INDRA v1.4.0

Representation features:

• RegulateAmount (to represent synthesis/transcription, degradation) INDRA Statements collected from inputs and assembled into models
• RegulateActivity INDRA Statements now generalize activation/inhibition
• New subclasses of Modification INDRA Statements
• Bioentities extended and is mapped to in INDRA input processors

Input processors:

• BEL processor extracts indirect Statements
• New API and processor for Sparser NLP system in indra.sparser
• Various improvements in all existing input processors

Output assemblers:

• Cytoscape JS assembler
• PySB assembler generalized and extended with PysbPreassembler
• Various extensions in all existing output assemblers

Core assembly modules:

• Improved and generalized BeliefEngine implementation in indra.belief
• Improved, generalized and extended MechLinker implementation in indra.mechlinker
• Optimized Preassembler in indra.preassembler with multiprocessing option

Tools:

• Assemble corpus tool in indra.tools.assemble_corpus exposes all assembly functionalities and adds many Statement filters
• Model Checker in indra.tools.model_checker verifies executable models with respect to observations represented as indirect INDRA Statements
• Expand family tool in indra.tools.expand_families using Bioentities relationships
• Improved high-throughput reading tools in indra.tools.reading

Other:

• REST API exposing main INDRA functionalities as a web service
• New example models in models
• Extended documentation and tutorials in doc