Hello,
I'm trying to do some differential equation modeling in R using the
package 'deSolve.' Briefly, I'm trying to use the law of mass
action
(the details of which aren't really important) to structure a vector
of rate equation which will be passed into an ODE function and solved
with associated functions from 'deSolve.' Roughly what this entails
is scanning through a very large stoichiometric matrix containing
integers which map metabolites to reactions and then assembling a
series of monomials that describe the rates of the reactions. I'm
running into trouble because R does not like doing numerical
operations on characters, but I need the rate to be in symbolic form.
Below I've described an example.
The input is a matrix like this one, but a lot bigger:
rxn1 rxn2 rxn3
met1 -2 0 2
met2 -1 -1 0
met3 0 -1 -1
and the goal is to generate a vector of monomials representing the
rate of each reaction 1 - 3:
rateRxn1 = (met1)^2 * (met2)^1
rateRxn2 = (met2)^1 * (met3)^1
rateRxn3 = (met3)^1
The rates need to be represented symbolically for me to pass into the
ODE solver where the metabolites will be assigned starting values. I
tried using the functions "quote" and "substitute" but
unfortunately
they are tough to use within a loop because if I pass in a metabolite
label generated from a loop (e.g. metaboliteNames[i]) it's taken
verbatim in "quote()," so I get "metaboliteNames[i]^-stoich[i,
j]"
instead of "met1^2."
My goal is to make a package of functions for modeling and simulation
of chemical kinetics and I want to make sure that they are open-source
and freely available to all researchers, so any advice on how to
proceed would be greatly appreciated!
Erin
--
Erin Rachael Shellman
The University of Michigan
Bioinformatics PhD Candidate
http://www.erinshellman.com
shellman at umich.edu
(937) 321.1129
Hello,
I'm trying to do some differential equation modeling in R using the
package 'deSolve.' Briefly, I'm trying to use the law of mass
action
(the details of which aren't really important) to structure a vector
of rate equation which will be passed into an ODE function and solved
with associated functions from 'deSolve.' Roughly what this entails
is scanning through a very large stoichiometric matrix containing
integers which map metabolites to reactions and then assembling a
series of monomials that describe the rates of the reactions. I'm
running into trouble because R does not like doing numerical
operations on characters, but I need the rate to be in symbolic form.
Below I've described an example.
The input is a matrix like this one, but a lot bigger:
rxn1 rxn2 rxn3
met1 -2 1 2
met2 -1 -1 0
met3 1 -1 -1
and the goal is to generate a vector of monomials representing the
rate of each reaction 1 - 3:
rateRxn1 = (met1)^2 * (met2)^1
rateRxn2 = (met2)^1 * (met3)^1
rateRxn3 = (met3)^1
The rates need to be represented symbolically for me to pass into the
ODE solver where the metabolites will be assigned starting values. I
tried using the functions "quote" and "substitute" but
unfortunately
they are tough to use within a loop because if I pass in a metabolite
label generated from a loop (e.g. metaboliteNames[i]) it's taken
verbatim in "quote()," so I get "metaboliteNames[i]^-stoich[i,
j]"
instead of "met1^2."
My goal is to make a package of functions for modeling and simulation
of chemical kinetics and I want to make sure that they are open-source
and freely available to all researchers, so any advice on how to
proceed would be greatly appreciated!
Erin
--
Erin Rachael Shellman
The University of Michigan
Bioinformatics PhD Candidate
http://www.erinshellman.com
shellman@umich.edu
(937) 321.1129
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