Fig. 9

RetroPath2.0 KNIME workflow. Inner view of the “Core” node where the computation takes place. The “Source, Sink…” and “Rules” nodes parse the source, sink and rules input files provided by the user and standardize data so that it can be processed by downstream nodes. Definitions for source, sink, and rule sets are provided in the text. The outer loop (“Source” loop) iterates over each source compounds, while the inner loop (“Length” loop) allows to iterate the process up to a maximum number of steps predefined by the user. The nodes (1) “FIRE”, (2) “PARSE”, (3) “UPDATE SOURCE…” and (4) “BUILD” are sequentially executed at each inner iteration. Respectively, they (1) apply all the rules on source compounds, (2) parse and standardize new products, (3) update the lists of source and sink compounds for the next iteration and (4) merge results that will be written by the node “Write global results”. Once the maximum number of steps is reached (or no new product is found), the “Compute scope” node identify the scope linking each source to the sink compounds, then these results are written by the node “Write per source results”. Only the main nodes involved in the process are shown