emmaa 1.1.0

Ecosystem of Machine-maintained Models with Automated Analysis

# EMMAA EMMAA is an Ecosystem of Machine-maintained Models with Automated Analysis.

## Documentation For a detailed documentation of EMMA, visit http://emmaa.readthedocs.io

## Concept The main idea behind EMMAA is to create a set of computational models that are kept up-to-date using automated machine reading, knowledge-assembly, and model generation. Each model starts with a prior network of relevant concepts connected through a set of known mechanisms. This set of mechanisms is then extended by reading literature or other sources of information each day, determining how new information relates to the existing model, and then updating the model with the new information.

Models are also available for automated analysis in which relevant queries that fall within the scope of each model can be automatically mapped to structural and dynamical analysis procedures on the model. This allows recognizing and reporting changes to the model that result in meaningful changes to analysis results.

## Applications The primary application area of EMMAA is the molecular biology of cancer, however, it can be applied to other domains that the INDRA system and the reading systems integrated with INDRA can handle.

## Installation The primary dependency of EMMAA is INDRA which can be installed using pip. Depending on the application, third-party dependencies of INDRA may need to be installed and configured separately.

## Funding The development of EMMAA is funded under the DARPA Automating Scientific Knowledge Extraction (ASKE) program.