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Kappa-Dev / KappaTools

Tool suite for kappa models. Documentation and binaries can be found in the release section. Try it online at
http://kappalanguage.org/
GNU Lesser General Public License v3.0
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how to debug reactions #590

Closed nilsbecker closed 5 years ago

nilsbecker commented 5 years ago

hi, i have a set of reactions which yield a product species which i did not expect to be possible. to debug my rules, i have created a stopping condition that stops when the offending species first appears. what i would like is to be able to see what reaction event created it. is there a way to achieve this?

(please feel free to close this and point me to a different place if this question is not appropriate for the github issues list)

nilsbecker commented 5 years ago

from the recent bioinformatics article i gathered that 'stories' are probably what i could use, however i was unable to find documentation on those?

nilsbecker commented 5 years ago

after some digging in outdated docs, i found a way to make it work using the CLI programs KaSim and KaStor. still no luck with the GUI. for now, i can work with my solution.

pirbo commented 5 years ago

If your simulation is not too big, you can do that in the GUI. Check "Store the trace" in the "preferences" (top right of the screen). redo your simulation with $TRACK directive. Now the tab "story" is available...

nilsbecker commented 5 years ago

ah i see, nice. it would be great to make this feature more discoverable