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Toolbox History and Explanation
Welcome to a work in progress. We are making available a copy of The Chemical Reaction Network Toolbox, Version 2.3. The Toolbox is intended to implement in Windows various parts of Chemical Reaction Network Theory that have appeared in the literature. Naturally, literature articles are the primary source for detailed information about what the Toolbox is intended to do, but the Guide that comes packaged with the program does provide some information for newcomers.
Version 2.X is a descendent of Version 1.X, which was written many years ago for the Microsoft DOS operating system. (Yes, DOS!) In some respects, the earlier version remains more powerful. In particular, the DOS version contained a ChemLab component, which provided numerical solutions (and their graphical display) for the differential equations that derive from mass action systems. People who want those capabilities can still download the DOS version. It can be run very nicely in Windows, on a Mac, or on a Unix machine -- all under the freely available DOSBox.
One advantage of Version 2.X is, of course, that it is written for Windows, not DOS. But it also extends considerably the power of the old Network Analyst component of Version 1.X, which was centered around deficiency-oriented parts of Chemical Reaction Network Theory. (The deficiency is a non-negative integer index with which reaction networks can be classified.)
The very first version of the Toolbox -- Version 1.0 -- was aimed at implementing theory for networks of deficiencies zero and one. For those networks it could determine whether there could be any set of rate constants for which the corresponding differential equations admit two distinct positive steady states that are stoichiometrically compatible. Version 1.1 was intended to implement work in Phillipp Ellison's Ph.D. thesis, which extended deficiency one theory to large classes of higher deficiency networks. Version 2.X goes further: It implements theory in the Ph.D. thesis of Haixia Ji, which extends Phillipp Ellison's work.
And Version 2.X goes further still: Among other things, it implements a different strand of Chemical Reaction Network Theory that had its origins in work of Ph.D. student Paul Schlosser and that took another direction in the Ph.D. work of Gheorghe Craciun. With Gheorghe's work a central question became whether a network has "the mass action injectivity property." (For technical reasons, an important presumption then was that each species is subject to a "degradation reaction.") If the network does have the mass action injectivity property, then multiple positive stoichiometrically compatible steady states are impossible, no matter what the rate constants are. In Version 2.X, the Toolbox will tell you whether a network does (or does not) have the mass action injectivity property. No presumption about degradation reactions are necessary, and the denial of multiple steady states for injective mass action networks still obtains.
As of Version 2.1, still another strand of reaction network theory was implemented in the Toolbox, this one the result of work with Guy Shinar. Unlike the others, this strand is not tied to the presumption of mass action kinetics. If a network is endowed with a subtle structural property called concordance, then -- so long as the kinetics falls within a large and natural class (which embraces the mass action class as a special case) -- the resulting dynamical equations must have certain attributes. In particular, there is no possibility of switch-like transitions between two distinct stoichiometrically compatible positive steady states. In Version 2.1 there were modules that told you whether or not a network has the concordance property (or the more powerful strong concordance property). In Version 2.2 there are improvements to the user interface and also an additional module that implements still more general aspects of concordance theory (related to concordance with respect a species influence specification -- that is, a user-provided specification of which species are to be regarded as inducers or inhibitors of the various reactions). Version 2.3 has further enhancements and provides more incisive reports.
Network entry in Version 2.X is fairly intuitive. Networks can be saved in *.net files (but these are not compatible with Version 1.X.) After entering the network, you should go to the Reports menu and run the Basic Report. That report will guide you to other reports that might be relevant for the network at hand. (The Mass Action Injectivity Report and the various Concordance Reports are always options after the Basic Report has been run.)
You can download the current version along with the Guide here: The Chemical Reaction Network Toolbox Ver. 2.3. Programming for Version 2.X was the result of dedicated work by Phillipp Ellison, Haixia Ji, and Daniel Knight.
Here is a link to the older DOS version: The Chemical Reaction Network Toolbox, Version 1.1.
I can be reached at the following email address: email@example.com.
Work underlying development of the Toolbox has been supported by the United States National Science Foundation, most recently through grant EF-1038394, and by the National Institutes of Health through grant 1 R01 GM086881-01.