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[[Major assumptions and points of contention]]<br> | [[Major assumptions and points of contention]]<br> | ||
[[Extracting the model]]<br> | [[Extracting the model]]<br> | ||
Revision as of 16:15, 23 April 2007
Welcome to YeastPheromoneModel.org
The YeastPheromoneModel.org wiki is a modeling resource for the pheromone response pathway in Saccharomyces cerevisiae. This wiki was created for several purposes.
- It is meant to serve as a centralized repository of information that is relevant to computational modeling of the pheromone response pathway.
- The wiki also contains an embedded computational model that we are striving to make as detailed and accurate as possible. This rule-based model can be extracted into a single file, edited, and simulated or processed into an SBML file. As such, it is meant to serve as a base from which more narrowly focused models can be built.
This wiki is meant to serve as a community resource, where anyone can sign up for an account and edit the wiki. We would like the users to add missing information, correct any incorrect information, and express ideas as to how the knowledge garnered from the literature can be formulated into a mechanistic model. In this way the site can continue to evolve to meet the community's needs. To request an account so you can edit the wiki, just click on the Log in / create account link in the top right corner of any page, and follow the instructions found there.
Embedding the model elements (reactions and parameter definitions, relationships, and values) within the documentation of the pathway literature and modeling assumptions facilitates coordinated changes to the model and its documentation. Such thorough documentation of the judgments and evidence used to construct a computational model enables other investigators (and even the original authors) to evaluate and revise models more easily. The automated, rule-based generation of a computational model from the model elements embedded in the documentation has several advantages, including avoidance of manually-introduced errors and the ability to include a very large set of reactions that are easily specified by a small number of rules.
The Model
Yeast pheromone response model
Wiki organization and use
Brief overview of the organization of the model
Major assumptions and points of contention
Extracting the model
Modeling tags
BioNetGen
Moleculizer
Extracted models
Late December 2006 MAPK pathway model - tmt
Model Validation
Parameter Fitting
Timecourses for fitting model
Mutants for fitting model
Assumptions to re-test with full model
