Imported:YPM/Extracting the model

Overview

To use the model embedded in the site, you first need to extract the model. The process of extraction generates a BioNetGen Language (BNGL) model file, and a static copy of the relevant pages in the site to act as unchanging documentation for the model.

To extract the model from the wiki, please click on the link below. Note that the process of extracting the model takes a bit over 20 minutes. The link below calls a Python script (extract_model). This script adds links to the soon-to-be-created model file and static documentation in the Extracted model log. The script then initiates another Python script, wiki_parser, which traverses the wiki, and creates the model file and static documentation.

Extracting a copy of the model

Note that this process takes over 20 minutes... To extract a copy of the model, click HERE.

Editing the BNG file

Once you've got a BNG file, you'll likely want to edit it for a few reasons. Firstly, there are many parameters in the wiki with no associated value. You'll need to fill in values in order for BNG to correctly process the file. Secondly, the full model from this wiki specifies over 200,000 different complexes. If you're going to simulate with ODEs, this is impossible/unmanageable. Even stochastic simulation with BNG will probably run your computer out of RAM. But either way, the point of the model in this wiki is to provide the base model from which specific, more targeted models could be built. So the point is that you'll probably want to edit the BNG file. For help with the BNG syntax, see the BioNetWiki tutorial. You can document changes to the model that you extract on a Model Process page on the site (see Instances of models).