{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2015:PV6MAKI5UMTLJX3RU7XPJPS5I4","short_pith_number":"pith:PV6MAKI5","canonical_record":{"source":{"id":"1511.01268","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2015-11-04T10:18:23Z","cross_cats_sorted":["q-bio.MN","q-bio.SC"],"title_canon_sha256":"4c5be4158608a7e811910c391dbef13d119b5fae18b09895d6c87da8bdc7315d","abstract_canon_sha256":"b234167def52a62f81280ba7b8958edac23f67e3da406c85c7525bc0976da5f1"},"schema_version":"1.0"},"canonical_sha256":"7d7cc0291da326b4df71a7eef4be5d470f1ae5d5a95c60b201ce293b8683c222","source":{"kind":"arxiv","id":"1511.01268","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1511.01268","created_at":"2026-05-18T01:03:50Z"},{"alias_kind":"arxiv_version","alias_value":"1511.01268v1","created_at":"2026-05-18T01:03:50Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1511.01268","created_at":"2026-05-18T01:03:50Z"},{"alias_kind":"pith_short_12","alias_value":"PV6MAKI5UMTL","created_at":"2026-05-18T12:29:37Z"},{"alias_kind":"pith_short_16","alias_value":"PV6MAKI5UMTLJX3R","created_at":"2026-05-18T12:29:37Z"},{"alias_kind":"pith_short_8","alias_value":"PV6MAKI5","created_at":"2026-05-18T12:29:37Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2015:PV6MAKI5UMTLJX3RU7XPJPS5I4","target":"record","payload":{"canonical_record":{"source":{"id":"1511.01268","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2015-11-04T10:18:23Z","cross_cats_sorted":["q-bio.MN","q-bio.SC"],"title_canon_sha256":"4c5be4158608a7e811910c391dbef13d119b5fae18b09895d6c87da8bdc7315d","abstract_canon_sha256":"b234167def52a62f81280ba7b8958edac23f67e3da406c85c7525bc0976da5f1"},"schema_version":"1.0"},"canonical_sha256":"7d7cc0291da326b4df71a7eef4be5d470f1ae5d5a95c60b201ce293b8683c222","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T01:03:50.936559Z","signature_b64":"/OZMtQBkdVmgvDDmNGd1JZwXyBczKYWF99GdDPbjWXznWwxRXHsw71h83PWXdEmXAMRV9rnz+maOemX0f25mCg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"7d7cc0291da326b4df71a7eef4be5d470f1ae5d5a95c60b201ce293b8683c222","last_reissued_at":"2026-05-18T01:03:50.935855Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T01:03:50.935855Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1511.01268","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":"2026-05-18T01:03:50Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"QrSHIRFeAhGqtiZ1LZF7vPz0qCjJ/1jDGK2vUoYwfRIsBZGf0KVC0RHDaCt9c6LEMRaBwihCNcsFqfruDA2sDg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T17:42:48.270902Z"},"content_sha256":"0dff2d8e8b616dea85150c18b2fc84d78878c3aa146f8235beff44cb579e65d1","schema_version":"1.0","event_id":"sha256:0dff2d8e8b616dea85150c18b2fc84d78878c3aa146f8235beff44cb579e65d1"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2015:PV6MAKI5UMTLJX3RU7XPJPS5I4","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Stochastic Simulation of Biomolecular Networks in Dynamic Environments","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.MN","q-bio.SC"],"primary_cat":"q-bio.QM","authors_text":"Clive G. Bowsher, Margaritis Voliotis, Philipp Thomas, Ramon Grima","submitted_at":"2015-11-04T10:18:23Z","abstract_excerpt":"Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction prope"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1511.01268","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":"2026-05-18T01:03:50Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"gj/YTRTRUIUH4CuyRIq3fBOz8d4lXEihEFxnf5prjrj+IFxvS22GyRkSlG70DqiBJsg1+6T2K2yTQELSNJkBCg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T17:42:48.271641Z"},"content_sha256":"fba8dfd34d7eedda8299238b406221e9fcbbd176b78418f2976fc4820e9965d2","schema_version":"1.0","event_id":"sha256:fba8dfd34d7eedda8299238b406221e9fcbbd176b78418f2976fc4820e9965d2"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/PV6MAKI5UMTLJX3RU7XPJPS5I4/bundle.json","state_url":"https://pith.science/pith/PV6MAKI5UMTLJX3RU7XPJPS5I4/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/PV6MAKI5UMTLJX3RU7XPJPS5I4/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":"2026-05-28T17:42:48Z","links":{"resolver":"https://pith.science/pith/PV6MAKI5UMTLJX3RU7XPJPS5I4","bundle":"https://pith.science/pith/PV6MAKI5UMTLJX3RU7XPJPS5I4/bundle.json","state":"https://pith.science/pith/PV6MAKI5UMTLJX3RU7XPJPS5I4/state.json","well_known_bundle":"https://pith.science/.well-known/pith/PV6MAKI5UMTLJX3RU7XPJPS5I4/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2015:PV6MAKI5UMTLJX3RU7XPJPS5I4","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":"b234167def52a62f81280ba7b8958edac23f67e3da406c85c7525bc0976da5f1","cross_cats_sorted":["q-bio.MN","q-bio.SC"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2015-11-04T10:18:23Z","title_canon_sha256":"4c5be4158608a7e811910c391dbef13d119b5fae18b09895d6c87da8bdc7315d"},"schema_version":"1.0","source":{"id":"1511.01268","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1511.01268","created_at":"2026-05-18T01:03:50Z"},{"alias_kind":"arxiv_version","alias_value":"1511.01268v1","created_at":"2026-05-18T01:03:50Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1511.01268","created_at":"2026-05-18T01:03:50Z"},{"alias_kind":"pith_short_12","alias_value":"PV6MAKI5UMTL","created_at":"2026-05-18T12:29:37Z"},{"alias_kind":"pith_short_16","alias_value":"PV6MAKI5UMTLJX3R","created_at":"2026-05-18T12:29:37Z"},{"alias_kind":"pith_short_8","alias_value":"PV6MAKI5","created_at":"2026-05-18T12:29:37Z"}],"graph_snapshots":[{"event_id":"sha256:fba8dfd34d7eedda8299238b406221e9fcbbd176b78418f2976fc4820e9965d2","target":"graph","created_at":"2026-05-18T01:03:50Z","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":"Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction prope","authors_text":"Clive G. Bowsher, Margaritis Voliotis, Philipp Thomas, Ramon Grima","cross_cats":["q-bio.MN","q-bio.SC"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2015-11-04T10:18:23Z","title":"Stochastic Simulation of Biomolecular Networks in Dynamic Environments"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1511.01268","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":"sha256:0dff2d8e8b616dea85150c18b2fc84d78878c3aa146f8235beff44cb579e65d1","target":"record","created_at":"2026-05-18T01:03:50Z","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":"b234167def52a62f81280ba7b8958edac23f67e3da406c85c7525bc0976da5f1","cross_cats_sorted":["q-bio.MN","q-bio.SC"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2015-11-04T10:18:23Z","title_canon_sha256":"4c5be4158608a7e811910c391dbef13d119b5fae18b09895d6c87da8bdc7315d"},"schema_version":"1.0","source":{"id":"1511.01268","kind":"arxiv","version":1}},"canonical_sha256":"7d7cc0291da326b4df71a7eef4be5d470f1ae5d5a95c60b201ce293b8683c222","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"7d7cc0291da326b4df71a7eef4be5d470f1ae5d5a95c60b201ce293b8683c222","first_computed_at":"2026-05-18T01:03:50.935855Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T01:03:50.935855Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"/OZMtQBkdVmgvDDmNGd1JZwXyBczKYWF99GdDPbjWXznWwxRXHsw71h83PWXdEmXAMRV9rnz+maOemX0f25mCg==","signature_status":"signed_v1","signed_at":"2026-05-18T01:03:50.936559Z","signed_message":"canonical_sha256_bytes"},"source_id":"1511.01268","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:0dff2d8e8b616dea85150c18b2fc84d78878c3aa146f8235beff44cb579e65d1","sha256:fba8dfd34d7eedda8299238b406221e9fcbbd176b78418f2976fc4820e9965d2"],"state_sha256":"52b94a216b3f1dbcf9b9944c42df9a81819339a8599024695f1ba9c6aa4faa2f"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"japUngdSLXf3McfHTq3y8fDTBw6ueCTCuxc6dOCGd4KYL7vw1dYTyV94B1R5ij2xwmhwHZuS6Y5AYOMxg0zcBg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-28T17:42:48.275753Z","bundle_sha256":"bfc8eaa0be575e47b0b4589e8109d18844ca17e3540579412e117a54b3f2e116"}}