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If PPP atom types are needed, this list is parsed and matched with the structure using the CDK SMARTS matcher or specially implemented graph searches.
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We study the problem of implementing graph algorithms efficiently on Pregel- like systems, which can be surprisingly challenging.
Surfaces are represented by vertex vertex systems (Smith et al., 2004), which implement graph rotation systems.
If that solution were implemented during graph processing, then focused attention would be required to compute relations over those bound features (e.g., the user only explicitly knows that the left object is the taller one by shifting attention to a single object).
Images of dendritic networks (MAP2 staining) were manually converted into graphs (Figure 3a1,2) by implementing a graph deduction paradigm similar to the one used by Shefi et al. [17], where vertices were marked mainly at dendro-dendritic intersections, cell bodies, bifurcations, or growth cones (Figure 3a1,2).
My own submission was a web app that implemented a graphing calculator in JavaScript.
SD participated in study design and implemented the graphing algorithm.
We implemented the graphs using arrays in the Python Numeric [ 41] package.
We implemented the graph-based storage according to the architecture depicted in Figure 5.
We have implemented a graph-theoretic method that identifies the critical fragments of the bipartite digraph of a biochemical mechanism.
We have implemented a graph-theoretic method that allows for parameter-free model testing of biochemical mechanisms with mass action kinetics for multistability, oscillations and Turing instability.
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