li08_solution

The file contains the solution over time (3 oscillatory cycles) for the 
ordinary differential equation model as given in func_li08. In addition, 
events as constructed in the 
original publication [Li et al., 2008] are considered.

datasets

Detect feedback loops (cycles, circuits) between species (nodes) in ordinary differential equation (ODE) models. Feedback loops are paths from a node to itself without visiting any other node twice, and they have important regulatory functions. Loops are reported with their order of participating nodes and their length, and whether the loop is a positive or a negative feedback loop. An upper limit of the number of feedback loops limits runtime (which scales with feedback loop count). Model parametrizations and values of the modelled variables are accounted for. Computation uses the characteristics of the Jacobian matrix as described e.g. in Thomas and Kaufman (2002) <doi:10.1016/s1631-0691(02)01452-x>. Input can be the Jacobian matrix of the ODE model or the ODE function definition; in the latter case, the Jacobian matrix is determined using 'numDeriv'. Graph-based algorithms from 'igraph' are employed for path detection.

Katharina Baum

LoopDetectR

Comprehensive Feedback Loop Detection in ODE Models

Sandra Kr<c3><bc>ger

li08_solution function

A dataframe with 634 rows and 19 columns<dl class="dl-horizontal">
 <dt>time</dt><dd>time variable</dd>
 <dt>y1</dt><dd>first variable value</dd>
 <dt>y2</dt><dd>second variable value,</dd>
 <dt>etc.</dt><dd>etc.</dd>
 <dt>y18</dt><dd>18th variable value</dd>
</dl>

Format

Solution for the cell cycle model related to func_li08 — li08_solution

A dataframe with 634 rows and 19 columns<dl class='dl-horizontal'>
 <dt>time</dt><dd>time variable</dd>
 <dt>y1</dt><dd>first variable value</dd>
 <dt>y2</dt><dd>second variable value,</dd>
 <dt>etc.</dt><dd>etc.</dd>
 <dt>y18</dt><dd>18th variable value</dd>
</dl>

li08_solution: Solution for the cell cycle model related to func_li08

Description

Usage

Arguments

Format