LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
doc/Makefile
doc/conf.py
doc/getting_started.rst
doc/index.rst
doc/indra_logo.png
doc/installation.rst
doc/license.rst
doc/make.bat
doc/requirements.txt
doc/rest_api.rst
doc/ext/citations.py
doc/images/assembly.png
doc/images/example_graph.png
doc/modules/index.rst
doc/modules/pipeline.rst
doc/modules/resources.rst
doc/modules/statements.rst
doc/modules/assemblers/bmi_wrapper.rst
doc/modules/assemblers/cx_assembler.rst
doc/modules/assemblers/cyjs_assembler.rst
doc/modules/assemblers/english_assembler.rst
doc/modules/assemblers/graph_assembler.rst
doc/modules/assemblers/html_assembler.rst
doc/modules/assemblers/index.rst
doc/modules/assemblers/index_card_assembler.rst
doc/modules/assemblers/indranet_assembler.rst
doc/modules/assemblers/kami_assembler.rst
doc/modules/assemblers/pybel_assembler.rst
doc/modules/assemblers/pysb_assembler.rst
doc/modules/assemblers/sbgn_assembler.rst
doc/modules/assemblers/sif_assembler.rst
doc/modules/assemblers/tsv_assembler.rst
doc/modules/belief/belief_engine.rst
doc/modules/belief/index.rst
doc/modules/belief/skl_belief.rst
doc/modules/databases/index.rst
doc/modules/explanation/index.rst
doc/modules/explanation/model_checker.rst
doc/modules/explanation/pathfinding.rst
doc/modules/explanation/reporting.rst
doc/modules/literature/index.rst
doc/modules/mechlinker/index.rst
doc/modules/ontology/bio_ontology.rst
doc/modules/ontology/index.rst
doc/modules/ontology/ontology.rst
doc/modules/ontology/ontology_service.rst
doc/modules/ontology/standardize.rst
doc/modules/ontology/virtual_ontology.rst
doc/modules/preassembler/grounding_mapper.rst
doc/modules/preassembler/index.rst
doc/modules/preassembler/preassembler.rst
doc/modules/preassembler/site_mapper.rst
doc/modules/sources/index.rst
doc/modules/sources/trrust.rst
doc/modules/sources/bel/index.rst
doc/modules/sources/biofactoid/index.rst
doc/modules/sources/biogrid/index.rst
doc/modules/sources/biopax/index.rst
doc/modules/sources/crog/index.rst
doc/modules/sources/ctd/index.rst
doc/modules/sources/dgi/index.rst
doc/modules/sources/drugbank/index.rst
doc/modules/sources/eidos/index.rst
doc/modules/sources/geneways/index.rst
doc/modules/sources/gnbr/index.rst
doc/modules/sources/hprd/index.rst
doc/modules/sources/hypothesis/index.rst
doc/modules/sources/indra_db_rest/index.rst
doc/modules/sources/isi/index.rst
doc/modules/sources/medscan/index.rst
doc/modules/sources/minerva/index.rst
doc/modules/sources/ndex_cx/index.rst
doc/modules/sources/omnipath/index.rst
doc/modules/sources/phosphoelm/index.rst
doc/modules/sources/reach/index.rst
doc/modules/sources/rlimsp/index.rst
doc/modules/sources/signor/index.rst
doc/modules/sources/sparser/index.rst
doc/modules/sources/tas/index.rst
doc/modules/sources/tees/index.rst
doc/modules/sources/trips/index.rst
doc/modules/sources/virhostnet/index.rst
doc/modules/tools/index.rst
doc/modules/util/index.rst
doc/tutorials/gene_network.rst
doc/tutorials/html_curation.rst
doc/tutorials/index.rst
doc/tutorials/nl_modeling.rst
doc/tutorials/images/apikey_curatorID.png
doc/tutorials/images/bad_submission.png
doc/tutorials/images/curation_row_created_circled.png
doc/tutorials/images/curation_select_error_circled.png
doc/tutorials/images/curation_submit_circled.png
doc/tutorials/images/curation_submitted_successfully.png
indra/__init__.py
indra/config.py
indra/java_vm.py
indra.egg-info/PKG-INFO
indra.egg-info/SOURCES.txt
indra.egg-info/dependency_links.txt
indra.egg-info/entry_points.txt
indra.egg-info/requires.txt
indra.egg-info/top_level.txt
indra/assemblers/__init__.py
indra/assemblers/cx/__init__.py
indra/assemblers/cx/assembler.py
indra/assemblers/cx/hub_layout.py
indra/assemblers/cyjs/__init__.py
indra/assemblers/cyjs/assembler.py
indra/assemblers/english/__init__.py
indra/assemblers/english/assembler.py
indra/assemblers/graph/__init__.py
indra/assemblers/graph/assembler.py
indra/assemblers/html/__init__.py
indra/assemblers/html/assembler.py
indra/assemblers/html/templates/indra/statements_view.html
indra/assemblers/html/templates/indra/template.html
indra/assemblers/index_card/__init__.py
indra/assemblers/index_card/assembler.py
indra/assemblers/indranet/__init__.py
indra/assemblers/indranet/assembler.py
indra/assemblers/indranet/net.py
indra/assemblers/kami/__init__.py
indra/assemblers/kami/assembler.py
indra/assemblers/pybel/__init__.py
indra/assemblers/pybel/assembler.py
indra/assemblers/pysb/__init__.py
indra/assemblers/pysb/assembler.py
indra/assemblers/pysb/base_agents.py
indra/assemblers/pysb/bmi_wrapper.py
indra/assemblers/pysb/common.py
indra/assemblers/pysb/export.py
indra/assemblers/pysb/kappa_util.py
indra/assemblers/pysb/preassembler.py
indra/assemblers/pysb/sites.py
indra/assemblers/sbgn/__init__.py
indra/assemblers/sbgn/assembler.py
indra/assemblers/sif/__init__.py
indra/assemblers/sif/assembler.py
indra/assemblers/tsv/__init__.py
indra/assemblers/tsv/assembler.py
indra/belief/__init__.py
indra/belief/skl.py
indra/benchmarks/__init__.py
indra/benchmarks/benchmark_db_coverage.py
indra/benchmarks/benchmark_trips.py
indra/benchmarks/bioprocesses/__init__.py
indra/benchmarks/bioprocesses/__main__.py
indra/benchmarks/phosphorylations/__init__.py
indra/databases/__init__.py
indra/databases/cbio_client.py
indra/databases/chebi_client.py
indra/databases/chembl_client.py
indra/databases/context_client.py
indra/databases/doid_client.py
indra/databases/drugbank_client.py
indra/databases/efo_client.py
indra/databases/go_client.py
indra/databases/hgnc_client.py
indra/databases/hp_client.py
indra/databases/identifiers.py
indra/databases/ido_client.py
indra/databases/lincs_client.py
indra/databases/mesh_client.py
indra/databases/mirbase_client.py
indra/databases/ndex_client.py
indra/databases/obo_client.py
indra/databases/owl_client.py
indra/databases/pubchem_client.py
indra/databases/taxonomy_client.py
indra/databases/uniprot_client.py
indra/explanation/__init__.py
indra/explanation/reporting.py
indra/explanation/model_checker/__init__.py
indra/explanation/model_checker/model_checker.py
indra/explanation/model_checker/pybel.py
indra/explanation/model_checker/pysb.py
indra/explanation/model_checker/signed_graph.py
indra/explanation/model_checker/unsigned_graph.py
indra/explanation/pathfinding/__init__.py
indra/explanation/pathfinding/pathfinding.py
indra/explanation/pathfinding/util.py
indra/literature/__init__.py
indra/literature/adeft_tools.py
indra/literature/biorxiv_client.py
indra/literature/crossref_client.py
indra/literature/elsevier_client.py
indra/literature/newsapi_client.py
indra/literature/pmc_client.py
indra/literature/pmids_auth_xml.txt
indra/literature/pmids_fulltext.txt
indra/literature/pmids_oa_txt.txt
indra/literature/pmids_oa_xml.txt
indra/literature/pubmed_client.py
indra/literature/s3_client.py
indra/mechlinker/__init__.py
indra/ontology/__init__.py
indra/ontology/ontology_graph.py
indra/ontology/standardize.py
indra/ontology/app/__init__.py
indra/ontology/app/app.py
indra/ontology/bio/__init__.py
indra/ontology/bio/__main__.py
indra/ontology/bio/ontology.py
indra/ontology/virtual/__init__.py
indra/ontology/virtual/ontology.py
indra/pipeline/__init__.py
indra/pipeline/decorators.py
indra/pipeline/pipeline.py
indra/preassembler/__init__.py
indra/preassembler/custom_preassembly.py
indra/preassembler/refinement.py
indra/preassembler/sitemapper.py
indra/preassembler/grounding_mapper/__init__.py
indra/preassembler/grounding_mapper/analysis.py
indra/preassembler/grounding_mapper/disambiguate.py
indra/preassembler/grounding_mapper/gilda.py
indra/preassembler/grounding_mapper/mapper.py
indra/resources/README.txt
indra/resources/__init__.py
indra/resources/add_grounding_resources_from_csv.py
indra/resources/amino_acids.tsv
indra/resources/bel_chebi_map.tsv
indra/resources/biomappings.tsv
indra/resources/cas_to_chebi.tsv
indra/resources/chebi.json
indra/resources/chebi_to_chembl.tsv
indra/resources/chebi_to_pubchem.tsv
indra/resources/chembl_tas.csv
indra/resources/curated_site_map.csv
indra/resources/db_refs_map.csv
indra/resources/default_belief_probs.json
indra/resources/default_config.ini
indra/resources/doid.json
indra/resources/drugbank_mappings.tsv
indra/resources/efo.json
indra/resources/famplex_map.tsv
indra/resources/go.json
indra/resources/greek_alphabet.py
indra/resources/hgnc_entries.tsv
indra/resources/hmdb_to_chebi.tsv
indra/resources/hms_lincs_extra.tsv
indra/resources/hp.json
indra/resources/identifiers_patterns.json
indra/resources/ido.json
indra/resources/index_card_schema.json
indra/resources/kinases.tsv
indra/resources/lincs_proteins.json
indra/resources/lincs_small_molecules.json
indra/resources/lspci.tsv
indra/resources/mesh_id_label_mappings.tsv
indra/resources/mesh_mappings.tsv
indra/resources/mesh_supp_id_label_mappings.tsv
indra/resources/mirbase.tsv
indra/resources/ncit_allele_map.tsv
indra/resources/ncit_map.tsv
indra/resources/phosphatases.tsv
indra/resources/ras_pathway_proteins.csv
indra/resources/source_info.json
indra/resources/source_mapping.json
indra/resources/statements_schema.json
indra/resources/transcription_factors.csv
indra/resources/uniprot_subcell_loc.tsv
indra/resources/update_resources.py
indra/resources/famplex/entities.csv
indra/resources/famplex/equivalences.csv
indra/resources/famplex/gene_prefixes.csv
indra/resources/famplex/grounding_map.csv
indra/resources/famplex/relations.csv
indra/resources/grounding/agents.json
indra/resources/grounding/covid_grounding.csv
indra/resources/grounding/extra_gmap_files.json
indra/resources/grounding/gene_grounding.csv
indra/resources/grounding/grounding_map.csv
indra/resources/grounding/ignore.csv
indra/resources/grounding/misgrounding_map.csv
indra/sources/__init__.py
indra/sources/biogrid.py
indra/sources/utils.py
indra/sources/bel/__init__.py
indra/sources/bel/api.py
indra/sources/bel/processor.py
indra/sources/biofactoid/__init__.py
indra/sources/biofactoid/api.py
indra/sources/biofactoid/processor.py
indra/sources/biopax/__init__.py
indra/sources/biopax/api.py
indra/sources/biopax/processor.py
indra/sources/crog/__init__.py
indra/sources/crog/__main__.py
indra/sources/crog/api.py
indra/sources/crog/processor.py
indra/sources/ctd/__init__.py
indra/sources/ctd/api.py
indra/sources/ctd/processor.py
indra/sources/dgi/__init__.py
indra/sources/dgi/__main__.py
indra/sources/dgi/api.py
indra/sources/dgi/processor.py
indra/sources/drugbank/__init__.py
indra/sources/drugbank/api.py
indra/sources/drugbank/processor.py
indra/sources/eidos/__init__.py
indra/sources/eidos/api.py
indra/sources/eidos/bio_processor.py
indra/sources/eidos/cli.py
indra/sources/eidos/client.py
indra/sources/eidos/processor.py
indra/sources/eidos/reader.py
indra/sources/eidos/server.py
indra/sources/geneways/__init__.py
indra/sources/geneways/action_parser.py
indra/sources/geneways/actionmention_parser.py
indra/sources/geneways/api.py
indra/sources/geneways/find_full_text_sentence.py
indra/sources/geneways/processor.py
indra/sources/geneways/symbols_parser.py
indra/sources/gnbr/__init__.py
indra/sources/gnbr/api.py
indra/sources/gnbr/processor.py
indra/sources/hprd/__init__.py
indra/sources/hprd/api.py
indra/sources/hprd/processor.py
indra/sources/hypothesis/__init__.py
indra/sources/hypothesis/annotator.py
indra/sources/hypothesis/api.py
indra/sources/hypothesis/processor.py
indra/sources/index_cards/__init__.py
indra/sources/index_cards/processor.py
indra/sources/indra_db_rest/__init__.py
indra/sources/indra_db_rest/api.py
indra/sources/indra_db_rest/exceptions.py
indra/sources/indra_db_rest/processor.py
indra/sources/indra_db_rest/query.py
indra/sources/indra_db_rest/query_results.py
indra/sources/indra_db_rest/util.py
indra/sources/isi/__init__.py
indra/sources/isi/api.py
indra/sources/isi/experiments.py
indra/sources/isi/isi_verb_to_indra_statement_type.tsv
indra/sources/isi/preprocessor.py
indra/sources/isi/processor.py
indra/sources/minerva/__init__.py
indra/sources/minerva/api.py
indra/sources/minerva/id_mapping.py
indra/sources/minerva/minerva_client.py
indra/sources/minerva/processor.py
indra/sources/ndex_cx/__init__.py
indra/sources/ndex_cx/api.py
indra/sources/ndex_cx/processor.py
indra/sources/omnipath/__init__.py
indra/sources/omnipath/api.py
indra/sources/omnipath/processor.py
indra/sources/phosphoelm/__init__.py
indra/sources/phosphoelm/api.py
indra/sources/phosphoelm/phosphoelm_mapping.py
indra/sources/phosphoelm/processor.py
indra/sources/reach/__init__.py
indra/sources/reach/api.py
indra/sources/reach/processor.py
indra/sources/reach/reach_rule_regexps.txt
indra/sources/reach/reader.py
indra/sources/rlimsp/__init__.py
indra/sources/rlimsp/api.py
indra/sources/rlimsp/processor.py
indra/sources/signor/__init__.py
indra/sources/signor/api.py
indra/sources/signor/processor.py
indra/sources/sparser/__init__.py
indra/sources/sparser/api.py
indra/sources/sparser/processor.py
indra/sources/sparser/xml_processor.py
indra/sources/tas/__init__.py
indra/sources/tas/api.py
indra/sources/tas/processor.py
indra/sources/tees/__init__.py
indra/sources/tees/api.py
indra/sources/tees/parse_tees.py
indra/sources/tees/processor.py
indra/sources/trips/__init__.py
indra/sources/trips/analyze_ekbs.py
indra/sources/trips/api.py
indra/sources/trips/client.py
indra/sources/trips/drum_reader.py
indra/sources/trips/processor.py
indra/sources/trrust/__init__.py
indra/sources/trrust/api.py
indra/sources/trrust/processor.py
indra/sources/virhostnet/__init__.py
indra/sources/virhostnet/api.py
indra/sources/virhostnet/processor.py
indra/statements/__init__.py
indra/statements/agent.py
indra/statements/concept.py
indra/statements/context.py
indra/statements/delta.py
indra/statements/evidence.py
indra/statements/io.py
indra/statements/resources.py
indra/statements/statements.py
indra/statements/util.py
indra/statements/validate.py
indra/tests/__init__.py
indra/tests/make_mock_ontology.py
indra/tests/test_adaptive_assembly.py
indra/tests/test_adeft_tools.py
indra/tests/test_assemble_corpus.py
indra/tests/test_belief_engine.py
indra/tests/test_belief_sklearn.py
indra/tests/test_benchmarks.py
indra/tests/test_biofactoid.py
indra/tests/test_biogrid.py
indra/tests/test_biopax.py
indra/tests/test_bmi_wrapper.py
indra/tests/test_cbio_client.py
indra/tests/test_chebi_client.py
indra/tests/test_chembl_client.py
indra/tests/test_context.py
indra/tests/test_crossref_client.py
indra/tests/test_ctd.py
indra/tests/test_custom_preassembly.py
indra/tests/test_cx_assembler.py
indra/tests/test_cyjs_assembler.py
indra/tests/test_db_rest.py
indra/tests/test_delta.py
indra/tests/test_docs_code.py
indra/tests/test_drugbank.py
indra/tests/test_eidos.py
indra/tests/test_elsevier_client.py
indra/tests/test_english_assembler.py
indra/tests/test_expand_families.py
indra/tests/test_fix_invalidities.py
indra/tests/test_geneways.py
indra/tests/test_gnbr.py
indra/tests/test_go_client.py
indra/tests/test_graph_assembler.py
indra/tests/test_grounding_resources.py
indra/tests/test_groundingmapper.py
indra/tests/test_hgnc_client.py
indra/tests/test_hprd.py
indra/tests/test_html_assembler.py
indra/tests/test_hypothesis.py
indra/tests/test_identifiers.py
indra/tests/test_incremental_model.py
indra/tests/test_index_card_assembler.py
indra/tests/test_indranet_assembler.py
indra/tests/test_isi.py
indra/tests/test_json_schema.py
indra/tests/test_kami_assembler.py
indra/tests/test_kappa_util.py
indra/tests/test_lincs_client.py
indra/tests/test_literature.py
indra/tests/test_mechlinker.py
indra/tests/test_medscan.py
indra/tests/test_mesh.py
indra/tests/test_minerva.py
indra/tests/test_mirbase_client.py
indra/tests/test_model_checker.py
indra/tests/test_ndex_client.py
indra/tests/test_ndex_cx_processor.py
indra/tests/test_omnipath.py
indra/tests/test_ontology.py
indra/tests/test_pathfinding.py
indra/tests/test_phosphoelm_processor.py
indra/tests/test_pipeline.py
indra/tests/test_pmc_client.py
indra/tests/test_preassembler.py
indra/tests/test_pubchem_client.py
indra/tests/test_pubmed_client.py
indra/tests/test_pybel_api.py
indra/tests/test_pybel_assembler.py
indra/tests/test_pysb_assembler.py
indra/tests/test_rasmachine.py
indra/tests/test_reach.py
indra/tests/test_rest_api.py
indra/tests/test_rlimsp.py
indra/tests/test_s3_client.py
indra/tests/test_sbgn_assembler.py
indra/tests/test_sif_assembler.py
indra/tests/test_signor.py
indra/tests/test_sitemapper.py
indra/tests/test_sparser.py
indra/tests/test_sparser_xml.py
indra/tests/test_statement_validate.py
indra/tests/test_statements.py
indra/tests/test_statements_serialization.py
indra/tests/test_tas.py
indra/tests/test_taxonomy_client.py
indra/tests/test_tees.py
indra/tests/test_trips.py
indra/tests/test_trips_ekbs.py
indra/tests/test_trrust.py
indra/tests/test_tsv_assembler.py
indra/tests/test_uniprot_client.py
indra/tests/test_util.py
indra/tests/test_virhostnet.py
indra/tests/util.py
indra/tests/test_obo_clients/__init__.py
indra/tests/test_obo_clients/test_doid_client.py
indra/tests/test_obo_clients/test_efo_client.py
indra/tests/test_obo_clients/test_hp_client.py
indra/tests/test_obo_clients/test_ido_client.py
indra/tools/__init__.py
indra/tools/adaptive_assembly.py
indra/tools/analyze_ontology.py
indra/tools/assemble_corpus.py
indra/tools/executable_subnetwork.py
indra/tools/expand_families.py
indra/tools/extract_grounding_map.py
indra/tools/fix_invalidities.py
indra/tools/gene_network.py
indra/tools/hypothesis_annotator.py
indra/tools/incremental_model.py
indra/tools/mechlinker_queries.py
indra/tools/machine/__init__.py
indra/tools/machine/__main__.py
indra/tools/machine/cli.py
indra/tools/machine/config.py
indra/tools/machine/default-config.yaml
indra/tools/machine/gmail_client.py
indra/tools/machine/machine.py
indra/tools/machine/twitter_client.py
indra/util/__init__.py
indra/util/_require_python3.py
indra/util/aws.py
indra/util/get_version.py
indra/util/multiprocessing_traceback.py
indra/util/nested_dict.py
indra/util/perm_cache.py
indra/util/plot_formatting.py
indra/util/repickle_stmts.py
indra/util/statement_presentation.py
models/hello_indra.py
models/indra_statements_demo.ipynb
models/model_complexity_demo.ipynb
models/braf_model/assemble_model.py
models/braf_model/braf_rxn_analysis.py
models/braf_model/model1.txt
models/braf_model/model2_from1.txt
models/braf_model/model3_from2.txt
models/braf_model/run_model.py
models/p53_model/ATM_v1.txt
models/p53_model/ATM_v2.txt
models/p53_model/ATM_v3.txt
models/p53_model/ATM_v4a.txt
models/p53_model/ATM_v4b.txt
models/p53_model/ATR_v1.txt
models/p53_model/ATR_v2.txt
models/p53_model/ATR_v3.txt
models/p53_model/POMI_tutorial.ipynb
models/p53_model/param_analysis.py
models/p53_model/run_p53_model.py
models/ras_pathway/CyJS_Assembler.ipynb
models/ras_pathway/correction.txt
models/ras_pathway/extension.txt
models/ras_pathway/ras_pathway.txt
models/ras_pathway/run_ras_boolnet.py
models/ras_pathway/run_ras_pathway.py
models/ras_pathway/cyjs/base_script.js
models/ras_pathway/cyjs/index.html
models/ras_pathway/cyjs/style.css
models/worldmodel/text_to_model.ipynb
rest_api/__init__.py
rest_api/api.py