Command line stochastic simulator for kappa models. Documentation and binaries can be found in the release section below.
Yes it somehow work. I've written a file vars
containing
-var foo 0
-var bar 1
and a model test.ka that use 'foo' and 'bar'. Then I KaSim -make-sim test.sim $(cat vars) test.ka
Now if I change the value of 'foo' and 'bar' in vars
and run KaSim $(cat vars) -load-sim test.sim
, it does run the simulation with the new values!
KaSim $(cat vars) -load-sim test.sim
inside a for loop in bash because missing whitespaces: it should say KaSim $( cat vars ) -load-sim test.sim
. That little mistake prevented KaSim read new values.
%obs: 'obs_name' 'var_name'
syntax error
s, invalid use of character [
or Invalid internal state
with models in the model folder with the master branch but no error with KaSim4 rc1.
Parsing synth.ka...
done
File "synth.ka", line 42, characters 0-0:
Incorrect beginning of sentence
%mod: repeat ... do ... until ...
construction. You can make the test/application time based instead of event based by using %mod: alarm ... repeat ... do ... until ...
.
Hello everyone. Finally I could show you my work. We developed a tool to calibrate Rule-Based Models and it supports KaSim (v4). Please, I you have doubts, things to improve or anything, don't hesitate and contact me (or to Alberto). I'm writing my PhD thesis and your feedback will be considered further. Thank you in advance. Best regards.
https://www.nature.com/articles/s41598-019-51546-6
https://pleione.readthedocs.io/en/latest/
init
s, it simply consider them as what they are internally: Rules of introductions." and its rational is "Dead rules warnings are there to prevent omissions/bugs, if a user explicitly says %init: 0 A()
it is interpreted as saying "I'm not forgetting A() but I want none" so static analyses considers A as "taken into account"".