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INDRA v1.2.0

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@bgyori bgyori released this 10 Jul 21:46
1.2.0
4f143ef

Documentation now available at http:// http://indra.readthedocs.io/

New features:

  • Refactored assemblers module (indra.assemblers) containing PySB, CX, English, IndexCard, Graph and SBGN assemblers
  • Literature module (indra.literature) with PubMed, PMC, Elsevier and CrossRef clients
  • Mechanism linker (indra.mechlinker) to simplify and infer missing links between mechanisms
  • Generalized representation for active forms of proteins (indra.statements.ActiveForm) and activation events (indra.statements.Activation)
  • Representation for Agent cellular location and translocation processes (indra.statements.Translocation)
  • Relevance service from NDEx based on network heat diffusion
  • JSON serialization and deserialization of INDRA Statements (indra.statements.Statement.to_json)

New tools:

  • Ras Machine (models/rasmachine) - a framework for building incrementally updated use case-specific models based on a prior network and new literature as it appears
  • Incremental model (indra.tools.incremental_model) - a class for assembling a model incrementally as new mechanisms become available
  • Gene network (indra.tools.gene_network) - a tool for extracting and assembling a network of known mechanisms given a gene list of interest from the PathwayCommons database and the BEL Large Corpus
  • Executable subnetwork (indra.tools.executable_subnetwork) - a tool for extracting a subnetwork of limited scope from a large set of INDRA Statements and instantiating it as a rule-based executable model
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