The problem
A rule-based model cannot be built in VCell without the graphics editor. That makes rule-based modelling the one part of the client that is unreachable from a script, from a test, or from anyone who would rather type than draw — and it is not a small gap, since reaction rules are the whole point of a rule-based model.
Two separate things close the door, and both are worth stating because either one alone would be enough:
1. The BioNetGen definition column is read-only for rules. BioModelEditorReactionTableModel.isCellEditable allows the equation/BNGL column only when the row is a ReactionStep:
if (column == COLUMN_EQUATION) {
if(process instanceof ReactionStep) {
return true;
} else {
return false;
}
}A ReactionRule is not a ReactionStep, so the cell is never editable — not even on first specification, which is the rule for every other table. Directly below this method sits a commented-out version that was reaching for exactly this: it would have allowed the edit while the rule's molecules had no components. So the idea has been here before.
2. The rule editor exposes nothing to address. Its entire reactant/product pattern area is a single anonymous component:
ReactionRuleEditorPropertiesPanel$1 777x200 px children = 0
Every molecule, site, state and bond is painted onto that one component. The only real Swing controls in the panel are Add Reactant, Add Product, Reversible and three display toggles — so pressing New Rule gives you an empty rule and no way to fill it in except by right-clicking painted pixels.
Notably, Molecules, Species and Observables do not have this problem. Their BioNetGen definition columns are writable, and the 7.7 tutorial says so itself: "Every table has a column BioNetGen definition… It is useful if you have separate BNGL code you want to paste, but do not want to import for some reason." Setting one cell to EGFR(ecd,tmd,Y1~u~p,Y2~u~p) replaces about a dozen right-click gestures. Only rules are missing.
What this blocks today
While scripting the two rule-based tutorials (#2067) both models had to be built by writing BNGL to a file and using File > Import, because there is no other way in. That works — both reproduce their public reference models exactly — but it means:
- the tutorials cannot be scripted the way they are taught;
- there is no way to make a small edit to one rule without the graphics editor;
- rule-based models are effectively untestable through the UI.
The obvious fix, and why it is not sufficient on its own
Making the BioNetGen definition column writable for ReactionRule is a small change and would unblock all of the above. But raw BNGL is a poor primary interface for the people this feature is for:
- it needs autocomplete over the molecule patterns actually available in the model, or the user is typing identifiers from memory;
- site states, bonds, and bound / unbound / "bound to anything" (
!+, !?, unbound) have to be applied consistently across reactant and product patterns — the editor currently enforces that by construction, and greys out combinations that are impossible;
- an expert can get it right, but the syntax is technical and unintuitive for a new user, which is precisely who the graphics editor serves well.
So this should not land as "make the cell editable" and stop there. That would create a second way to build a rule that is easy to get subtly wrong and hard to diagnose.
What is actually wanted
A more accessible textual (or hybrid) route to specifying a rule, with the consistency the graphics editor currently guarantees. There are a few plausible shapes for it and picking between them deserves a proper design pass rather than a first guess — autocomplete-backed BNGL entry, a structured non-graphical editor, a text form that round-trips against the existing editor, or some combination.
Out of scope for #2067; opening this to record the finding and the constraints.
/cc for design discussion — this one needs a plan before any code.
The problem
A rule-based model cannot be built in VCell without the graphics editor. That makes rule-based modelling the one part of the client that is unreachable from a script, from a test, or from anyone who would rather type than draw — and it is not a small gap, since reaction rules are the whole point of a rule-based model.
Two separate things close the door, and both are worth stating because either one alone would be enough:
1. The BioNetGen definition column is read-only for rules.
BioModelEditorReactionTableModel.isCellEditableallows the equation/BNGL column only when the row is aReactionStep:A
ReactionRuleis not aReactionStep, so the cell is never editable — not even on first specification, which is the rule for every other table. Directly below this method sits a commented-out version that was reaching for exactly this: it would have allowed the edit while the rule's molecules had no components. So the idea has been here before.2. The rule editor exposes nothing to address. Its entire reactant/product pattern area is a single anonymous component:
Every molecule, site, state and bond is painted onto that one component. The only real Swing controls in the panel are
Add Reactant,Add Product,Reversibleand three display toggles — so pressing New Rule gives you an empty rule and no way to fill it in except by right-clicking painted pixels.Notably, Molecules, Species and Observables do not have this problem. Their BioNetGen definition columns are writable, and the 7.7 tutorial says so itself: "Every table has a column BioNetGen definition… It is useful if you have separate BNGL code you want to paste, but do not want to import for some reason." Setting one cell to
EGFR(ecd,tmd,Y1~u~p,Y2~u~p)replaces about a dozen right-click gestures. Only rules are missing.What this blocks today
While scripting the two rule-based tutorials (#2067) both models had to be built by writing BNGL to a file and using
File > Import, because there is no other way in. That works — both reproduce their public reference models exactly — but it means:The obvious fix, and why it is not sufficient on its own
Making the BioNetGen definition column writable for
ReactionRuleis a small change and would unblock all of the above. But raw BNGL is a poor primary interface for the people this feature is for:!+,!?, unbound) have to be applied consistently across reactant and product patterns — the editor currently enforces that by construction, and greys out combinations that are impossible;So this should not land as "make the cell editable" and stop there. That would create a second way to build a rule that is easy to get subtly wrong and hard to diagnose.
What is actually wanted
A more accessible textual (or hybrid) route to specifying a rule, with the consistency the graphics editor currently guarantees. There are a few plausible shapes for it and picking between them deserves a proper design pass rather than a first guess — autocomplete-backed BNGL entry, a structured non-graphical editor, a text form that round-trips against the existing editor, or some combination.
Out of scope for #2067; opening this to record the finding and the constraints.
/cc for design discussion — this one needs a plan before any code.