Example Data

How to use?

To download the following files, please right-click on them and choose "Save As..."

Step 1a) Set CSML/SBML and Parameter Search Space

This step is to load the model file (CSML or SBML) and define the distribution and range for parameters that users wish to estimate.

CSML sample set:
  1. Click on "Set SBML/CSML and Parameter Search Space" button.
  2. Click on "Load CSML" button and select the downloaded Circadian model.
  3. Click on the rightmost column of 'e16 ' entity. A "Parameter Search" dialog will popup.
  4. Change the "Max" text field to 10.
  5. Click on "Apply" button.
  6. Repeat the same for e17 entity but this time set the "Max" text field to 10.
  7. Click on "Continue" button to proceed.
SBML sample set:
  1. Click on "Set SBML/CSML and Parameter Search Space" button.
  2. Click on "Load SBML" button and select the downloaded ITR model.
  3. Click on the rightmost column of parameter_reaction_v5_parameter_lminus2 entity. A "Parameter Search" dialog will popup.
  4. Change the "Min" text field to 0.
  5. Change the "Max" text field to 1.
  6. Click on "Apply" button.
  7. Click on "Continue" button to proceed.

Step 1b) Set Time-Series Data

This step is to input the observed time-series data. Accepted formats include EDF, CSV and TSV. Functions such as smoothing and sampling are included to improve the quality of observed data for better estimation results.

CSML sample set:
  1. Click on "Set Time-Series Data" button. A message dialog will popup. Select "EDF".
  2. Go to menu bar and select "File->Load".
  3. Choose the downloaded observed data for Circadian model.
  4. Click on "Continue" button to proceed.
SBML sample set:
  1. Click on "Set Time-Series Data" button. A message dialog will popup. Select "EDF".
  2. Go to menu bar and select "File->Load".
  3. Choose the downloaded observed data for ITR model.
  4. Click on "Continue" button to proceed.

Step 2) Link CSML with Time-Series Data

This step is needed to pair the model entities with observed data. An auto-map function is available to match corresponding entities and observed data with same names.

CSML sample set:
  1. Click on "Link SBML/CSML with Time-Series" button.
  2. Click on "Auto-Map" button.
  3. Click on "Done" button to proceed.
SBML sample set:
  1. Click on "Link SBML/CSML with Time-Series" button.
  2. Click on "Auto-Map" button.
  3. Click on "Done" button to proceed.

Step 3) Run Data Assimilation

A variety of settings for the particle filter and simulation are enabled to allow for flexibility based on the user's needs.

CSML sample set:
  1. Click on "Run Data Assimilation" button.
  2. Change the "Number of Seeds" text field to around 10000.
  3. Click on "Run" button.
SBML sample set:
  1. Click on "Run Data Assimilation" button.
  2. Change the "Number of Seeds" text field to around 10000.
  3. Change the "Simulation Time" text field to 1.
  4. Change the "Simulation Interval" text field to 0.001.
  5. Click on "Run" button.

View Result

After running the particle filter algorithm, the simulation runs results using estimated parameters will be plotted for ease of comparison between the original and fitted models. The parameters' distribution plot is also displayed.

CSML sample set:
SBML sample set: