The purpose of this page is to serve as an introduction to accessing simulation results from the Enteric Immunity SImulator (ENISI) and conducting simulations.
The ENISI model is provided to the user as a network depiction of inflammatory and regulatory immune cell interactions with epithelial cells and bacteria in the four tissue compartments; lumen, epithelium, lamina propria, and lymph node.
Cell Designer image: ENISI model of H. pylori
In the network red nodes indicate cells that participate in the inflammatory pathways and blue indicate those in the regulatory pathways. Green nodes are cell-types that may participate in either response. Black arrows between nodes in the same tissue compartment represent differentiation from one cell-type to another. Black arrows between nodes in different compartments indicate migration from one tissue site to another. Green arrows point from cell-types to the differentiation and migration processes in which they participate.
The network is created in CellDesigner, a structured diagram editor for drawing regulatory networks. MIEP uses this software to create the structural model. If you are interested in using CellDesigner to build your structural models you can download and install the program.
An interactive version of the network is created with CellPublisher and provided to the user. Users can navigate through different cells types and interactions on the network and get useful information though the info windows.
ENISI is a simulator of the mucosal immune pathways in a tissue sample. As a tool, ENISI allows users to modify model parameters creating a customized in silico environment in which infection dynamics can be predicted given the specific experimental conditions represented.
There are three options for viewing model predictions of outcomes given specific infection scenarios:
1. One may view the results of a simulated infections under hypothetical experimental conditions that have been pre-configured for past in silico studies at http://www.modelingimmunity.org/modeling/enisi/
Navigation and interpretation of these results are described in the tutorial video at http://www.youtube.com/watch?v=ZdNuS-G8rqo.
2. One may run own simulations setting the host immunological set point and controlling the does and time of infection with different strains using the graphical user interface. Instructions for using ENISI are give in the tutorial: http://www.youtube.com/watch?v=ZdNuS-G8rqo.
3. One may download the code and customize their in silico enviornment further by manipulating any of the 87 parameters of the middle to fit specific experimental conditions. This involves a scripting language that is described in the on-line documentation.
