Skip to content

Home

Jump to bottom
Eugenia Oshurko edited this page May 1, 2020 · 10 revisions

Welcome to the KAMIStudio developer's wiki!

KAMIStudio is a bio-curation environment for modelling cellular signalling implementing the KAMI framework. It is also a part of a larger Kappa project. See a short tool paper.

KAMIStudio is a web-based Python application built using the Flask microframework. Its backend uses the ReGraph and KAMI Python libraries developed in the same project. The above-mentioned libraries use Neo4j database and, in addition, KAMIStudio itself uses MongoDB to store persistently some auxiliary data structures (rules, protein definitions, meta-data of corpora and models).

Its frontend uses d3.js and React JavaScript frameworks. To debug the React-related functionality, you may consider using a browser plugin react developer tools.

KAMIStudio can be installed locally by following the installation instructions here. These instructions allow the user to either install it manually or use a Docker container that can be built using the provided image. The latter option is preferable for the users that don't want to go through the tedious process of installing and configuring Neo4j and MongoDB.

A read-only demo is available at http://kamistudio.ens-lyon.fr/.

Here are some pages that may interest you:

TODO

  • Add a possibility to select seed genes when instantiating a new model (so that we can use only a subset of all protoforms).
  • Add Kappa generation directly from a corpus (see CorpusKappaGenerator in kami.exporters.kappa).
  • Add Kappa initial conditions to the interface (see KappaInitialCondition in kami.exporters.kappa, possibility to specify initial conditions by clicking on the nodes of the action graph, maybe similar to the way new protein definitions are added).
  • Add Kappa observables to the interface (ass in the previous bullet point).
  • Add an interfaces for making queries in KamiQL (see kamiql in the KAMI repository).
Clone this wiki locally