1. Part III How to use SHAKEN

2. How to Use SHAKEN These slides walk you through each item in SHAKEN’s main menu We will show how each item works with a demo Then you can try to do the same thing from your laptop

3. Main Menu Enter Knowledge Ask a Question Test Knowledge Logout

4. Enter Knowledge Functions: add a new biological process or edit an existing one When working with processes, you can: –Name the process, define it in terms of predefined terms –Define the objects involved in the process –Define the subevents in the process and their ordering See a demo of how this works in SHAKEN Try doing it yourself

5. Ask Questions Function: Check what the system knows by asking questions about the knowledge entered Example questions: –What are the parts of an object? –What causes a certain thing to happen? Each question is formulated by –selecting a question template from a menu –customizing the question to the scenario at hand by assigning objects used in the scenario See a demo of how this works in SHAKEN Try doing it yourself

6. Test Knowledge Function: Check what the system knows by executing a simulation of the process entered Example: –Checks that preconditions of each step are satisfied –Check that all expected effects are obtained SHAKEN will show a report for each step: –Whether all its preconditions are satisfied –Whether all its effects are obtained SHAKEN will also show: –Different execution paths that are possible See a demo of how this works in SHAKEN Try doing it yourself

7. Test Knowledge: What if there is an error? Errors can appear in process models: –Steps may fail to execute: A precondition of the step is not satisfied An expected effect is not obtained –There may be unintended loops –There may be steps that are never reached during simulation SHAKEN will show an error report: –Failed steps –Unreachable steps –Loop alerts See a demo of how this works in SHAKEN Try doing it yourself Suppose we made an error and forgot to say that the virus needs to be next to the cell

8. Test Knowledge: How to fix an error? SHAKEN will show suggestions for fixing each error: –Add a new step before the failed step The new step would achieve the failed precondition –Modify the current step Objects assigned may be too general –… Suggestions are customized to each error’s context –Ex: Add a Move step that will change the Virus location You can make any of these changes using the editor You can also choose other fixes not suggested by SHAKEN See a demo of how this works in SHAKEN Try doing it yourself

9. How Do You Know You Are Done Teaching SHAKEN? No errors are reported when you run the simulation You ask a few key questions and the answers are as you expected

10. Part IV Hands-on Practice