5 documents found, page 1 of 1
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organisms metabolism under different conditions1. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites and reactions that are assigned to subcellular locations. Geneproteinreaction (GPR) rules and annotations using database information can add meta-information to GEMs. GEMs with ...
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian; Beber, Moritz E.; Olivier, Brett G.; Bergmann, Frank T.; Ataman, Meric; Babaei, Parizad; Bartell, Jennifer A.; Blank, Lars M.An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The Systems Biology Markup Language (SBML): Language Specification for Level 3 ...
Hucka, Michael; Bergmann, Frank T.; Chaouiya, Claudine; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M.; König, Matthias; Novère, Nicolas LeComputational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, includin...
SBML qualitative models: a model representation format and infrastructure to fo...
Chaouiya, Claudine; Bérenguier, Duncan; Keating, Sarah M; Naldi, Aurélien; van Iersel, Martijn P; Rodriguez, Nicolas; Dräger, Andreas; Büchel, FinjaQualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qual...
Path2Models: large-scale generation of computational models from biochemical pa...
Büchel, Finja; Rodriguez, Nicolas; Swainston, Neil; Wrzodek, Clemens; Czauderna, Tobias; Keller, Roland; Mittag, Florian; Schubert, MichaelSystems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.