Library for rule-based meta-modelling in cellular signalling
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README.md

KAMI: Knowledge Aggregator and Model Instantiator

KAMI: Knowledge Aggregator and Model Instantiator is a semi-automatic bio-curation platform which provides a user with tools for gradual aggregation of biological facts about individual protein- protein interactions of different provenance, their annotation, visualisation and further instantiation for building rule-based models of concrete systems and performing hypothesis testing.

About project

The platform allows to input annotated biological facts through the graphical interface or pro- grammatically through the API. The input facts can be automatically merged with an existing model in a context-dependent manner (the knowledge present in the model influences the way these facts are interpreted and, therefore, merged with the model). The model itself is a graph hierarchy (an instance of ReGraph’s core data structure). Apart from the user input knowledge, the hierarchy con- tains expert knowledge used by KAMI for the interpretation of interactions, for example, definitions of protein families, protein variants definitions, the semantics of particular protein domains. This expert knowledge is obtained from both publicly available data (such as UniProt, Pfam, InterPro databases) and from collaboration with biologists. From the knowledge aggregated by a user in the hierarchy, KAMI allows to automatically instantiate models expressed with Kappa rules and perform simulations with KaSim.

Configuration

KAMI Hierarchy

Imports from other formats

INDRA

Exports to other formats

Kappa

INDRA

KAMI Gui

The RegraphGui is a javascript library for Regraph Hierarchy can be added, edited, merged and removed. The UI is dumb : due to the current implementation of regraph, it reload the whole graph or hierarchy on each update. This UI is autonomus and only need itself to work.... and a regraph server.

Configuration

To configure the ui, simply edit the index.js file. Change the server url and if needed the root node name.

Usage

Top tab allow hierachy navigation and loading,adding and exporting graph or hierarchy. to select a graph, click on its name, to go inside it, double click on its name. to go back, select another level in the hierarchy selector on the right

The side menu allow to remove selected graph and all the hierarchy behind. It also allow graph merging using matching : (beta format).

The main div contain the graph associated with the selected tab. This graph can be edited with right click The ui can be zoomed and dragged with mousewheel Nodes and edges are editable. some node edition require to select other nodes : to do so : shift click on it. To lock or unlock a node : ctrl click on it. The main graph is associated with a force simulator witch is reseted at each graph modification.