Search Results for "encoding"

...It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures. . CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed for the ecosystem modelling. ...

...It performs several steps of the reconstruction process, including the functional genomic annotations of the whole genome. Moreover, merlin includes tools for the identification and annotation of transport proteins encoding genes, as well as the generation of transport reactions for such carriers. Also, merlin includes tools for the compartmentation of the model that predict the localisation of the proteins encoded in the genome, and thus the localisation of the metabolites involved in the reactions induced by such proteins. Finally, merlin expedites the transition from genome-scale data to SBML metabolic models, allowing the user to have a preliminary view of the biochemical network.

...AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism. For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. This provides an alternative to pathway/gene set enrichment analyses which is simultaneously more flexible and more specific.

TaxonX is an XML schema for encoding taxonomic treatments to: create open, persistent full digital surrogates of treatments; identify treatments and their major structures; identify textual data such as names, localities, characters, and citations Maintenance of TaxonX has moved to: https://github.com/tcatapano/TaxonX