For metabolites experimentally shown to be used by the organism but not predicted as such by the model (see Applications of metabolic models on growth phenotype predictions for methods to perform these predictions), their method automatically proposes minimal sets of reactions from a repository of reactions that, if added, would allow the model to exploit the external metabolites.
We looked for evidence of the protein-coding ability in a variety of other sources, in a large-scale proteomics experiment using human placental tissue (36), in the Passel selected reaction monitoring data repository (37) in the Human Protein Atlas (13) and in the UniProt Knowledgebase literature resource (34).
This interaction matrix encodes regulatory information that is deployed dynamically by the networks through biochemical reactions; hence, this repository of analog information can be thought of as representing a regulatory genotype defined, somehow, in biochemical terms (see Figure 1B).
In the latter category, the GapFill method was specifically developed to identify dead-ends in models, and correct them by adding reaction from a global repository of reactions, changing the reversibility status of reactions, or adding transporters (Kumar et al., 2007).
MCM: Minichromosome maintenance; GBM: Glioblastoma; qRT-PCR: Quantitative real-time reverse transcription polymerase chain reaction assays; TCGA: The Cancer Genome Anatomy Rembrandtt: Repository of Molecular Brain Neoplasia Data; OS: Overall survival.
To assess the long term behaviour of spent fuel in a French nuclear waste repository, the chemical reactions between the fuel and possible intruding water must be understood and the resulting radionuclide release must be quantified.
As the largest repositories of pathway reaction data, KEGG and Reactome represent the best starting points for building large-scale models of cellular function.
The experts, from the federal Chemical Safety and Hazard Investigation Board, also found that there is no single repository of information on runaway chemical reactions, making it difficult for industries and government agencies to identify patterns that might promote safer handling.
Canister corrosion and the chemical interactions of corrosion products with bentonite are key reactions for the long term performance of a repository.
Open-access databases are thus the main repositories of the large-scale pathway reaction and interaction data necessary for cellular-scale systems modelling.
This ion pumping is linked directly to the hydrolysis of adenosine triphosphate (ATP), the cell's repository of metabolic energy (see above Coupled chemical reactions).
