Basic Introduction

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Prerequisites
Creating Standard User Account
Importing a Model or File
Creating a New Model
Running a Simulation and Visualizing results

Prerequisites

This tutorial will guide you through the basic features of StochSS 2.0. You will become familiar with the Model Editor and the Workflow Manager. You will learn how to create your own model, which can be population, concentration or hybrid population/concentration-based, and how to simulate it using either an ordinary differential equation (ODE) solver, the stochastic simulation algorithm (SSA), the basic tau leaping (Tau Leaping) solver or the basic tau hybrid (Hybrid ODE/SSA) solver.

Creating Standard User Account


From the StochSS home page you can click Click here to login to get to the login page.  Here you can login using an existing google account or create a new google account.  If you are new to StochSS 2.0 StochSS will create an account for you using the google account you logged in with.

Figure 1. Home page.
Figure 1. Home page.

 

Importing an existing Model or File

Import to root

Option 1: StochSS Model

  1. Navigate to the File Browser page.
  2. Click + button at the bottom of the file tree.
  3. Click Upload StochSS Model from the options.
  4. Select a StochSS model and click Upload.

Option 2: SBML Model

  1. Navigate to the File Browser page.
  2. Click + button at the bottom of the file tree.
  3. Click Upload SBML Model from the options.
  4. Select a SBML model and click Upload.

Option 3: File

  1. Navigate to the File Browser page.
  2. Click + button at the bottom of the file tree.
  3. Click Upload File from the options.
  4. Select a file and click Upload.
Figure 2. Upload file to root.
Figure 2. Upload file to root.
Import to a directory

To upload a StochSS Model, SBML Model or File to a particular directory replace step 2 above with these steps.

  1. Click on the directory you wish to upload too.
  2. Click Actions for … button at the bottom of the file tree.
  3. Click Upload File in the provided menu.

Figure 3. Actions button.
Figure 3. Actions button.

Figure 4. Upload file to directory.
Figure 4. Upload file to directory.

Note that StochSS model files have the .mdl extension, however, a model file with the .json extension may also be uploaded.
Note that SBML files in StochSS use the extension .sbml, however, SBML files with the .xml extension may also be uploaded
Note that due to limitations with the SBML standard, StochSS only supports non-spatial models in this format.
If you upload a zip file StochSS will unzip the file in the same directory you uploaded the zip file to.
After importing the model, StochSS should highlight the imported file in the file browser.

Creating a New Model

The Model Editor will let you create new or modify existing stochastic biochemical models as well as deterministic models.  The best way to get started with the model editor is to open an example model and look at the different sections.

An example population model is defined by the following two reactions:

Figure 5. Reaction r1.
Figure 5. Reaction r1.

 

Figure 6. Reaction r2.
Figure 6. Reaction r2.

To create this model:

  1. Navigate to the File Browser.
  2. Click + and select Create Model or select a directory, click Actions for … and select Non-Spatial from the New Model menu.
  3. Name the model to example and click OK to navigate to the Model Editor.
  4. Once in the Model Editor click Population for the default species mode.
    Figure 7. Default species mode.
    Figure 7. Default species mode.
  5. Click Add Species twice to create two species.
  6. By default the species are named s1 and s2. Set the initial condition for s1 to 1000 and the initial condition for s2 to 0.
  7. Similarly to above, click Add Parameter twice to add two parameters.
  8. By default they will be named k1 and k2. Set k1 to 0.0001 and k2 to 0.05.
  9. Click Add Reaction to add two reactions. Select the reactants, products, rates and reaction types corresponding to Figures 5 and 6. Compare to Figures 8 and 9 to verify the settings.
    Figure 8. Dimerization reaction.
    Figure 8. Dimerization reaction.


    Figure 9. Decay reaction.
    Figure 9. Decay reaction.
  10. Click Run Preview to view a sample time series of the model.

Running a workflow and Visualizing results

For this section, create or import a model using the directions above.

  1. Navigate to the File Browser page.
  2. Select the model you wish to simulate and click Actions for … to navigate to the Workflow Selection page.
  3. Click on the type go workflow you would like to run to navigate to the Workflow Manager page.
  4. Setup your simulation parameters: seed, trajectories, algorithm, etc.
    Figure 10. Simulation Settings.
    Figure 10. Simulation Settings.
  5. Settings for Simulation Algorithms:
    1. If you choose ODE for the Simulation Algorithm you will be able set any of the Deterministic Settings.
    2. If you choose SSA for the Simulation Algorithm you will be able to set the Trajectories and Seed under the Stochastic Settings.  Setting the algorithm to Tau-Leaping will allow you to additionally set the Tau Tolerance.
    3. The Hybrid ODE/SSA  and the Choose for me algorithm options will allow you to sett any of the settings under Deterministic and Stochastic Settings.
    4. If you choose the Choose for me option StochSS will select the algorithm best suited for your simulation.  StochSS makes this decision based on the model components, the default species mode, and which settings you chose to set (change from default values).
  6. Click Start Workflow. The Workflow Manager page will refresh, displaying the status of the workflow as well as the date and time of when the workflow was started..
  7. When the workflow has completed you will be able to visualize the results in the Results section.  If you set the Trajectories to a value greater than one you will have multiple ways to represent the results.
  8. In the Results section you will also be able to modify the plots, download the plot image or raw plot data and download the raw results in a CSV format.
  9. To download the full workflow:
    1. Navigate to the File Browser.
    2. Select the workflow you wish to download.
    3. Click the Actions for … button.
    4. Select Download as .zip from the menu

Note that in StochSS workflows are represented with the .wkfl extension.

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