Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. It is performed for heterologous pathways generated by RetroPath2.0. The tool performs the following steps: -Merges a user-defined GEM SBML model with each given heterologous pathway individually. -Performs FBA using the CobraPy package. Three different analysis methods are proposed; two of which are native CobraPy methods - standard FBA and Parsimonious FBA, the other one proposed ...

Given the mono-component reactions generated by the tool "Pathways to SBML", this node adds the cofactors associated with each mono-component reaction generated by RetroPath2.0. The advanced parameters include the name of the heterologous pathway defined by "Pathways to SBML" node, the compartment ID of the SBML file (default is MNXC3, the MetaNetX ID for the cytoplasm). The tool also updates the reaction rule to include the SMILES cofactors to the reaction rule.

This tool takes for input the outputs of both RetroPath2.0 and RP2paths and generates a series of SBML files with mono-component reactions. Since more than one reaction rule may be associated with a single reaction, the best scoring reaction steps are considered before combining them to individual pathways. The number of combinations is controlled by the "Max reaction rules per reaction" parameter in the Advanced Options. The default value is 2, with a minimum of 1 with no maximum. A higher substep ...

RP2paths extracts the set of pathways that lies in a metabolic space file output by the RetroPath2.0 workflow. The advanced options include a time out parameter in minutes to limit the execution time of the tool. Similar to the RetroPath2.0 node, an internal limit is set on RAM usage for this server version of the tool.

This tool performs retrosynthesis search for possible metabolic routes between a source molecule and a collection of sink molecules. It takes as input, files from RetroRules, source and sink compounds (can be generated as explained in SynBioCAD Utilities), and the maximal pathway length (i.e; the number of steps). Only a single source molecule is processed at this time. Using Advanced Options, you can define the maximum number of compounds to keep for a next iteration (TopX), the minimal (dmin) ...