KaStor documentation

[Erika Herrera]

Hello guys!

I'm Erika, I'm a phd student in cheminformatics. I'm interested in the concept of the Kappa stories. I'm familiar with Kappa, but I'm unsure how to use KaStor and have been unable to find any documentation. I would specifically like to explore KaStor on the command line. 

Could anyone point me in some direction? Thank you in advance :).

[Albin Salazar]

Hi Erika,

Nice to meet you.

I found useful Chapter 5 of this version of the Kappa manual: https://tools.kappalanguage.org/docs/KaSim-manual-4.0.pdf

Also, the work of,

Matthieu et al: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011858

Sébastien et al: https://hal.science/hal-03357485v1/file/abstract-CMSB2021-b.pdf, https://inria.hal.science/hal-03389052/document

Jonathan: https://github.com/jonathan-laurent/KaFlow

have also provided some nice insights when using KaStor for our models.

From my understanding there is still quite a bit of work to do in dealing with large numbers of potential stories (esp. if using counter sites), but maybe others can provide better insights on this.

I recall that a newer version of the Kappa manual is also underway.

Hopefully this provides some direction-- have fun!

Best,

Albin

[Jérôme Feret]

Dear Erika, 

KaStor can be used through KaSim, and this is the easiest way to proceed in command-line. 

1) The intervention TRACK enables the tracking of a pattern : the causal history of any new occurrence of the pattern when the tracking is enabled will be investigated. 

2) The level of compression is tuned with the following directive : 

%def: "displayCompression" "none" "weak" « strong"

Basicaly: « none » will prompt any event that are causality related to the tracked event, without any compression 

                «  weak » will extract a minimal scenario 

               «  strong » will consider agents up to permutation, which induces a lot of computational time, but may reduce the scenario further. 

Examples may be found in the git repository:  tests/integration/cflows 

You may also have a look at the resources of my M2 course (including the slides and some toy examples). 

See Session 4 in https://www.di.ens.fr/~feret/teaching/2024-2025/MPRI.2.19/

Would you need further help, please let us know, or if you have specific development needs. 

Best. 

Jérôme.

[Erika Herrera]

Thank you so much for the answers!!