Imported:YPM/Main Page v2
Welcome to YeastPheromoneModel.org
The YeastPheromoneModel.org wiki is a modeling resource for the pheromone response pathway in Saccharomyces cerevisiae.
This resource serves as a centralized repository of information for modeling the pheromone response pathway, and contains an embedded computational model of the pheromone response pathway that anybody in the community can use.
This site is meant to serve as a community resource, where anyone can sign up for an account and contribute. We encourage 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 contribute, please email Ty Thomson at tmt AT mit DOT edu. Include your preferred username in the email.
Getting Started
There are a couple of key parts of the site to check out, depending on your interests. If you want to go check out the information in the site, go straight to the main model page. If you're interesting in learning how you can use the model encoded within the site, go to the using the model page. Or see below for more information about this site.
We initially build this site as a means to document our own model. But working with the folks involved in OpenWetWare, we realized the potential power of allowing the community to use and ultimately run the site. Since this site contains a well documented model, using the model encoded in the site as a base model (from which to make more specific models - see Instances of models below) means that groups need only document their departures from this base model. More importantly, this site provides a forum in which different members of the community can discuss the evidence and weigh the likelihood of different interactions and mechanisms. We believe that open discussion of evidence will lead to deeper understanding of the pathway function and better computational models.
Contributing to this Site
Users should not be shy about contributing to this site, especially when adding information, correcting mistakes, and adding comments. See site conventions for more information on editing pages.
For information about basic editing, see Wiki conventions and Help:Contents.
If you want more information about the embedded model, or you want to edit the embedded model elements, see Brief overview of the organization of the model and Modeling tags.
Instances of models
The Extracted model log keeps track of every time a model is extracted from the site.
We have also used this site to document the changes that we have made to extracted models. We call these pages Model Process pages.
Model Process page for 2007 04 22 12h14m39s
Additional Resources
The model encoded in this site is in BioNetGen language. Some parts of the model have also been implemented in Moleculizer. The Moleculizer model is linked from the appropriate Reaction pages.
About the model
Major assumptions and points of contention
Parameter Fitting
Timecourses for fitting model
Mutants for fitting model
Assumptions to re-test with full model
