Software

Bioagents

 

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
  • ...
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INDRA

 

INDRA (the Integrated Network and Dynamical Reasoning Assembler) assembles information about biochemical mechanisms into a common format that can be used to build several different kinds of explanatory models. Sources of mechanistic information include pathway databases, natural language descriptions of mechanisms by human curators, and findings extracted from the literature by text mining. Mechanistic information from multiple sources is de-duplicated, standardized and assembled into sets of mechanistic Statements with associated evidence. Sets of...

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OpenComet

OpenComet is an open-source software tool providing automated analysis of comet assay images.

OpenComet is a plugin for the image processing program ImageJ. The latest version of OpenComet (v1.3) can be obtained from the Downloads page. Follow the instructions to install and launch OpenComet. OpenComet can analyze a batch of comet assay images, identify the comets and measure their parameters. Refer to the...

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