Dear Matthias, On Thu, May 26, 2016 at 09:46:54AM +0200, Matthias Nilsson wrote: > Jan Kim <[email protected]> wrote on Wed [2016-May-25 19:35:38 +0100]: > > Dear Matthias, dear All, > > > > probably a question tangential to the subject of this thread but -- > > are SBML models data, or are they software? Personally I'm inclined > > to categorise them as the latter. > > Dear Jan, > > Can you elaborate? My gut feeling is that it's closer to a database > than to a software library, since there is only static data.
Briefly, my thinking is that SBML models are essentially machine-executable representations of differential equation systems, and I consider a DE system as the equivalent of an algorithm and therefore its machine-executable implementation seems like software to me. The data, i.e. input taken by this software is comprised of the initial conditions and other parameters (coefficients etc.). So perhaps SBML files typically contain both software and the data, so that may help explain how they can be perceived to be one or the other -- or indeed both. I think that this lack of separation of code from data is an issue for computational systems biology to grapple with, mixing the two is never a good idea. I'd be very happy to discuss this in more detail but suggest to take that off this list. Best regards, Jan > Best regards, > Matthias > > -- +- Jan T. Kim -------------------------------------------------------+ | email: [email protected] | | WWW: http://www.jtkim.dreamhosters.com/ | *-----=< hierarchical systems are for files, not for humans >=-----* _______________________________________________ Discuss mailing list [email protected] http://lists.software-carpentry.org/listinfo/discuss
