INDRA v1.22.0

Package structure and dependencies

• Protmapper and Gilda version requirements increased, PySB dependency restriction relaxed

Core assembly modules

• Ontology graph represents obsolete ID replacements in indra.ontology
• Improved BioOntology graph which now includes MONDO, ECCODE, and improves OBO hierarchy import to avoid cycles indra.ontology.bio
• Identifier standardization now applies replaced IDs in indra.ontology.standardize
• Refactor preassembler refinement finding to expose more endpoints in indra.preassembler.refinement
• Refinement finding optimized when split index isn used in indra.preassembler.refinement
• Grounding mapping disambiguation additional back-end options in indra.preassembler.grounding_mapper
• Ontology analysis extends to finding cycles indra.tools.analyze_ontology

Statement representation

• Additional functions for JSON (de)serialization of single Statements in indra.statements
• Validation: multiple validators supported, refactored to use classes indra.statements.validate

Knowledge sources

• New API and processor for running the SemRep reading system and processing its outputs indra.sources.semrep
• New API and processor for CREEDS data in indra.sources.creeds
• New API and processor for UbiBrowser in indra.sources.ubibrowser
• New API and processor for the ACSN database in indra.sources.acsn
• BEL processor now uses Selventa IDs instead of names in indra.sources.bel
• Improved identifier extraction from BioPAX in indra.sources.biopax
• Eidos reader/CLI updated to work with the latest Eidos version in indra.sources.eidos
• Improved HPRD API with option to process compressed archive directly in indra.sources.hprd
• MINERVA client improved to process latest project automatically in indra.sources.minerva
• Improved OmniPath processing to decouple evidences among Statements in indra.sources.omnipath
• Streamlined RLIMS-P API with improved identifier extraction in indra.sources.rlimsp
• SIGNOR processor is now compatible with latest data format indra.sources.signor

Model assemblers

• Refactored (more options, better consistency) styling for the HTML Assembler in indra.assemblers.html
• New option in IndraNetAssembler to represent self loops indra.assemblers.indranet

Model analysis

• Additional options added to ModelChecker to control explanation paths indra.explanation.model_checker

Tools

• Additional cases handled in validity fixing of identifiers indra.tools.fix_invalidities

Resources and database clients

• New client to access Bioregistry content in indra.databases.bioregistry_client
• New client to access the Expasy enzyme (EC code) database in indra.databases.ec_client
• New client to interact with the Biolookup web service in indra.databases.biolookup_client
• Extended HGNC client to provide enzyme code mappings for genes in indra.databases.hgnc_client
• Extended MeSH client to access CAS mappings for compounds indra.databases.mesh_client
• New client to interact with MONDO diseases indra.databases.mondo_client
• Extended OBO client allowing access to more ontologies indra.databases.obo_client
• Extended PubChem client with additional functionalities indra.databases.pubchem_client
• Multiple resource files updated including for Biomappings, ChEBI, FamPlex, HGNC,
  identifiers.org, MeSH, and Selventa entries

Literature clients

• PubMed client extended to provide substance-specific publications indra.literature.pubmed_client
• New client to access COCI data from OpenCitations in indra.literature.coci_client

INDRA v1.21.0

Package structure and dependencies

• Multiple modules for the world modeling use case separated out into the INDRA World package (https://github.com/indralab/indra_world). For the specific modules affected, see #1278 and #1283.
• rdflib is no longer a requirement.
• Increased protmapper version (0.0.22) with updated protein resources.

Core assembly modules

• Multiple updates to the INDRA BioOntology (version incremented from 1.12 to 1.18) including adding entity types for nodes, UniProt-Entrez mappings for non-human proteins, chemical family relations from LSPCI in indra.ontology.bio.
• Belief engine significantly refactored to allow more flexibility in statement scoring in indra.belief.
• New belief scorer module added which learns and applies scorers using sklearn models based on curation data in indra.belief.skl.

Statement representation

• Improved statement validation checking and exception messages in indra.statements.validate.

Knowledge sources

• New input API and processor for the GNBR reading system in indra.sources.gnbr.
• INDRA DB client module in indra.sources.indra_db_rest significantly refactored with changes to the API, improved control over e.g., limits and logging, and a new query module in indra.sources.indra_db_rest.query to allow complex query construction.
• Improved evidence extraction for CrOG in indra.sources.crog.
• Improved processing of statement polarities from CTD in indra.sources.ctd.

Model assemblers

• Improved hub layout generation for CX networks in indra.assemblers.cx.
• HtmlAssembler extended to generate links out for database sources, display belief badges, and improve knowledge source badges in indra.assemblers.html.
• IndraNet assembler extended to provide better aggregation logic for
  Statements into network edges in indra.assemblers.indranet.
• PyBEL assembler extended to include additional annotations on edges in indra.assemblers.pybel.

Tools

• Assemble corpus extended with mechanism linking functions in indra.tools.assemble_corpus.
• Validity fixing tools indra.tools.fix_invalidities.

Resources and database clients

• Expose GO namespaces for terms in indra.databases.go_client.
• Expose locus types in HGNC client in indra.databases.hgnc_client.
• Improved prefix/id format handling in identifiers.org client indra.databases.identifiers.
• New Infectious Disease Ontology client in indra.databases.ido_client.
• MeSH client extended to provide supplementary concept mappings to primary terms and tree numbers for supplementary concepts in indra.databases.mesh_client.
• New client for ingesting OWL ontologies in indra.databases.owl_client and corresponding refactoring OBO client in indra.databases.obo_client.
• Resource file content updates for FamPlex, HGNC and MeSH.

INDRA v1.20.0

Package structure and dependencies

• INDRA is now tested with Python 3.9 (supports 3.6-3.9).
• Increased protmapper version (0.0.21) with updated protein resources.
• Moved out deprecated evaluation scripts (#1283).

Core assembly modules

• Preassembler refactored to support refinement filter classes to enable incremental assembly indra.preassembler.
• Belief engine refactored to support incremental assembly indra.belief.
• New function to get standard Agent from name and references in indra.ontology.standardize.
• Support for intermediate node annotations and local file parsing in YAML ontology indra.ontology.world.
• INDRA BioOntology updated from v1.7 to v1.12 with bug fixes and resource updates indra.ontology.bio.
• New function to re-map DB refs within the same namespace in indra.tools.assemble_corpus.

Statement representation

• New pretty print and statement statistics functions in indra.statements.io.
• Fixes related to refinement finding and hash calculation in indra.statements.
• Fixed refinement finding for multiple agents with the same name in bound conditions indra.statements.agent.

Knowledge sources

• New API and processor for the Drug Gene Interaction (DGI) database at indra.sources.dgi.
• New API and processor for the Chemical Roles Graph (CRoG) at indra.sources.crog.
• New API and processor for MINERVA models at indra.sources.minerva.
• New function to process a single BEL statement string in indra.sources.bel.
• Improved chemical grounding in BioPAX processor indra.sources.biopax.
• New process from web function for DrugBank indra.sources.drugbank.
• EidosBioProcessor refactored into a separate class indra.sources.eidos.
• Eidos processor allows using custom grounder when processing into bio statements indra.sources.eidos.bio_processor.
• New feature to turn Statements into Hypothes.is annotations and upload them in indra.sources.hypothesis.
• Support for processing BEL script annotations from Hypothes.is in indra.sources.hypothesis.
• New processor to process remote INDRA JSON files indra.sources.utils.

Model assemblers

• Statement presentation refactored to support custom grouping and sorting indra.util.statement_presentation.
• HTML assembler builds on new statement presentation to support custom sorting indra.assemblers.html.
• IndraNet assembler supports adding extra columns/properties to the output indra.assemblers.indranet.
• PySB assembler allows reverse-engineering Agents from an assembled model indra.assemblers.pysb.

Model analysis / explanation

• INDRA is now compatible with Kappy 4.1.2 (which changes the contact map format).
• New Kappa contact map analysis to diagnose cycles in indra.assemblers.pysb.kappa_util.
• New NodeContainer class for model checking to carry node annotations in indra.explanation.model_checker.
• Support for custom edge filters in path finding in indra.explanation.path_finding.
• Support for reporting refinement edges in path finding in indra.explanation.reporting.

Tools

• New tool to upload annotations to Hypothes.is from INDRA Statements in indra.tools.hypothesis_annotator.

Resources and database clients

• Resource updates to Biomappings, ChEBI and EFO resources.
• Many new grounding curations added to grounding resources (mappings, misgrounding, ignores).
• Better handling for external namespaces in the OBO client indra.databases.obo_client.

Literature clients

• The DART client was moved into the INDRA World package.
• New function to get titles for PMC articles in indra.literature.pmc_client.

INDRA v1.19.0

Package structure and dependencies

• Setup adjusted to require newer versions of PyBEL (0.15), PyBioPax (0.0.5), and Protmapper (0.0.19).
• Automated testing has been migrated from Travis CI to Github Actions.

Core assembly modules

• The statement refinement finding algorithm has been reimplemented for a speedup of multiple orders of magnitude depending on application in indra.preassembler.
• The Preassembler now supports a series of user-supplied filter functions to speed up refinement finding in a use case-specific way in indra.preassembler.
• The BioOntology's version has increased to 1.7 with many resource updates and new sources (e.g., Biomappings included in indra.ontology.
• The IndraOntology no longer contains connected component labels (faster initialization and loading), in indra.ontology.
• The grounding disambiguation code is refactored with improved prioritization in indra.preassembler.grounding_mapper.
• Grounding disambiguation has been refactored into a separate module in indra.preassembler.grounding_mapper.disambiguate.
• New Statement validation module for automated consistency checks of Statements, Agents, and their attributes in indra.statements.validate.
• Improvements to WorldOntology extension during runtime in indra.ontology.world.

Knowledge sources

• Structured meta-information on INDRA's sources is now available as a resource file in indra/resources/source_info.json.
• The deprecated LINCS Small Molecules (indra.sources.lincs_drug) source module has been removed; replaced by TAS in indra.sources.tas.
• The BEL processor is now compatible with PyBEL 0.15+ in indra.sources.bel.
• Updaed BioGRID processor, more extractions and compatibility with the TAB 3.0 format in indra.sources.biogrid.
• Improvements to BioPAX processing to support e.g., BioPAX from Reactome in indra.sources.biopax.
• Support for compositional grounding from the CWMS, Eidos, Sofia, and Hume readers.
• Support for event type filter for the CWMS, Eidos, Sofia, and Hume readers.
• Grounding cache feature added for re-grounding in indra.sources.eidos.
• Support for using obtained evidence counts in INDRA DB REST client and HTML assembler.
• Support for specifying organism priority for protein grounding in Reach processor in indra.sources.reach.
• Handle protein chain/fragment grounding in Reach processor in indra.sources.reach.
• Improvements to extracting some forms of regulation in Reach processor in indra.sources.reach
• Many improvements to Signor processor in indra.sources.signor.
• New EKB forms extracted in TRIPS processor indra.sources.trips.

Model assemblers

• New HTML look implemented (with support for old/simplified view) in the HTML Assembler in indra.assemblers.html.

Model analysis / explanation

• Many new path finding algorithms implemented in indra.explanation.pathfinding.
• Support for semantic filters on paths implemented for model checking in indra.explanation.model_checker.

Resources and database clients

• indra.resources is now a proper module with helper functions to load resource files.
• New client for interacting with identifiers.org namespaces, IDs and URLs in indra.databases.identifiers.
• Many resources have been updated (e.g., HGNC entries, FamPlex, new grounding mappings) in indra.resources.

Literature clients

• Better MeSH annotation extraction, including supplementary concepts in PubMed client indra.literature.pubmed_client.
• Local storage feature for DART client in indra.literature.dart_client.

INDRA v1.18.0

Package structure and dependencies

• Starting with this release, INDRA supports Python 3.6+ only.
• The live curation service for the World Modelers use case is now in a separate repository at https://github.com/indralab/indra_wm_service.
• New dependencies for this release include obonet, tqdm and pybiopax.
• Pyjnius is no longer a necessary requirement for any INDRA module (though it can still be optionally used for local JAR-based reading with Eidos and Reach).

Core assembly modules

• A major change in the current release is the introduction of the indra.ontology module which replaces the indra.preassembler.hierarchy_manager module, for more details, see #1100.
• New BioOntology at indra.ontology.bio which implements naming, identifier mapping and hierarchical relationships among 2.1 million relevant entities (up from 250k in the previous release). The BioOntology also subsumes the old cellular component hierarchy, activity hierarchy, and modification hierarchy, which has now been removed.
• New WorldOntology at indra.ontology.world which replaces multiple reader-specific ontologies for the WorldModelers use case.
• New ontology web service in indra.ontology.app which allows using the IndraOntology as a service for ID mapping, isa/partof queries, name lookups, etc.
• New VirtualOntology indra.ontology.virtual which acts as a client for the ontology web service.
• The name standardization and grounding standardization code has been reimplemented to use the IndraOntology, and is now under the indra.ontology.standardize module with significantly extended mapping capabilities, and many new functions.
• The Preassembler has been adapted to use the IndraOntology and is extended with new options in indra.preassembler.
• The indra.preassembler.ontology_mapper module along with a host of other scripts for making hierarchies (all replaced by the new IndraOntology) have been deprecated and removed.
• Improved grounding mapping and disambiguation logic when multiple texts are available for an agent in indra.preassembler.grounding_mapper.
• Many extensions to grounding mapping resources in indra.resources.grounding.
• Bug fixes in indra.pipeline for handling some corner cases.

Knowledge sources

• With the relase of PyBioPAX (https://github.com/indralab/pybiopax), the BioPAX processor has been fully reimplemented, and is now a pure-Python module that no longer requires pyjnius to operate. See indra.sources.biopax.
• New API and processor for the Comparative Toxicogenomics Database (CTD) at indra.sources.ctd.
• Improved extraction of grounding from PyBEL models in indra.sources.bel.
• New API and processor for the DrugBank database at indra.sources.drugbank.
• New API and processor for the OmniPath web service at indra.sources.omnipath.
• New API and processor for Biofactoid at indra.sources.biofactoid.
• Overhauled API and processor for the Target Affinity Spectrum in indra.sources.tas with significantly extended content and improved naming and grounding.
• The BEL RDF processor has been deprecated and removed with the PyBEL processor continuing to serve as the entrypoint for processing BEL content in indra.sources.bel.
• Multiple new biology-oriented endpoints in the Eidos API in indra.sources.eidos.
• The CWMS RDF processor has been removed in factor of the EKB/XML processor which continues to operate at indra.sources.cwms.

Model assemblers

• Extended support for knowledge sources and simplified support for evidence count and source count annotations in the HtmlAssembler in indra.assemblers.html. There are also several bug fixes in handling some statement types in this module, as well as improved links out to literature content.
• Extended support for knowledge source annotations in the CX assembler in indra.assemblers.cx.
• Handling negative modification conditions in the EnglishAssembler indra.assemblers.english.
• Improved signed graph assembly from BEL graphs in indra.assemblers.pybel.

Model analysis / explanation

• New dedicated module for causal path finding methods in indra.explanation.pathfinding.
• Generalized and improved statement checking in all submodules of indra.explanation.model_checker
  with support for open-ended search.

Resources and database clients

• New Taxonomy client in indra.databases.taxonomy_client
• New DrugBank client in indra.databases.drugbank_client
• Reimplemented ChEBI client based on OBO in indra.databases.chebi_client.
• Extended ChEBML client with naming information in indra.databases.chembl_client.
• Extended LINCS client with more naming and mapping information in indra.databases.lincs_client.
• The BioGRID client has been removed from indra.databases.biogrid_client since it has become redundant with indra.sources.biogrid.
• Support for the PubChem JSON web service endpoint in indra.databases.pubchem_client.
• The network relevance client has been removed from indra.databases.relevance_client since it relied on a web service that is no longer operational.
• Many extensions to mapping and naming resources, in particular for chemicals.

Literature clients

• New client for the DART document infrastructure used in the World Modelers use case in indra.literature.dart.
• Better search by MeSH terms in the PubMed client in indra.literature.pubmed_client.

REST API

• The INDRA REST API has been completely reimplemented in a new framework, and has been extended significantly in its functionalities. It also comes with improved Swagger documentation with a public instance
  running at http://api.indra.bio:8000.

INDRA v1.17.0

Package structure and dependencies

• The high-throughput reading tools in indra.tools.reading have been
  moved into an independent repository at
  https://github.com/indralab/indra_reading.
• The obonet package is now a required dependency.

Input processors

• New VirHostNet API and processor in indra.sources.virhostnet.
• New Hypothes.is API and processor allowing processing
  annotations into INDRA Statements in indra.sources.hypothesis.
• Integrated new version of Sparser reader with improved and adapted
  processor in indra.sources.sparser.
• Refactored Eidos API into separate reader, client and server with
  significantly extended usage instructions in indra.sources.eidos.
• New endpoints in Eidos API implementing biology-oriented processing, as
  well as regrounding with respect to a user-supplied ontology in
  indra.sources.eidos.
• Overhauled Reach API supporting the latest Reach version and prioritizing
  using Reach as a (local) web service over JAR-based reading
  in indra.sources.reach, also with significantly extended usage
  instructions.
• Support for extracting Conversion statements from Reach output in
  indra.sources.reach.
• ISI reader processor in indra.sources.isi no longer requires a Python 2
  runtime and the separate nxml2text tool.
• Updated RLIMS-P API in indra.sources.rlimsp to work with latest web service at
  https://research.bioinformatics.udel.edu/itextmine/api/data/rlims/.

Resources and clients

• Overhauled GO resources and client to be based on OBO in
  indra.databases.go_client.
• MeSH tree numbers, isa relationships and determination of
  subtree implemented in indra.databases.mesh_client.
• Extended mappings added between MeSH and GO, ChEBI, EFO, DOID, HP.
• All resource files updated to latest version in indra.resources.

Core assembly modules

• New Pipeline module in indra.pipeline allowing building
  and running custom assembly pipelines programmatically or from a JSON file.
• UniProt protein features and EFO, DOID, HP ontologies
  integrated with name/grounding standardization.
• Overhauled integration of Gilda (https://github.com/indralab/gilda) with
  indra.preassembler.grounding_mapper allowing selective re-grounding
  of statements as well as disambiguation.
• New one-statement-per-line JSON output mode in indra.statements.io to
  support streaming large INDRA Statement JSONs.

Literature

• New bioRxiv/medRxiv client to monitor collections and download PDF/XML/text
  content in indra.literature.biorxiv_client.
• Significantly improved text extraction from PMC NXML in
  indra.literature.pmc_client.

Output assemblers

• Refactoried English assembler to allow keeping track of
  entity coordinates within each assembled sentence in
  indra.assemblers.english.
• Improved construction of entity links in HTML assembler
  in indra.assemblers.html.
• More annotations propagated into PyBEL graph in
  indra.assemblers.pybel.
• Made the upload and update of CX networks more robust in
  indra.assemblers.cx.

Explanation

• Improvements to finding all paths of a given length in
  indra.explanation.

Tools

• Refactored LiveCuration service into a separate module in
  indra.tools.live_curation.
• Updated outdated assembly approach in GeneNetwork tool in
  indra.tools.gene_network.

Other

• Updated and extended README, usage examples and tutorials.

INDRA v1.16.0

Input processors

• New PhosphoELM API and processor in indra.sources.phosphoelm.
• PyBEL API and processor updated for PyBEL 0.14 compatibility in indra.sources.bel.
• Improvements in regrounding approach with Eidos in indra.sources.eidos.
• Bug fixes to offline reading via the REACH API in indra.sources.reach.
• Refactor ISI reader API and processor for containerization in indra.sources.isi.

Core assembly modules

• Full integration of Gilda disambiguation with grounding mapper both as
  a package and a web service in indra.preassembler.grounding_mapper.
• Refactor grounding mapper module to separate out standardization functions
  in indra.preassembler.grounding_mapper.standardize.

Output assemblers

• Many improvements to the HTML assembler including refactoring,
  improved grouping and heading generation, and support Influences in
  indra.assemblers.html.
• Improvements to grounding and introduction of part_of relations in
  PyBEL assembler in indra.assemblers.pybel.

Resources

• Integrate a set of known MeSH to GO mappings.

Explanation

• Improvements to reporting paths in the explanation module in
  indra.explanation.

Tools

• Many new features in the Live curation, including actively loading
  and saving corpora on S3 in indra.tools.live_curation.
• Add new high-throughput reader management for ISI and TRIPS readers
  in indra.tools.reading
• Significant refactoring of indra.tools.reading to separate reader
  classes and improve containerization.

INDRA v1.15.2

Package structure

• Remove the top-level data folder from version control (not part of package)
• Make INDRA compatible with networkx 2.4 (which removed several deprecated
  features).

Input processors

• Refactoring of the BEL input API in indra.sources.bel.
  Access to Selventa corpora is now via https://github.com/cthoyt/selventa-knowledge.
• Multitude of improvements to the CWMS processor in indra.sources.cwms,
  including extracting migration events.
• Refactoring of INDRA DB REST API in indra.sources.indra_db_rest to use
  a class-based processor structure for all endpoints.
• Add Gilda grounding option to the ISI reader in indra.sources.isi.

Core assembly modules

• Normalization across equivalent and opposite concepts in indra.preassembler
  based on an ontology.
• Improved custom preassembly functions for location and time matching in
  indra.preassembler.custom_preassembly.
• Preliminary integration of a Gilda client with Grounding mapper in
  indra.preassembler.grounding_mapper.gilda.

Output assemblers

• Improved headings and grounding display in the HTML assembler in
  indra.assemblers.html.
• Generalize INDRA Net assembler to causal influences and associations in
  indra.assemblers.indranet.
• Make PySB assembler compatible with PySB 1.9 in indra.assemblers.pysb.

Resources

• Integrate new WorldModelers ontologies with INDRA in
  indra.preassembler.make_wm_ontologies.
• Updates to FamPlex and other grounding resources.

INDRA v1.14.1

Representation

• New MovementContext class to represent movement time/places for Events
• New QuantitativeState class to represent specific quantities associated with Events

Input sources

• Support for extracting Migration statements from CWMS in indra.sources.cwms
• Adaptation to changes in Eidos API and output format in indra.sources.eidos
• Adaptation to changes in Hume API and output format in indra.sources.hume
• Custom processor for migration tables in indra.sources.eidos.migration_table_processor
• Support for representing source counts in INDRA DB REST in indra.sources.indra_db_res

Internal assembly

• Significantly improved and generalized DB refs name standardization, and preassembly matching/refinement for all entities including chemicals and biological processes
• New custom matches/refinement function feature in Preassembler in indra.preassembler and BeliefEngine in indra.belief
• Support for new World Modelers ontology
• Grounding mapper refactored with new misgrounding map functionality in indra.preassembler.grounding_mapper

Model assemblers

• New IndraNet assembler to assemble custom networks for path finding in indra.assemblers.indranet
• New NiceCxAssembler for streamlined CX network assembly in indra.assemblers.cx
• Significantly improved HTML assembler with source count badges and support for templates indra.assemblers.html
• Refactored index card assembler with extended metadata support in indra.assemblers.index_card

Database/literature clients

• New PubChem client in indra.databases.pubchem_client
• New miRBase client in indra.databases.mirbase_client
• New Experimental Factor Ontology (EFO) client in indra.databases.efo_client
• New Phenotype Ontology (HP) client in indra.databases.hp_client
• New Disease Ontology (DOID) client in indra.databases.doid_client
• New mapping functionalities in HGNC, MeSH and ChEBI clients
• ScienceDirect search feature added in Elsevier client in indra.literature.elsevier_client
• Additional article info extraction and support for getting MeSH annotations in PubMed client in indra.literature.pubmed_client.

Model analysis

• Refactored ModelChecker with four new subclasses for analysis of specific model/network types in indra.explanation

Tools

• S3 corpus upload feature in LiveCuration tool in indra.tools.live_curation

INDRA v1.13.0

Representation

• INDRA Events introduced as arguments of Influences or as standalone statements
• Influence statements are no longer derived from IncreaseAmount
• New object model for representing Delta/QualitativeDelta in Events

Input processors

• Support for standalone Events and Migration events extracted from CWMS in indra.sources.cwms
• Support for extracting standalone Events from Eidos in indra.sources.eidos
• Support for extracting standalone Events from Hume in indra.sources.hume
• Support for extracting standalone Events from Sofia in indra.sources.sofia

Database/Literature clients

• Support for determining type of gene in indra.databases.hgnc_client
• Support for mapping outdated gene names to current ones in indra.databases.hgnc_client
• Improved extraction of text from Elsevier XMLs in indra.literature.elsevier_client
• Additional annotations and metadata extraction support in indra.literature.pubmed_client

Dependencies

• Use Open JDK instead of Oracle JDK with pyjnius
• deft renamed to adeft

Assemblers

• All relevant assemblers adapted to new Influence/Event/Concept representation
• Support for generating Kappa influence and contact maps in PySB assembler in indra.assemblers.pysb
• Support for Influence statements in CX assembler in indra.assemblers.cx

Model analysis

• Additional logic in ModelChecker for Kappa influence map pruning in indra.explanation.model_checker

Reading tools

• Refactoring of AWS-based reading tools