Web demos PhDSeeker

Resources

Source code: (1) | Related publications: [submitted]

Pheromone-Directed Seeker (PhDSeeker) is a bio-inspired algorithm for synthesizing linear and branched metabolic pathways. It allows to relate several compounds simultaneously, ensuring the availability of substrates for every reaction in the solution. This web-demo allows to use PhDSeeker similarly as the desktop version. It requires three files as input:

  • Reactions file: List of reactions to be used for synthesizing a metabolic pathway.
  • Compounds file: List of freely available compounds (i.e. water), and compounds to related.
  • Settings file: Configuration parameters of the algorithm.

An example for each file is provided with the webdemo. As outputs, PhDSeeker returns an interactive graph, whose elements can be re-arranged manually online, and two files:

  • Summary: Text file containing the sets of compounds involved in the search, and a detailed description of the reactions belonging to the pathway found.
  • Pathway: Downloadable version of the interactive graph.

Contact: Matias Gerard