Appendix B

Chapter B: Reconstruction of biological networks #

  1. The correct order of the key steps in metabolic reconstruction is:
    a. Gene functional annotations > model construction > model refinement > model simulation > evaluate model
    b. Gene functional annotations > model refinement > model simulation > evaluate model > model construction
    c. Gene functional annotations > model construction > model simulation > model refinement > evaluate model
    d. Gene functional annotations > model refinement > model construction > model simulation > evaluate model
    e. Gene functional annotations > model construction > model simulation > evaluate model > model refinement
    Ans: a

  2. Given a stoichiometric matrix \( \mathbf{S} \) of dimensions \(a \times b\)
    a. Number of metabolites are \(a\)
    b. Number of metabolites are \(b\)
    c. Number of reactions are \(a\)
    d. If \(v\) is the vector of fluxes, \(\mathbf{S}\mathbf{v} = \mathbf{0}\) at steady state
    Ans: a, d

  3. Which of these can you find in a reconstructed metabolic model of an organism?
    a. List of all genes
    b. List of all reactions
    c. GPRs
    d. Stoichiometry of all reactions
    e. Reaction directionality/thermodynamics
    Ans: a, b, c, d, e