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Biological reasoning agents

A collection of agents for biological reasoning in a communication system. The following agents are currently available:

  • MRA (Mechanistic Reasoning Agent): The MRA uses INDRA to construct mechanistic models of biochemical systems from user input, publications and databases. It can also propose changes to model structure autonomously.
  • TRA (Temporal Reasoning Agent): The TRA executes dynamical models built by the MRA under variable experimental conditions and verifies whether the dynamics meets a given temporal pattern
  • DTDA (Disease, Target and Drug Agent): The DTDA's task is to search for targets known to be implicated in a disease and to look for drugs that are known to affect that target.

KQML messaging classes used by the agents are available at: https://github.com/bgyori/pykqml

Installing the bioagents

Note that currently the bioagents have limited usage on their own. They are meant to be launched in the context of a communication system.

The bioagents depend on the following non-default python packages: objectpath, rdflib, functools32, requests, lxml, pandas.

The MRA uses INDRA to assemble models based on a natural language description of mechanisms. Please follow the more detailed instructions on the INDRA page to install it and its dependencies:

pip install git+https://github.com/sorgerlab/indra.git

INDRA depends on PySB, which is best installed from Github:

pip install git+https://github.com/pysb/pysb.git

PySB depends on BioNetGen. Make sure that BioNetGen is unzipped into /usr/local/share/BioNetGen, such that BNG2.pl is located at /usr/local/share/BioNetGen/BNG2.pl. Alternatively, set BNGPATH to the folder in which BNG2.pl is.