Advanced features, such as model scripting and an optimization tool, are also described.
An extensive description of the methodology is provided in the Extended Experimental Procedures, and the modeling scripts and models are available at http://salilab.org/40S-eIF1-eIF3 //salilab.org/40S-eIF1-eIF3 //salilab.org/40S-eIF1-eIF3
It provides not only the detailed information about all descriptors and how to calculate them but also several tutorials and corresponding model scripts for different applications.
(3) BioTriangle provides several tutorials and corresponding model scripts for different applications.
The models and parameters used are described in detail in Additional file 4 and in the model scripts which can be downloaded from the STEPS website.
The main purpose of the language is to publish the modeling algorithms of the application in the designer knowledge domain to let the designer create parametric model scripts.
The kinetic model (MATLAB scripts and in SBML format) and parameter sets for simulating both experiments are provided in Additional file 2. We applied the method to construct condition-specific kinetic models of the metabolic network of S. cerevisiae.
The modeling relies on FAMILIAR (FeAture Model scrIpt Language for manIpulation and Automatic Reasoning) (Acher et al. 2013), a scripting language and tool dedicated to the management of feature models.
Logistic regression analysis was run using the JMP nominal logistic model script, loading species, order of prompts, and the cross between species and order of prompts as construct model effects, and whether the observation was in the TA category or PS rubric concept as the response variable.
The governing ODEs are solved by MATLAB ODE solver and the implementation can be found in Additional file 5: Model Script 1.
