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 varscontaining
-var foo 0
-var bar 1and 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 varsand run KaSim $(cat vars) -load-sim test.sim, it does run the simulation with the new values!
@pirbo Thank you for your help. Today I finished the Genetic Algorithm that parametrize models. I had a bad time using the command
KaSim $(cat vars) -load-sim test.siminside 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.
btw, the code was
%obs: 'obs_name' 'var_name'
Hello everyone. I'm here to share my happiness and say thank you for let me work and discuss my Ph.D. project about RBMs and the use of KaSim to advance in it. I'm now Ph.D. candidate and part of this accomplish is yours. Best to all and I'll be keep in touch asking you doubts ;). Best wishes!
Hello everyone. What is happening with the syntax option in the master branch? is deprecated (with respect the rc1) and now every model should be written in syntax 4, am I right? Also, I'm getting
syntax errors, invalid use of character [ or Invalid internal state with models in the model folder with the master branch but no error with KaSim4 rc1.
@pirbo sorry. you're right, is was a problem with my path. Also, I didn't see the syntax option in help (probably to tired yesterday). Now, only synth.ka raised an error in the master branch. Thank you.
Parsing synth.ka...
done
File "synth.ka", line 42, characters 0-0:
Incorrect beginning of sentence
error really really weird because is the end of the file
Hello everyone, I have a small problem with comments. In KaSim3, I could do comments at the end of the line with #. However, in KaSim4, it complain that there is an illegal definition of the variable. Removing the comment resolve the issue. How can I include a comment at the end of a line? Thanks
what do you mean by continuous? You can repeatedly (try to) apply a perturbation every event by using the
%mod: repeat ... do ... until ... construction. You can make the test/application time based instead of event based by using %mod: alarm ... repeat ... do ... until ....
I'm developing now a python script and I solved how to call KaSim with subprocess, and parallelize simulations with SLURM and multiprocessing
Hello everyone. I finished the script that calculates sensitivities to model parameters. It simulates samples of models created with the pyhon SALib package and from the dynamical influence network (din hits and din fluxs) and after simulations, the same SALib package determines the sensitivities. You can download at https://test.pypi.org/project/sterope/ and here it's an example model that comes from the BioNetFit paper. https://github.com/glucksfall/sterope/tree/master/example/kasim. Please, don't hesitate to tell me if you have any suggestion, doubt, or anything. My plan is submit a paper with results using the package, not the package itself because I think it isn't enough. Thank you and best regards.
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/
(and don't look much at the code...)
Hi, sorry for the delay. I'm not sure it is OK but it is expected yes :-) The technical reason is "KaSa does not look at numbers in the
inits, 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"".
Or there is a way to declare that all agents in a rule must share the same state for their location
thank you very much in advance. Best regards
Hello everyone. I tried to find a good place to get started using Kappa in a graphical environment, but could not find anything useful. Tried to use KaSim, but in the downloaded version, I cannot even get the editor working. No editing enabled, file dropdown is disabled, and no loading available. In-browser version is said to be preloaded with a sample grammar, but I cannot get it showing up in the editor. Are there any tutorials on the UI available? Other visualization tools? Thanks for your help.
Hi @scoolpic_twitter, did you try https://tools.kappalanguage.org/try/?model=https%3A//raw.githubusercontent.com/Kappa-Dev/KappaTools/master/examples/abc-pert.ka?
Which operating system are you using? Is the Kappapp available at https://github.com/Kappa-Dev/KappaTools/releases/tag/v4.1 working?
(tried it under ubuntu 20.04)