A small editor App to automatically format JSON files

I've been very remiss in my postings. Grant proposals and administration consume a huge amount of time. I estimate paperwork now takes up between 4 and 5 months a year of my time. ChatGPT is starting to help with some mundane tasks and hopefully, that will increase over time. Ideally, I’d like to live in a world where all bureaucratic chores are relegated to an AI assistant so we AI humans can focus on more creative activities.

I’m not sure how much you’ve had to work with JSON files, they pop up everywhere and I’ve also ended up using them to store information. The problem I always face is being able to edit them. JSON in its purest form is just a single line of text so that when loaded into your favorite editor you just see one long line of text which isn’t great for editing. Usually, I will paste the text into an online formatter and paste the pretty version of the JSON back into my editor where I can work with it. Yes, I could load the JSON into a specialist editor, but they are even more tedious to use. Yes, I could install a plugin for Notepad++ and try to remember keystrokes to format the JSON or I could figure out how to install yet another plugin in the sublime text and remember yet another keystroke.

I therefore spent probably an hour creating a simple editor that when I load a JSON file it automatically formats the text. I uploaded it to GitHub. More important here is the link to the binaries. Appologies to Mac owners, it ony works on Windows. I don't have a good open source editor component for the Mac platform.

Another way to find unstable steady states

James Glazier recently told me of a trick he uses to find unstable steady states. Consider the following model which has two stable and one unstable steady state (it's a bistable system using postiive feedback). Note that $Xo means the species Xo is fixed.

import tellurium as te

r = te.loada('''
    $Xo -> S1; (0.1 + k1*S1^4/(k2+S1^4));
    S1 ->; k3*S1;
    
    k1 = 0.9; k2 = 0.3; k3 = 0.7; S1 = 0.5;
''')

If we run a simulation of this system it evolves to one of the stable steady states, in this case 0.144635. If we set the initial conditon to S1 = 10, we can also get the other stable state at S1 = 1.3095. There is the code to do that:

import tellurium as te

r = te.loada('''
    $Xo -> S1; ( 0.1 + k1*S1^4/(k2+S1^4));
    S1 ->; k3*S1;
    
    k1 = 0.9; k2 = 0.3; k3 = 0.7; S1 = 0.5;
''')

r.steadyState()
print (r.S1)

# Find theother steady state
r.S1 = 10
r.steadyState()
print (r.S1)

But how can we find the unstable one? There as an old trick where if one integrates backwards in time, stable states became repelers and unstable states attractors. However we don't allow someone to specfiy a start time that is bigger then the eed time. Instead James Glazier realized one chould just a put minus sign in front of every rate law to mimic the same effect. For example, a simulation of the following modiified model:

import tellurium as te

r = te.loada('''
    $Xo -> S1; -(0.1 + k1*S1^4/(k2+S1^4));
    S1 ->; -k3*S1;
    
    k1 = 0.9; k2 = 0.3; k3 = 0.7; S1 = 0.5;
''')
m = r.simulate (0, 50, 100)
print (r.S1)

will yield the unstable state at S1 = 0.68256.

Generating random networks

Here is a simple script that will generate a large number of random mass-action models and plot simulations of each in a grid.

Each grid has a number written on it so that you can grab the associated model if you find some interesting beahvior. In this case we see model 81 is oscillatory. You'll need the teUtils package for this in order to access the random network generator.

import tellurium as te
import roadrunner
import teUtils as tu
import matplotlib.pyplot as plt
import numpy as np

numRows = 15
numCols = 15
plt.subplots(numRows, numCols, figsize=(19,16)) 
count = 0
models = []
while count < numRows*numCols:
    model = tu.buildNetworks.getRandomNetwork(10,20)
    r = te.loada(model)
    try:
        m = r.simulate (0, 160, 200)
        try:            
            models.append (model)
            if count % 20 == 0:
               print (count)
            ax = plt.subplot (numRows, numCols, count+1)
            ax.tick_params(axis='both', which='major', labelsize=7)
            ax.tick_params(axis='both', which='minor', labelsize=7)
            ax.set_xlabel('Time')    
            te.plotArray(m, show=False)
            maxy = ax.get_ylim ()
            ax.text (50, maxy[1]/2, str(count), fontsize=14)            
            count = count + 1
        except:
            # failed to find a steady state so probably a bad model
            pass
    except:
        print ('Something very wrong with the model')
plt.show()

There is one run I did and you'll model 81 ihas some intersting dynamics:

This is model 81 pulled out and resimulated to show the dynamics more clearly:

import tellurium as te

# Get the model using:
#   print (models[81])

# Then copy and paste the model as below:

r = te.loada("""
var S0, S1, S2, S4, S5, S6, S7, S8, S9
ext S3;
J0: S9 + S8 -> S6; E0*(k0*S9*S8);
J1: S6 -> S7 + S9; E1*(k1*S6);
J2: S2 + S0 -> S8; E2*(k2*S2*S0);
J3: S4 + S4 -> S6; E3*(k3*S4*S4);
J4: S5 -> S2 + S1; E4*(k4*S5);
J5: S9 -> S4 + S0; E5*(k5*S9);
J6: S1 -> S0 + S5; E6*(k6*S1);
J7: S0 -> S4 + S4; E7*(k7*S0);
J8: S3 -> S9; E8*(k8*S3);
J9: S5 -> S1 + S9; E9*(k9*S5);
J10: S5 -> S0 + S4; E10*(k10*S5);
J11: S5 -> S4 + S9; E11*(k11*S5);
J12: S5 + S1 -> S0; E12*(k12*S5*S1);
J13: S2 + S9 -> S4; E13*(k13*S2*S9);
J14: S1 -> S8; E14*(k14*S1);
J15: S8 + S0 -> S1; E15*(k15*S8*S0);
J16: S7 -> S8; E16*(k16*S7);
J17: S8 + S6 -> S7; E17*(k17*S8*S6);
J18: S4 -> S6 + S6; E18*(k18*S4);
J19: S5 -> S1 + S4; E19*(k19*S5);

k0 = 0.6158; k1 = 0.0524;  k2 = 0.7206;  k3 = 0.0261
k4 = 0.4946; k5 = 0.2428;  k6 = 0.3249;  k7 = 0.4854
k8 = 0.6743; k9 = 0.6320;  k10 = 0.8954; k11 = 0.435
k12 = 0.580; k13 = 0.0298; k14 = 0.850;  k15 = 0.342
k16 = 0.556; k17 = 0.3221; k18 = 0.584;  k19 = 0.681

E0 = 1;  E1 = 1;  E2 = 1;  E3 = 1
E4 = 1;  E5 = 1;  E6 = 1;  E7 = 1
E8 = 1;  E9 = 1;  E10 = 1; E11 = 1
E12 = 1; E13 = 1; E14 = 1; E15 = 1
E16 = 1; E17 = 1; E18 = 1; E19 = 1

S3 = 1
S0 = 6; S1 = 3; S2 = 3; S4 = 2
S5 = 6; S6 = 2; S7 = 6; S8 = 2
S9 = 1
""")

m = r.simulate (0, 180, 100)
r.plot()

Here is the simulation from running the above code. Note that not every reaction is contributing to this behavior. You can remove J2, J3, J4, J6, J9, J10, J11, J12, J13, J14, J15, and J19 and the system will still oscillate.

What you can now is use another function in teUtils to look at a single model and plot a grid of simulations using random parameter values for that model. To do this just call plotRandSimGrid as follows. We apply it to model 81:

r = te.loada (models[81])
tu.plotting.plotRandSimGrid (r, endTime-500, ngrid=8, maxRange=1)

maxRange limits the range of random parmateer values. In this model, if the range is bigger, sometimes we get bad parameter sets which don't simulate. A maxRange of 1 seems to gives simulatable models. Most of the time the defaults are sufficient and you only have to pass in the roadrunner object, r. Here is a sample run: