Hector Medina
Hector Medina
In the GUI, the tab "polymers" displays a list of bonds that yield arbitrarily large complexes. Meanwhile, the contact map tab displays all bonds. It would be useful to have...
In the GUI, the contact map has an "interactive mode". It allows one to highlight specific bonds in the contact map. However, it disallows self-bonds. For example, in: ``` Bob(site0[./1]),...
Similar in spirit to #598, but requiring a whole lotta **_computer science_**! A trace can be a very large file, notably as they're written in JSON. Traces of biological-style models...
A message that asks for confirmation when leaving the UI would save some models from unintended cybernetic oblivion when mis-clicking a Home, or Bookmark button. I.e. Gmail's when composing an...
It would be useful to have more functions available to the interactive mode / toplevel: * compile to simulation package * change plot period As this mode is intended for...
`Kappa Simulator: v4.0rc1-414-gfc032a0` The behavior of `-mixture` has several bugs. Let's take the model: ``` %agent: A(s) %agent: B(s) %init: 100 A(), B() A(s[./1]),B(s[./1]) @ 1e-3 A(s[1/.]),B(s[1/.]) @ 1e-1 %obs:...
For example: ``` %agent: A(a,b) A(a[./1]), A(b[./1]) @ 1 A(a[1/.]), A(b[1/.]) @ 1 %init: 10 A(a[.],b[.]) %mod: [E] > 3 do ($SNAPSHOT "foo" ; $STOP) ``` Browser: Firefox 57.0.4
The following code runs and produces an inputs file. The inputs file contains illegal kappa statements (according to the UI and CL version of KaSim), and suggest kinetics that I...
Using KaSimWeb (whatever version is running 7:30pm Boston time), using the test suite model under `models/test_suite/compiler/counters_2_levels/counter_2.ka`, changing the default value of the counter to `2`, produces the above cryptic error...
When the UI encounters tokens, it seems WebSim crashes. The console reads about 150 of these error messages: `...{"severity":"error","text":"file_name: KaSa_rep/frontend/preprocess/prepreprocess.ml; message: line 743: Tokens are not implemented in KaSa yet;...