Metabolic Pathway for CEN3031 section: 1491

In this project you are going to develop a software for Metabolic Pathway analysis. Metabolic pathways describe a series of reactions that take place inside the cell. A pathway can be represented as a graph with directed edges. The type of nodes in the graph are: enzymes (catalyzes reactions), reactions, metabolites/compounds, and pathways. The possible edges are:

The software should provide the following functionalities:

  1. Pathway creation and manipulation (including file operations such as new, open, save, save as, and close)
  2. Query evaluation and report generation
    1. Membership queries (e.g., List the pathways in which a particular enzyme/reaction/compound participates
    2. Dependency queries (e.g., What happens when a particular enzyme is inhibited?)

The software will be implemented in Java and it must have a GUI. Whenever it will be useful, the software should generate a graphical report where the results of the query are highlighted. The pathways will be stored in XML files.