (14995)
- Cancer Biology (12118)
- Cell Biology (17428)
- Clinical Trials (138)
- Developmental Biology (9432)
- Ecology (14194)
- Epidemiology (2067)
- Evolutionary Biology (18326)
- Genetics (12258)
- Genomics (16813)
- Immunology (11882)
- Microbiology (28122)
- Molecular Biology (11615)
- Neuroscience (61044)
- Paleontology (452)
- Pathology (1874)
- Pharmacology and Toxicology (3239)
- Physiology (4967)
- Plant Biology (10434)
- Synthetic Biology (2889)
- Systems Biology (7346)
- Zoology (1653)