Command line stochastic simulator for kappa models. Documentation and binaries can be found in the release section below.
Hello everyone, I hope you're fine. I started a project to model metabolism reactions, and because I'm soughting to extend it to genome-scale, reactions consume or produce tokens. The obvious problem is, because tokens could take negative values, make conditions to have a rate != 0. However, I still have negative values. Could you help me with a possible solution?
if you have some comment please tell me. Thank you!
@pirbo is API version 2 working well right now? I have realease current version of kappa-notebook here https://github.com/antonkulaga/kappa-notebook/releases/tag/0.20 but it is tailored for v1 of API.
It is not a problem for me to understand Ocaml code, the main issue is that I do not understand 1) the routing of API version2 2) which codefiles are v2-only 3) I have issues with pausing/stoping simulation as you changed something in routing
@glucksfall yes use command line option
-var name_of_variable value_of_variable
@antonkulaga We're getting there but we are SO late ...
Well... thanks anyway
arg, I see. No, indeed, you cannot mix
-load-sim an -i. I'm sure you can translate a file of name value into a list of -var name valueusing xargs (you can probably simply write you -var in a file and ask the shell to include it in the command line...) I'll try and give you my results
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.