Code to simulate the nutrient signaling model in yeast and carry out analysis based on literature curated data.

While this repository provides python scripts to interact with the model, we also provide the model in other formats for ease of use. These can be found in /data/model-formats

The alternate formats currently available are:

1. SBML

I recommend setting up a virtual environment for this project. The steps to be followed are listed below

1. Clone this repository:

   git clone https://github.com/amoghpj/nutrient-signaling.git
       

2. Go to repository:

   cd nutrient-signaling
       

3. Set up virtual environment called nsig (or whatever you prefer):

   virtualenv -p python3 nsig
       

1. Activate virtual environment

   source nsig/bin/activate
       

2. Install requirements:

   pip install -r requirements.txt   
       

3. Finally install the nutrient_signaling package which provides some useful functions and classes to interact with the model and the data

   pip install -e .
       

4. You can now import nutrient_signaling as a package in your other projects!

+--------------------+
| nutrient signaling |
+--------------------+
                      

 +--------------+                                  
 | /----------\ |                                  
 | |simulators| |           +------------------+            
 | |          | |           |                  |            
 | \----------/ |<----------+ Model definition |                                     
 |  |       |   |           |                  |       
 |+-+-+ +---+--+|           +------------------+            
 ||CPP| |Python||                                  
 |+---+ +------+|                                  
 +-----+--------+                                  
       |                    /-------------------------\                                        
       +--+                 |                         |                  
          |         +------>|   datacomparison.py     |                  
          V         |       |                         |                  
    +---------+     |       \--^--------^---------^---/                  
    |         |     |          |        |         |                      
    |  Model  +-----+          |        |         |                      
    |         |          +-----+        +---+     +--------+             
    +---------+          |                  |              |             
                  +------+-------+    +-----+-------+   +--+----------+  
                  |  Time course |    |Perturbation |   | Qualitative |  
                  +--------------+    +-------------+   +-------------+  
                        ^                       ^                  ^      
                        |                       |                  |     
         +--------------+                       |                  +---+            
         |               +----------------------+--+                   |            
  +------+-------+       |                         |      +------------+-----------+
  |    time      |       | perturbation-data.yaml  |      |                        |
  |  course      |       |                         |      | experimental_data.yaml |
  |              |       +-------------------------+      |                        |
  +--------------+                                        +------------------------+