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FAQ

T2B - Frequently Asked Questions (FAQs)

Click to expand You can use the `Search_models` tool to query the BioModels database for relevant models based on keywords. Here are some examples:
- Search for Crohn’s disease models: 
Search models on Crohn’s disease
- Find models on COVID-19: 
Find models on COVID-19

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

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

3. How do I retrieve annotations from a model?

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

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

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

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

Click to expand The `Custom_plotter` tool helps you focus on a subset of species in a simulation plot.
- Plot only CRP-related species: 
Make a custom plot to show only CRP-related species.
- Plot glucose-related species: 
Plot only glucose-related species.

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

Click to expand The `Steady_state` tool helps stabilize a model.
- 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.

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

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

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

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

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

Click to expand The `Query_article` tool helps analyze uploaded research articles.
- 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.

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

Click to expand Assign names to different experiments and compare results.
- 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.