The Kappa project involves several major satellite efforts.
The challenge of building models of complex biomolecular systems necessitates an intermediate stage to bridge between the biophysically and biochemically grounded descriptions in papers and databases on the one hand and the ungrounded abstract language of Kappa on the other. This intermediate staging area is a knowledge representation that enables the user-driven aggregation of nuggets encapsulating mechanistic information pertaining to protein-protein interactions, the visualization of their interrelations, identification of conflicts, etc. In essence, it aims at being the biologically grounded model the user reasons about. This model is then compiled into Kappa for execution. From this perspective, Kappa is seen as an "assembler" code rather than the primary language for building a model in the first place.
KAMI stands for Knowledge Aggregator and Model Instantiator. It is an ongoing development led by Russ Harmer at ENS Lyon. KAMI poses interesting challenges in knowledge representation and multi-level graph rewriting.
Visualization is of paramount importance when navigating and reasoning about complex interaction systems. Some of the visualization integrated in the Kappa UI has been developed in the Creative Coding Lab of Angus Forbes.
A major challenge is the visualization of networks that change dynamically. The Kappa simulator can track the dynamically evolving influences that rules exert on each other, yielding a Dynamic Influence Network (DIN). The Forbes group has developed an interactive visualization of the DIN. It currently requires a two-stage approach whereby a user first generates a zipped-up series of DIN matrices using KaSim and then uploads the zip-file to the DIN visualizer. In the future we hope to seamlessly integrate the Kappa UI with the DIN.
A wrapper kappy exposes the Kappa simulator API providing access to KaSim capabilities in Python scripts. It can be installed through the Python package manager with pip install kappy.
Several tools are not yet ready for preview. Most important among them is a nifty event trace analysis tool and a so-called co-simulator for counterfactual simulation. We will update these pages as soon as these tools are ready for prime time.
Pretty printing Kappa expressions in LaTeX
For LaTeX printing of Kappa code, there is a language definition for the listings package available here, and a demo texfile here.
For archaeologists, here is the source code of previous Kappa implementations.