### T2B - Frequently Asked Questions (FAQs)

#### 1. How can I find models related to a specific disease or topic?

<details>

  <summary>Click to expand</summary>

  You can use the `Search_models` tool to query the BioModels database for relevant models based on keywords. Here are some examples:

  <br>

  - Search for Crohn’s disease models:

    ```

    Search models on Crohn’s disease

    ```

  - Find models on COVID-19:

    ```

    Find models on COVID-19

    ```

</details>

#### 2. How can I get details about a specific model?

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  <summary>Click to expand</summary>

  Use the `Get_modelinfo` tool to retrieve information such as species names, parameters, initial values, and descriptions. Examples:

  <br>

  - Briefly describe a model:

    ```

    Briefly describe model 971

    ```

  - List all species and parameters in a model:

    ```

    List all the species and parameters in model 971

    ```

  - Get the initial concentration of a specific species:

    ```

    What is the initial concentration of Pyruvate in model 64?

    ```

  - List model name and units in a table format:

    ```

    List the name and units in model 537. Show them as a table.

    ```

</details>

#### 3. How do I retrieve annotations from a model?

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  <summary>Click to expand</summary>

  The `Get_annotations` tool extracts model annotations and provides descriptions from UniProt and OLS databases where possible.

  <br>

  - Show all annotations in a model:

    ```

    Show me all the annotations in model 64

    ```

  - Retrieve specific annotations related to interleukins:

    ```

    Show me annotations of only interleukin-related species in model 537

    ```

</details>

#### 4. How do I run a simulation on a model?

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  <summary>Click to expand</summary>

  Use the `Simulate_model` tool to simulate a model. You can specify duration, time intervals, and initial values for species/parameters.

  <br>

  - Basic simulation:

    ```

    Simulate model 64

    ```

  - Specify simulation time and interval:

    ```

    Simulate model 64 for 3 days with an interval of 10

    ```

  - Set initial concentration and add recurring events:

    ```

    Run a simulation on model 537 for 100 hours with a time interval of 50.

    Set the initial concentration of Ab{serum} to 100.

    Add a recurring event that resets Ab{serum} to 100 every 20 hours.

    ```

</details>

#### 5. Can I create custom plots from my simulation results?

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  <summary>Click to expand</summary>

  The `Custom_plotter` tool helps you focus on a subset of species in a simulation plot.

  <br>

  - Plot only CRP-related species:

    ```

    Make a custom plot to show only CRP-related species.

    ```

  - Plot glucose-related species:

    ```

    Plot only glucose-related species.

    ```

</details>

#### 6. How do I bring a model to steady state?

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  <summary>Click to expand</summary>

  The `Steady_state` tool helps stabilize a model.

  <br>

  - Basic steady-state analysis:

    ```

    Bring model 64 to a steady state

    ```

  - Set initial conditions before analysis:

    ```

    Bring model 64 to a steady state. Set the initial concentration of Pyruvate to 50.

    ```

</details>

#### 7. How do I ask questions about the simulation results?

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  <summary>Click to expand</summary>

  Use the `Ask_question` tool after running a simulation or steady-state analysis to retrieve insights.

  <br>

  - Steady-state concentration of a species:

    ```

    What is the steady-state concentration of Pyruvate?

    ```

  - Time required for a species to reach steady state:

    ```

    How long does glucose-related species take to reach steady state?

    ```

  - Final concentration in a simulation:

    ```

    What is the concentration of CRP-related species at the end of the simulation?

    ```

</details>

#### 8. How do I analyze how one species or parameter affects another?

<details>

  <summary>Click to expand</summary>

  The `Parameter_scan` tool allows you to analyze how changes in one parameter affect another.

  <br>

  - Effect of extracellular glucose on Pyruvate:

    ```

    How does the value of Pyruvate change in model 64 if the concentration of Extracellular Glucose is changed from 10 to 100 with a step size of 10? The simulation should run for 5 time units with an interval of 10.

    ```

  - Effect of dose changes on CRP concentration:

    ```

    Run a param scan in model 537 to observe change in concentration of CRP in serum over time if initial value of the parameter Dose is changed from 100 to 500 with a step size of 25.

    ```

</details>

#### 9. Can I ask questions about a research article I uploaded?

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  <summary>Click to expand</summary>

  The `Query_article` tool helps analyze uploaded research articles.

  <br>

  - Summarize key takeaways:

    ```

    What are the key takeaways of the uploaded article?

    ```

  - Find parameter descriptions in the article:

    ```

    Query the uploaded article to suggest possible description of the parameter gR in model 64.

    ```

</details>

#### 10. How can I compare different simulations or steady-state results?

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  <summary>Click to expand</summary>

  Assign names to different experiments and compare results.

  <br>

  - Compare simulations:

    ```

    Simulate model 537 for 2016 hours. Call it experiment Treatment4wk.

    ```

    ```

    Redo the simulation for 2016 hours but set the initial value of Dose to 0 and DoseQ2W to 300. Call it experiment Treatment2wk.

    ```

    ```

    What is the concentration of CRP in serum at the end of the simulation in all experiments done so far?

    ```

  - Compare steady-state results:

    ```

    Bring model 64 to a steady state. Call it Experiment_1.

    ```

    ```

    Bring model 64 to a steady state. Set initial concentration of NADH to 10. Call it Experiment_2.

    ```

    ```

    Compare the concentration of Pyruvate in both experiments at steady state.

    ```

</details>