{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2018:Q6B73KAGFT2YFL6YKGPDH6BCMV","short_pith_number":"pith:Q6B73KAG","canonical_record":{"source":{"id":"1809.08321","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2018-09-21T21:32:58Z","cross_cats_sorted":[],"title_canon_sha256":"65ba9563a1d3893bbc581c0228a8006514275cac5b222c0accae577ae21fc1d8","abstract_canon_sha256":"f9f8d47de73bd937a92edc85b17bafafff83493a9e14c72737e999c89377dd0d"},"schema_version":"1.0"},"canonical_sha256":"8783fda8062cf582afd8519e33f8226558b547e3d1eb5d05c7e7dcb3aa3fc489","source":{"kind":"arxiv","id":"1809.08321","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1809.08321","created_at":"2026-05-18T00:05:08Z"},{"alias_kind":"arxiv_version","alias_value":"1809.08321v1","created_at":"2026-05-18T00:05:08Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1809.08321","created_at":"2026-05-18T00:05:08Z"},{"alias_kind":"pith_short_12","alias_value":"Q6B73KAGFT2Y","created_at":"2026-05-18T12:32:46Z"},{"alias_kind":"pith_short_16","alias_value":"Q6B73KAGFT2YFL6Y","created_at":"2026-05-18T12:32:46Z"},{"alias_kind":"pith_short_8","alias_value":"Q6B73KAG","created_at":"2026-05-18T12:32:46Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2018:Q6B73KAGFT2YFL6YKGPDH6BCMV","target":"record","payload":{"canonical_record":{"source":{"id":"1809.08321","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2018-09-21T21:32:58Z","cross_cats_sorted":[],"title_canon_sha256":"65ba9563a1d3893bbc581c0228a8006514275cac5b222c0accae577ae21fc1d8","abstract_canon_sha256":"f9f8d47de73bd937a92edc85b17bafafff83493a9e14c72737e999c89377dd0d"},"schema_version":"1.0"},"canonical_sha256":"8783fda8062cf582afd8519e33f8226558b547e3d1eb5d05c7e7dcb3aa3fc489","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:05:08.817223Z","signature_b64":"iFf5YIi6skmrKS+V5/WXFwCowIlXkc31meDIabLEVcd6+B/PB077Uc7Fm1cCyp/Uw7HQWmnkSPgQhLxy2fFuAQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"8783fda8062cf582afd8519e33f8226558b547e3d1eb5d05c7e7dcb3aa3fc489","last_reissued_at":"2026-05-18T00:05:08.816698Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:05:08.816698Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1809.08321","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T00:05:08Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"RX0EuXc11RwmqupZqoXhwFIDKCwzSdmqemMv/Go9Kpsw4c2+lWh4ZQpSJiDZSUqKBxU2eLZicQTNRvfaWByrDg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-27T12:42:52.325486Z"},"content_sha256":"4ad849785552064545ada8894a6ad726e96b5ddad2ff71d4a06d6163dfee3df9","schema_version":"1.0","event_id":"sha256:4ad849785552064545ada8894a6ad726e96b5ddad2ff71d4a06d6163dfee3df9"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2018:Q6B73KAGFT2YFL6YKGPDH6BCMV","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"A Step-by-Step Guide to Using BioNetFit","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.QM","authors_text":"Alexander Ionkov, Brandon R. Thomas, Eshan D. Mitra, Jennifer Longo, Joshua Colvin, Keesha E. Erickson, Lewis R. Baker, Mar\\'ia del Carmen Ramos \\'Alamo, Raquel Dias, Richard G. Posner, Ryan Suderman, William S. Hlavacek","submitted_at":"2018-09-21T21:32:58Z","abstract_excerpt":"BioNetFit is a software tool designed for solving parameter identification problems that arise in the development of rule-based models. It solves these problems through curve fitting (i.e., nonlinear regression). BioNetFit is compatible with deterministic and stochastic simulators that accept BioNetGen language (BNGL)-formatted files as inputs, such those available within the BioNetGen framework. BioNetFit can be used on a laptop or standalone multicore workstation as well as on many Linux clusters, such as those that use the Slurm Workload Manager to schedule jobs. BioNetFit implements a meta"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1809.08321","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T00:05:08Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"GkwmH+tIG3qXzqWj72WcMzaVjR34BlmnCRQwAVydj+f0RySf0NMqSZNJ2vjGpCZSsNy704mOaDT1KuR8VmZOAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-27T12:42:52.326187Z"},"content_sha256":"58769765dc57df5ee777ad1a747c4f9a4a242d2f79d3d4655a85e7b71b7b2183","schema_version":"1.0","event_id":"sha256:58769765dc57df5ee777ad1a747c4f9a4a242d2f79d3d4655a85e7b71b7b2183"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/Q6B73KAGFT2YFL6YKGPDH6BCMV/bundle.json","state_url":"https://pith.science/pith/Q6B73KAGFT2YFL6YKGPDH6BCMV/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/Q6B73KAGFT2YFL6YKGPDH6BCMV/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-05-27T12:42:52Z","links":{"resolver":"https://pith.science/pith/Q6B73KAGFT2YFL6YKGPDH6BCMV","bundle":"https://pith.science/pith/Q6B73KAGFT2YFL6YKGPDH6BCMV/bundle.json","state":"https://pith.science/pith/Q6B73KAGFT2YFL6YKGPDH6BCMV/state.json","well_known_bundle":"https://pith.science/.well-known/pith/Q6B73KAGFT2YFL6YKGPDH6BCMV/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2018:Q6B73KAGFT2YFL6YKGPDH6BCMV","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"f9f8d47de73bd937a92edc85b17bafafff83493a9e14c72737e999c89377dd0d","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2018-09-21T21:32:58Z","title_canon_sha256":"65ba9563a1d3893bbc581c0228a8006514275cac5b222c0accae577ae21fc1d8"},"schema_version":"1.0","source":{"id":"1809.08321","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1809.08321","created_at":"2026-05-18T00:05:08Z"},{"alias_kind":"arxiv_version","alias_value":"1809.08321v1","created_at":"2026-05-18T00:05:08Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1809.08321","created_at":"2026-05-18T00:05:08Z"},{"alias_kind":"pith_short_12","alias_value":"Q6B73KAGFT2Y","created_at":"2026-05-18T12:32:46Z"},{"alias_kind":"pith_short_16","alias_value":"Q6B73KAGFT2YFL6Y","created_at":"2026-05-18T12:32:46Z"},{"alias_kind":"pith_short_8","alias_value":"Q6B73KAG","created_at":"2026-05-18T12:32:46Z"}],"graph_snapshots":[{"event_id":"sha256:58769765dc57df5ee777ad1a747c4f9a4a242d2f79d3d4655a85e7b71b7b2183","target":"graph","created_at":"2026-05-18T00:05:08Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"paper":{"abstract_excerpt":"BioNetFit is a software tool designed for solving parameter identification problems that arise in the development of rule-based models. It solves these problems through curve fitting (i.e., nonlinear regression). BioNetFit is compatible with deterministic and stochastic simulators that accept BioNetGen language (BNGL)-formatted files as inputs, such those available within the BioNetGen framework. BioNetFit can be used on a laptop or standalone multicore workstation as well as on many Linux clusters, such as those that use the Slurm Workload Manager to schedule jobs. BioNetFit implements a meta","authors_text":"Alexander Ionkov, Brandon R. Thomas, Eshan D. Mitra, Jennifer Longo, Joshua Colvin, Keesha E. Erickson, Lewis R. Baker, Mar\\'ia del Carmen Ramos \\'Alamo, Raquel Dias, Richard G. Posner, Ryan Suderman, William S. Hlavacek","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2018-09-21T21:32:58Z","title":"A Step-by-Step Guide to Using BioNetFit"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1809.08321","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:4ad849785552064545ada8894a6ad726e96b5ddad2ff71d4a06d6163dfee3df9","target":"record","created_at":"2026-05-18T00:05:08Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"f9f8d47de73bd937a92edc85b17bafafff83493a9e14c72737e999c89377dd0d","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2018-09-21T21:32:58Z","title_canon_sha256":"65ba9563a1d3893bbc581c0228a8006514275cac5b222c0accae577ae21fc1d8"},"schema_version":"1.0","source":{"id":"1809.08321","kind":"arxiv","version":1}},"canonical_sha256":"8783fda8062cf582afd8519e33f8226558b547e3d1eb5d05c7e7dcb3aa3fc489","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"8783fda8062cf582afd8519e33f8226558b547e3d1eb5d05c7e7dcb3aa3fc489","first_computed_at":"2026-05-18T00:05:08.816698Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T00:05:08.816698Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"iFf5YIi6skmrKS+V5/WXFwCowIlXkc31meDIabLEVcd6+B/PB077Uc7Fm1cCyp/Uw7HQWmnkSPgQhLxy2fFuAQ==","signature_status":"signed_v1","signed_at":"2026-05-18T00:05:08.817223Z","signed_message":"canonical_sha256_bytes"},"source_id":"1809.08321","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:4ad849785552064545ada8894a6ad726e96b5ddad2ff71d4a06d6163dfee3df9","sha256:58769765dc57df5ee777ad1a747c4f9a4a242d2f79d3d4655a85e7b71b7b2183"],"state_sha256":"1a6f2311df58909c816a8db57c486e72e2d043b8658da3ce12b08673cea9b82a"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"jENrZN2U7Fr0sEhZFqMUWQFwofQd7GmoqzrnoOApTItKuT9UrZ9woCLVnjR2aM3n0Lh90ZbVebW8Fwnb884EDg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-27T12:42:52.330102Z","bundle_sha256":"1c97469aa6e540681bf16163a0214821c554e8dcaf39a67522d88d85a11ff518"}}