txt2sto

Translate plain text file with reactions to stoichiometric matrix

Reaction rate dynamics can be retrieved from metabolite
concentration time courses. User has to provide corresponding stoichiometric
matrix but not a regulation model (Michaelis-Menten or similar).
Instead of solving an ordinary differential equation (ODE) system describing the evolution of concentrations,
we use B-splines to catch the concentration and rate dynamics then
solve a least square problem on their coefficients with non-negativity
(and optionally monotonicity) constraints.
Constraints can be also set on initial values of concentration.
The package 'dynafluxr' can be used as a library but also as
an application with command line interface dynafluxr::cli("-h") or graphical user interface dynafluxr::gui().

Serguei Sokol

dynafluxr

Retrieve Reaction Rate Dynamics from Metabolite Concentration
Time Courses

txt2sto function

<dl><dt>fn</dt>
<dd>String, file name</dd></dl>

Arguments

Translate plain text file with reactions to stoichiometric matrix — txt2sto

<dl>

<dt>fn</dt>
<dd>String, file name</dd>

</dl>

txt2sto: Translate plain text file with reactions to stoichiometric matrix

Description

Usage

Value

Arguments