Hector Medina
Hector Medina
There are several operations done in Kappa, e.g. binding, unbinding, link-swaps, state modifications, creation, and degradation. As a debugging tool, it would be useful if the editor informed the user...
When an observable has two symmetries, KaSim reports twice what's there. If I define with initial condition one single lone symmetric dimer, KaSim reports in the output there are two...
For user-friendliness, it would be nice if the Javascript proto-IDE would auto-complete (or offer suggestions) for variable names in the context of declaring a rule's rate. For example, when the...
For the Kappa Javascript simulator, it would be nice if the graphical rendering of the rule would be accompanied by the rates' definition and evaluation. See the attached image for...
Some years back, @russharmer developed a framework (or the proposal for one) that would allow one to modify a kappa program according to some rules of agent transformation. At the...
The kappa perturbation language is defined in the [KaSim Manual](http://dev.executableknowledge.org/docs/KaSim-manual-master/KaSim_manual.htm#x1-410071). It would be useful to have a builder utility for such perturbations and modifications. An example could be a pop-up...
When specifying a rule, one can write a LHS with two components that have no connection stated in that LHS. Depending on the model, those components might be already connected...
Previously, one could use `$UPDATE ` to change a rule's rate via a perturbation. This feature has since been removed. Although it remains technically possibly to do this via a...
It would be useful if KaSim had the option of a "continue" mode that could be launched with a snapshot and the inputs file (optionally the traces file). Here's the...
With pattern-notation, I can write 3 rules with: ``A(a),B(b) A(a!1),B(b!1) @ 'γ1' {γ2}, 'γ3'`` Shouldn't edit-notation also support reversible & ambiguous "overloading"? The following gives me a syntax error, but...