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We expect that the branch rate estimates from the simulated data should match the direct calculations from the reference graph.
To establish the optimal transformation of a participant graph into the reference graph, we have implemented the following automatic procedure.
Figure 5D shows the expected pattern for the database under HWE and can be used as a reference graph.
In Supplementary Figure S4, the variant and repeat branch rates for the reference graph, simulated reads and real NA12878 data is shown.
Educt-product pairs of the core metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG [ 31]) Pathway database and used to build a reference graph of 907 nodes.
The TRA measure is defined as the weighted sum of graph operations, normalized by the number of markers (i.e. by the number of nodes in the reference graph) to facilitate the comparison between videos (datasets) with different numbers of cells.
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The reference graphs were adopted from the literature [21, 25, 38, 41, 42].
Reference graphs include those of TDMA, STDMA, traffic-adaptive STDMA with temporal reuse and NC (STDMA-Adaptive-LET-NC), and traffic-adaptive node-assigned schedules with NC (Node-Assigned-NC).
To assess the number of bacteria tested in each experiment, reference graphs were created to determine the correlation between the number of colony-forming units (CFUs) in the standard medium and the optical density of the medium, measured by a spectrophotometer (SmartSpectm 3000, Bio-Rad).
Reference [30] used a citation graph to identify overlaps.
Reference [30] built a citation graph to analyze interrelated regulations, overlaps, and possible conflicts.
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