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T2B - Frequently Asked Questions (FAQs)
1. How can I find models related to a specific disease or topic?
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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?
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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?
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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?
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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?
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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?
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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?
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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?
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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?
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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?
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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. ```