In [3]:

    

from om import base, settings
from om.components import *
from om.data import *
from om.util import *

import pandas as pd
import numpy as np
import math,cobra

import escher
import escher.server
import json
import os
from IPython.display import HTML


session = base.Session()

from IPython.html.widgets import interact, interactive, fixed
from IPython.html import widgets
from IPython.display import clear_output, display, HTML

escher.clear_cache()
d = escher.server.directory
#with open(os.path.join(d, 'example_data/reaction_data_iJO1366.json')) as f:
#    reaction_data = json.load(f)


    

In [4]:

    

def show_name(dataset):
    rxn_data = {rxn_id:get_reaction_data(rxn_id, dataset)*20 for rxn_id in reaction_data.keys()}
    b2 = escher.Builder(map_json='/Users/dbuser/escher-maps/v1/iJO1366/iJO1366_central_metabolism.json',
                        model_json='/Users/dbuser/escher/escher/example_data/iJO1366.json',
                        reaction_data=rxn_data)
    display(b2.display_in_notebook())


    

In [5]:

    

x = interact(show_name, dataset=widgets.ToggleButtonsWidget(values=[x.name for x in session.query(DifferentialExpression).limit(3).all()]))


    

    




---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-4-619403fc5200> in show_name(dataset)
      1 def show_name(dataset):
----> 2     rxn_data = {rxn_id:get_reaction_data(rxn_id, dataset)*20 for rxn_id in reaction_data.keys()}
      3     b2 = escher.Builder(map_json='/Users/dbuser/escher-maps/v1/iJO1366/iJO1366_central_metabolism.json',
      4                         model_json='/Users/dbuser/escher/escher/example_data/iJO1366.json',
      5                         reaction_data=rxn_data)

NameError: global name 'reaction_data' is not defined

In [9]:

    

get_regulation_data('GAPD')


    

    
Out[9]:






  

    

      

      
dataset
      
regulator
      
strain
      
carbon_source
      
nitrogen_source
      
electron_acceptor
      
gene
      
type
      
value
    
  
  

    

      
2
      
 338
      
 Crp
      
 delta-crp
      
 fructose
      
 NH4Cl
      
 O2
      
 gapA
      
 transcriptional
      
 0.79729
    
    

      
3
      
 352
      
 Crp
      
 delta-crp
      
 glycerol
      
 NH4Cl
      
 O2
      
 gapA
      
 transcriptional
      
-1.00276
    
    

      
0
      
 352
      
 Crp
      
        wt
      
 glycerol
      
 NH4Cl
      
 O2
      
 gapA
      
 transcriptional
      
-1.00276
    
    

      
1
      
 338
      
 Crp
      
        wt
      
 fructose
      
 NH4Cl
      
 O2
      
 gapA
      
 transcriptional
      
 0.79729
    
  

In [ ]: