INDRA v1.4.1

Bug fixes and improvements in

• CyJS, CX, English and PySB Assemblers
• BioPAX, REACH and TRIPS Processors
• GeneNetwork tool and the SiteMapper
• The RAS Machine

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

INDRA v1.3.0

New features:

• Python 3 support in addition to maintaining compatibility with Python 2
• Universal handling of unicode within INDRA
• Bioentities added as a submodule as a basis for entity hierarchies (for protein family and complex relationships)
• Resources for performing high-throughput literature reading (indra.tools.reading) with Amazon cluster support
• Belief Engine (indra.belief) applies belief propagation based on evidence from multiple sources to score the believability of INDRA Statements
• Grounding Mapper (indra.preassembler.grounding_mapper) fixes named entity grounding to databases based on a use case specific mapping table
• New output assemblers added: SIF assembler (indra.assemblers.sif_assembler), Index Card assembler (indra.assemblers.index_card_assembler)
• Index Card processor as an input source (indra.index_cards)
• Several benchmarks are now available in indra.benchmarks

INDRA v1.2.0

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

1.1.1

New features:

• Site mapper for the preassembler
• CX assembler for visualization in Cytoscape and NDEx

Fixes:

• Resource files are now within the module
• Installation via setup.py now excludes jnius, which has to be manually installed
• Some fixes in the BioPAX processor