I want to reproduce an (old) biochemistry paper of Gilman and Ross, i.e. " Genetic algorithm selecetion of a regulatory structure that directs flux in a simple metabolic model." ( The following link leeds to the paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1236362/) I know this is an old paper, but maybe someone here remembers it. I really need the answers of the following questions because the enzymatic model explained in the paper is very important for my master thesis.

First: The author defines a system of two ODEs but the initial conditions of these ODEs are not printed in the paper. The author just writes: "Initial conditions for the integration are determined by letting the network relax to steady state. " (see p. 1324 on the lower right) . But how is this meant? In this paper the author wants to optimize the mentioned ODEs , so how can I find initial conditions, when there are not all parameters of the ODEs given?

Second: On the top of page 1324 are two needstate functions defined, called xi_T and xi_F. When I plot xi(F), the plot looks completely different from the one depicted in figure 3b in the paper. So the function defined in figure 3b) must be wrong. Did anyone realize that error and has a workaround for that? Of course I could define my own functions but I want to stay as close to the model in the paper as possible.

Thank you very much for your help.

  • 2
    $\begingroup$ The first thing, before asking on a random website, would be to see if you can track down the original authors and ask them. It was only published 20 years ago, so there's a good chance they're still alive. First try searching the website of their university, then expand from there. Look up other papers, find old postdocs, see if they know where to find them. Biology is a small world, and people have connections everywhere. With a little earnest work on your part you ought to be able to track them down. Hell, the contact info for Ross is given in the paper, shoot him an email. $\endgroup$ – MattDMo Jul 3 '16 at 3:17
  • $\begingroup$ @MattDMo Do you really think I didn't already do that? $\endgroup$ – maxE Jul 3 '16 at 10:37
  • $\begingroup$ no offense to you, but given the usual quality of 1-rep "Please do all of my research for me" questions we get, my answer would be yes. If you already have, then congratulations! $\endgroup$ – MattDMo Jul 3 '16 at 12:39

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