{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2016:ROHX3UU7ZYI3ZZCJKGOVC4WXZ6","short_pith_number":"pith:ROHX3UU7","canonical_record":{"source":{"id":"1602.02655","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2016-02-08T17:24:38Z","cross_cats_sorted":["physics.chem-ph","physics.comp-ph","q-bio.QM"],"title_canon_sha256":"5c4285a730c8f2347bcf7b7f71cf0864669bac9b1e63f776a8f1815be3109829","abstract_canon_sha256":"89f706988450156b897caff3c9f62f954a408aa48e39ffce452e5a57aef1ec8c"},"schema_version":"1.0"},"canonical_sha256":"8b8f7dd29fce11bce449519d5172d7cfb51b2831bc0f1e07912c0b936b3fcc52","source":{"kind":"arxiv","id":"1602.02655","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1602.02655","created_at":"2026-05-18T01:19:47Z"},{"alias_kind":"arxiv_version","alias_value":"1602.02655v1","created_at":"2026-05-18T01:19:47Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1602.02655","created_at":"2026-05-18T01:19:47Z"},{"alias_kind":"pith_short_12","alias_value":"ROHX3UU7ZYI3","created_at":"2026-05-18T12:30:41Z"},{"alias_kind":"pith_short_16","alias_value":"ROHX3UU7ZYI3ZZCJ","created_at":"2026-05-18T12:30:41Z"},{"alias_kind":"pith_short_8","alias_value":"ROHX3UU7","created_at":"2026-05-18T12:30:41Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2016:ROHX3UU7ZYI3ZZCJKGOVC4WXZ6","target":"record","payload":{"canonical_record":{"source":{"id":"1602.02655","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2016-02-08T17:24:38Z","cross_cats_sorted":["physics.chem-ph","physics.comp-ph","q-bio.QM"],"title_canon_sha256":"5c4285a730c8f2347bcf7b7f71cf0864669bac9b1e63f776a8f1815be3109829","abstract_canon_sha256":"89f706988450156b897caff3c9f62f954a408aa48e39ffce452e5a57aef1ec8c"},"schema_version":"1.0"},"canonical_sha256":"8b8f7dd29fce11bce449519d5172d7cfb51b2831bc0f1e07912c0b936b3fcc52","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T01:19:47.158054Z","signature_b64":"ZbulEawaclnaVSsyw3n7j+R3dkYUGhRHyNES2b5a0RsioJGySO44PF2a7YPybGsns5aEzykdaqICQvaCJ7f1Dg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"8b8f7dd29fce11bce449519d5172d7cfb51b2831bc0f1e07912c0b936b3fcc52","last_reissued_at":"2026-05-18T01:19:47.157612Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T01:19:47.157612Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1602.02655","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":"2026-05-18T01:19:47Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"uWaHgfnt7If8CyajmpO4wQ81XEbG8m26HD+WlXtev/rR5tHkuORUCBzO0ykA1lPN7JP7y4aBh0kRuNEoergqDQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-09T16:43:49.328023Z"},"content_sha256":"db2521b1fb1ce47cf3d69a27d5a02aa9d28447645ccfcc14acd3292a3b2c88f0","schema_version":"1.0","event_id":"sha256:db2521b1fb1ce47cf3d69a27d5a02aa9d28447645ccfcc14acd3292a3b2c88f0"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2016:ROHX3UU7ZYI3ZZCJKGOVC4WXZ6","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Optimisation of Simulations of Stochastic Processes by Removal of Opposing Reactions","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["physics.chem-ph","physics.comp-ph","q-bio.QM"],"primary_cat":"physics.bio-ph","authors_text":"Fabian Spill, Helen Byrne, Philip K. Maini","submitted_at":"2016-02-08T17:24:38Z","abstract_excerpt":"Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a large number of algorithms have been developed to speed up simulations. However, a drawback of many of these algorithms is that their implementation is more complicated than, for instance, the Gillespie algorithm, which is widely used to simulate the chemical master equation, and can be implemented with a few lines of code. Here, we present an algorithm which "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1602.02655","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":"2026-05-18T01:19:47Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"j1hFapsCX/b5dENzMwrQfvT4ZS6PaAFyI7xasvW3b+i2dQqgGnPgfp2FZTHJN0lK3+xP6DTI4xQn+cP8kd8yAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-09T16:43:49.328390Z"},"content_sha256":"e775638d5251fcab67f88c8b438aea358b771748bee5549881f3710ed49e91ed","schema_version":"1.0","event_id":"sha256:e775638d5251fcab67f88c8b438aea358b771748bee5549881f3710ed49e91ed"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/ROHX3UU7ZYI3ZZCJKGOVC4WXZ6/bundle.json","state_url":"https://pith.science/pith/ROHX3UU7ZYI3ZZCJKGOVC4WXZ6/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/ROHX3UU7ZYI3ZZCJKGOVC4WXZ6/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":"2026-06-09T16:43:49Z","links":{"resolver":"https://pith.science/pith/ROHX3UU7ZYI3ZZCJKGOVC4WXZ6","bundle":"https://pith.science/pith/ROHX3UU7ZYI3ZZCJKGOVC4WXZ6/bundle.json","state":"https://pith.science/pith/ROHX3UU7ZYI3ZZCJKGOVC4WXZ6/state.json","well_known_bundle":"https://pith.science/.well-known/pith/ROHX3UU7ZYI3ZZCJKGOVC4WXZ6/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2016:ROHX3UU7ZYI3ZZCJKGOVC4WXZ6","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":"89f706988450156b897caff3c9f62f954a408aa48e39ffce452e5a57aef1ec8c","cross_cats_sorted":["physics.chem-ph","physics.comp-ph","q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2016-02-08T17:24:38Z","title_canon_sha256":"5c4285a730c8f2347bcf7b7f71cf0864669bac9b1e63f776a8f1815be3109829"},"schema_version":"1.0","source":{"id":"1602.02655","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1602.02655","created_at":"2026-05-18T01:19:47Z"},{"alias_kind":"arxiv_version","alias_value":"1602.02655v1","created_at":"2026-05-18T01:19:47Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1602.02655","created_at":"2026-05-18T01:19:47Z"},{"alias_kind":"pith_short_12","alias_value":"ROHX3UU7ZYI3","created_at":"2026-05-18T12:30:41Z"},{"alias_kind":"pith_short_16","alias_value":"ROHX3UU7ZYI3ZZCJ","created_at":"2026-05-18T12:30:41Z"},{"alias_kind":"pith_short_8","alias_value":"ROHX3UU7","created_at":"2026-05-18T12:30:41Z"}],"graph_snapshots":[{"event_id":"sha256:e775638d5251fcab67f88c8b438aea358b771748bee5549881f3710ed49e91ed","target":"graph","created_at":"2026-05-18T01:19:47Z","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":"Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a large number of algorithms have been developed to speed up simulations. However, a drawback of many of these algorithms is that their implementation is more complicated than, for instance, the Gillespie algorithm, which is widely used to simulate the chemical master equation, and can be implemented with a few lines of code. Here, we present an algorithm which ","authors_text":"Fabian Spill, Helen Byrne, Philip K. Maini","cross_cats":["physics.chem-ph","physics.comp-ph","q-bio.QM"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2016-02-08T17:24:38Z","title":"Optimisation of Simulations of Stochastic Processes by Removal of Opposing Reactions"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1602.02655","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:db2521b1fb1ce47cf3d69a27d5a02aa9d28447645ccfcc14acd3292a3b2c88f0","target":"record","created_at":"2026-05-18T01:19:47Z","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":"89f706988450156b897caff3c9f62f954a408aa48e39ffce452e5a57aef1ec8c","cross_cats_sorted":["physics.chem-ph","physics.comp-ph","q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2016-02-08T17:24:38Z","title_canon_sha256":"5c4285a730c8f2347bcf7b7f71cf0864669bac9b1e63f776a8f1815be3109829"},"schema_version":"1.0","source":{"id":"1602.02655","kind":"arxiv","version":1}},"canonical_sha256":"8b8f7dd29fce11bce449519d5172d7cfb51b2831bc0f1e07912c0b936b3fcc52","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"8b8f7dd29fce11bce449519d5172d7cfb51b2831bc0f1e07912c0b936b3fcc52","first_computed_at":"2026-05-18T01:19:47.157612Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T01:19:47.157612Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"ZbulEawaclnaVSsyw3n7j+R3dkYUGhRHyNES2b5a0RsioJGySO44PF2a7YPybGsns5aEzykdaqICQvaCJ7f1Dg==","signature_status":"signed_v1","signed_at":"2026-05-18T01:19:47.158054Z","signed_message":"canonical_sha256_bytes"},"source_id":"1602.02655","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:db2521b1fb1ce47cf3d69a27d5a02aa9d28447645ccfcc14acd3292a3b2c88f0","sha256:e775638d5251fcab67f88c8b438aea358b771748bee5549881f3710ed49e91ed"],"state_sha256":"d001746502d37c6fd3a74521f76d70575ad9d20f19b177b436b6d74f3ac88fab"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5TigctLwHRhwK2iizgd9BXLuZIk1bNs3ZYGqdeU1vkV2uY3upfa81NpmqpV9cW86iO3GUojIP1P518ColG02CA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-09T16:43:49.330436Z","bundle_sha256":"f8895d012e524a619b3c5e6fcef47af7ae95222f45cdaff3f5e0a777399b9df3"}}