@datagrok/deqs v1.0.0

Deqs

Deqs is a package for the Datagrok platform. It provides in-browser tools for solving intial value problem for systems of ordinary differential equations (ODE).

• Go to Apps and run EquaSleek X
• Enter formulas or modify template
• Press Run button on the top panel

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 EquaSleek X
  • Press Run button on the top panel
• Modify a template:
  • Edit formulas or add new ones
  • Click F5 or Run button
• Use an advanced template:
  • Rigth click and select Templates > Advanced...
  • Modify formulas and click F5
• Save formulas in a local file:
  • Rigth click and select Save...
  • Find the file in Downloads
• Load equations from a local file:
  • Rigth click and select Load...
  • Select a file with formulas

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 the runOnOpen and runOnInput meta-features
• 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

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:

Platform applications

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

1. Press Export 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 annotations to get better UI. Append them, when defining parameters, initial values and argument.

Group inputs by specifying their category:

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

Add units:

#inits:
  x = 2 {units: C; category: Initial values}
  y = 0 {units: C; category: Initial values}

Define the desired caption:

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

Provide hints in brackets [ ]:

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

Apply scripting tools to get:

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

See also

• Compute
• Scripting
• Function annotations
• Viewers gallery