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@allison-li-1016 allison-li-1016 commented Jun 18, 2025

I am going to use this PR as a way to iterate on circuit implementation ideas. Any feedback would be greatly appreciated!

Description of major changes:

  • made combined combinatorial parent class for all 4 logical car circuits and refactored logical circuit classes under the parent class
  • added degradation of synnotch activation TF
  • new inhibitory circuit --> reaching bound synnotch threshold inactivates T cell --> inactivates inflammation pathway
  • new inducible circuit --> reaching bound synnotch threshold is the only way to activate T cell --> activates inflammation pathway

@allison-li-1016 allison-li-1016 marked this pull request as draft June 18, 2025 00:15
@allison-li-1016 allison-li-1016 marked this pull request as ready for review June 18, 2025 01:06
@allison-li-1016 allison-li-1016 requested a review from cainja June 18, 2025 01:06
@allison-li-1016 allison-li-1016 self-assigned this Jun 18, 2025
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More on the high level feedback:

  1. Not sure how I feel about there being 4 different classes here. Is there a way that we can combine them? I feel like this abstraction might be a little annoying to work with.
  2. I don't love the way that we're using super. I'm not sure it's more intuitive to specify super rather than not defining an overriding method at the same abstraction level.
  3. What's the benefit of the BindingEvent object? My impression is that it's implemented to track all binding events, but I think we are overcomplicating the irreversible behavior of synnotch? This is an incredibly expensive way to do this...

getTissueAgents(allAgents, bag);
super.age++;

if (state != PatchEnums.State.APOPTOTIC && age > apoptosisAge) {
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I think referencing PatchEnums makes this somewhat hard to read

super.unbind();
this.activated = false;
} else {
// if CD8 cell is properly activated, it can be cytotoxic
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don't love that comment refers to CD8

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3 participants