@datagrok/diff-studio v1.0.8

Diff Studio

Diff Studio is a package for the Datagrok platform. It provides in-browser tools for solving initial value problem for systems of ordinary differential equations (ODE) and its interactive exploration.

• Go to Apps and run Diff Studio
• Enter formulas or modify template
• Click F5 or go to Run tab

The solver takes a set of the differential equations in a declarative form, and creates a UI that solves the equations, visualizes the results, and lets you change parameters on the fly.

Quick start

Datagrok provides intuitive tools for the rapid solving ODEs.

• Run the solver:
  • Go to Apps and run Diff Studio
  • Go to Run tab to launch computations
• Modify a template:
  • Edit formulas or add new ones
  • Click F5 or go to Run tab
  • Cahnge inputs and explore your model
• Use an advanced template:
  • Press Open icon on the top panel
  • Select Templates > Advanced...
  • Modify formulas and click F5
• Save formulas in a local file:
  • Press Save icon on the top panel
  • Find the ivp-file in Downloads, modify it using any text editor
• Drag-n-drop:
  • Drag ivp-file with equations right into the browser
• Load equations from a local file:
  • Press Open icon on the top panel
  • Select From file...
  • Select a file with formulas
• Explore model:
  • Press Run sensitivity analysis icon
  • Analyze the relationship between inputs and outputs using one of the following methods:
    • Monte Carlo
    • Sobol
    • Grid

Create model from template

Start from one of these templates:

Use cases

The solver has built-in use cases. Get access to them via the context menu. You can use them as a template.

• Chem reactions
  • simulates mass-action kinetics
  • illustrates annotation of inputs
• Robertson's model
  • Robertson's chemical reaction model
  • stiff equations example
  • shows how Datagrok solves complicated ODEs
• Fermentation
  • models the kinetics of the biochemical reactions in fermentation
  • shows the usage of min and max in inputs annotation
• PK
  • pharmacokinetic (PK) simulation
  • one-compartment model
• PK-PD
  • simulates pharmacokinetics (PK), pharmacodynamics (PD), and their relationship
  • illustrates the usage of the loop feature for dosing specification
• Acid production
  • models gluconic acid production by Aspergillus niger
  • shows the usage of the update feature for multi-stage simulation
• Nimotuzumab
  • models population pharmacokinetic for nimotuzumab
  • demonstrates the output feature
• Bioreactor
  • simulates the bioreactor processes
  • illustrates the capability of modeling complex processes described by a large number of equations

Datagrok's ODEs suite has tools for solving both stiff and non-stiff equations. It provides a numerical solution.

Model structure

A model defines initial value problem. It contains name, differential equations, initial values and argument specifications:

#name: My ODEs
#equations:
  dx/dt = x + y + exp(t)
  dy/dt = x - y - cos(t)
#argument: t
  initial = 0
  final = 1
  step = 0.01
#inits:
  x = 2
  y = 5

Use the following sections to specify various problems:

Annotations

The Run tab of Diff Studio provides UI for interactive model exploration. Use annotations to improve usability. Append them, when defining parameters, initial values and argument.

Group inputs by specifying their category:

#parameters:
  P1 = 1 {category: Parameters}
  P2 = -1 {category: Parameters}

Define the desired caption:

#argument: t
  start = 0 {caption: Initial; category: Time}
  finish = 2 {caption: Final; category: Time}
  step = 0.01 {caption: Step; category: Time}

Specify min, max and step values to get sliders and clickers for the rapid model exploration:

#inits:
  x = 2 {min: 0; max: 5}
  y = 0 {min: -2; max: 2; step: 0.1}

Provide hints in brackets [ ]:

  P1 = 1 {category: Parameters} [P1 parameter tooltip]

Export to JavaScript script

Once you are satisfied with the result, you can convert your model to a Datagrok application. To do so:

1. Press JS button on the top panel
2. Press SAVE button
3. Script is created, and can be found in the "Scripts" section of the platform

Improve usability. Use #tags: model to add your model to Model Catalog. Provide a description in the #description-line:

#name: Bioreaction
#tags: model
#description: Complex bioreaction simulation

Apply scripting tools to get:

• non-elementary and special functions' use
• Datagrok packages' functions call

Find more features in Diff Studio docs.

See also

• Sensitivity analysis
• Viewers gallery
• Scripting