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    Anton Kulaga
    @antonkulaga
    could you keep the old one in "not unplugged mode" for a week or two? Switching to a new one will take some time for me and as they under different URIs they should not conflict much
    Anton Kulaga
    @antonkulaga
    I am updating to the latest version (using Ocaml code as reference). I wonder, why do you have so many nullables in the API?
    Rodrigo Santibáñez
    @glucksfall
    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?
    Rodrigo Santibáñez
    @glucksfall
    We made some changes and now the model run
    if you have some comment please tell me. Thank you!
    Anton Kulaga
    @antonkulaga
    @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
    Pierre Boutillier
    @pirbo
    Sorry @antonkulaga I come back to you very soon but I don't have a second with the release process of the command line tool. The API v2 has indeed huge unsolved problems...
    Anton Kulaga
    @antonkulaga
    @pirbo any progress on API v2. docs/explanation?
    Rodrigo Santibáñez
    @glucksfall
    Hello everyone. There's a way to compile a model without '%var' and the gave '%var' after compilation?
    Pierre Boutillier
    @pirbo
    I'm so sorry. Why did I never receive any notification about this last messages ...
    @glucksfall yes use command line option -var name_of_variable value_of_variable
    @antonkulaga We're getting there but we are SO late ...
    Rodrigo Santibáñez
    @glucksfall
    @pirbo could -var take a file with name_of variable value_of_variable?
    Pierre Boutillier
    @pirbo
    no but if you want to put them in a file why not creating a file with explicitly a list of%var name valueand simply put this file in the command before your model?
    Rodrigo Santibáñez
    @glucksfall
    I would try that alternative. I don't remember the exact combinations of load-sim and -i file_with_parameter that I tried to work together
    Well... thanks anyway
    Pierre Boutillier
    @pirbo
    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
    Pierre Boutillier
    @pirbo

    Yes it somehow work. I've written a file varscontaining

    -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 varsand run KaSim $(cat vars) -load-sim test.sim, it does run the simulation with the new values!

    Rodrigo Santibáñez
    @glucksfall
    Fantastic! That's great. I could run faster simulations with a lot of parameters. Thank!!!
    Rodrigo Santibáñez
    @glucksfall
    @PO
    Rodrigo Santibáñez
    @glucksfall
    @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.
    Rodrigo Santibáñez
    @glucksfall
    The script runs almost 3x faster
    Rodrigo Santibáñez
    @glucksfall
    Hello @pirbo, I have a doubt about simulation ending when the system has zero reactivity, but the time limit isn't reached: the output is truncated at the last simulated time, or the output is filled with repeated lines until the time limit?
    Pierre Boutillier
    @pirbo
    the output is truncated at the last simulated time
    Rodrigo Santibáñez
    @glucksfall
    thanks
    Rodrigo Santibáñez
    @glucksfall
    Hello @pirbo, I'm just wondering if there's a way to observe a variable (because it changes through the simulation)
    Rodrigo Santibáñez
    @glucksfall
    Don't worry. My friend was running an old model without observing variables and thought it was the model with observables variables
    btw, the code was %obs: 'obs_name' 'var_name'
    Rodrigo Santibáñez
    @glucksfall
    Hello everyone. I hope you're well. I have a problem trying to implement a perturbation. I have a condition and the effect but I don't know how to repeat the evaluation of the condition after every event until the end of the simulation. Do you have any example?
    Pierre Boutillier
    @pirbo
    Add repeat [true] after the effect. (In KaSim4) in kasim3 it was ˋrepeat cond do effects until [false]ˋ
    Rodrigo Santibáñez
    @glucksfall
    @pirbo thanks a lot
    Rodrigo Santibáñez
    @glucksfall
    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!
    Pierre Boutillier
    @pirbo
    @glucksfall Congratulation :tada:
    Rodrigo Santibáñez
    @glucksfall
    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.
    Pierre Boutillier
    @pirbo
    It looks like a bug... (or a problem with your path and you launch KaSim instead of KaSim-master) because 4rc1 and master use the same syntax and -syntax 3 is still present in master
    Rodrigo Santibáñez
    @glucksfall
    @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
    Rodrigo Santibáñez
    @glucksfall
    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
    Rodrigo Santibáñez
    @glucksfall
    Ok, I found the answer in the manual (// instead of #)
    Rodrigo Santibáñez
    @glucksfall
    Hello everyone. I have a doubt, is there a way to apply a "continuos" perturbation to the model?
    Pierre Boutillier
    @pirbo
    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 ....
    Rodrigo Santibáñez
    @glucksfall
    I mean a pertubation following a function like a sine or cosine.
    Rodrigo Santibáñez
    @glucksfall
    Sincerely, I had forgotten about the repeat until. Thanks about that. I should get closer to a solution with that.
    Rodrigo Santibáñez
    @glucksfall
    Hello everyone. I'm willing to develop a method to estimate parameter sensibility of a RBM simulated stochastically with KaSim. I'm open to discussion if you have any idea of how I can do that, or aid to develop or test the software.
    I'm developing now a python script and I solved how to call KaSim with subprocess, and parallelize simulations with SLURM and multiprocessing
    Rodrigo Santibáñez
    @glucksfall
    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.
    Pierre Boutillier
    @pirbo
    Nice work!