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LSC_109_QUALIFICATION.md
56.9 KB · Sep 30, 2026 · 23:01 UTC
# LSC-109 starter qualification report
Status: **passed** on 2026-07-02T14:57:33.986Z.
The shipped Sequence Viewer 0.1.26 marketplace bundle was the only installed bundle in each host and was exercised through both an actual GPT-5.6 SOL model-driven MCP App flow and a visible installed-browser host. The workspace began empty for every run; all three official-endpoint workflows produced exactly one viewer contribution, one card, and one active session.
## Qualified runtime
- Execution commit: d7fd06c59f3f232c1ca7ea982d2b219469212ef0 (tree 7690b55352fc38cccf2e97bbb1ee37e51cfbcc44)
- Submitted tracked-plugin source snapshot SHA-256: 815303ec54a02acec897d262b1aeba5997f1ccb724606a97e8b7910d507046ca (316 files, 2926698 bytes)
- Snapshot algorithm: sha256(sorted tracked relativePath NUL byteLength NUL fileSha256 LF)
- Snapshot exclusions are limited to the self-referential evidence files: LSC_109_QUALIFICATION.md, lsc-109-qualification.json
- Bundle SHA-256: 2d9e8b8cbf24b3ad07fb94fd2816bc83c7a21f00e30fa2ab1a14338b0267db8c (13 files, 3002439 bytes)
- Manifest SHA-256: e251955505f5b3c4c65b55d79ff24c051260c094d6dcc47bca6dd686e6c26848
- [Evidence manifest](https://drive.google.com/file/d/1HJmyJeBFtDrhWYczcA1OT8J4HKbckZuK/view?usp=drivesdk) SHA-256 643c76608cb4068bda74cc313231d09180bccd5ad06c3d84e1c9938a2bbc279c
- Starter contract SHA-256: cdfebb95e15ffad58710d9183c7fd850e51b04e72500c6ca1413dfaa557bfb8d
- [Qualification run](https://drive.google.com/file/d/13UwN-CT7_kGkWqAiCR8dZxJK6aRSUr-Y/view?usp=drivesdk) SHA-256 a79ff9202229bfdc2c39f1a28624d03205d447801e7d47c0ea14f69a740f0816
- [Complete raw evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) SHA-256 9561b6557faf616d2a6dc91da87f5f09f6b5874c6e46becb6aa3631474aefbc1
- Evidence folder: https://drive.google.com/drive/folders/134iz8GS9qHSjmheMb0l8WAtdNna357US
## Model-driven installed workflows
| Example | Mode | Stable authoritative IDs | Live scientific result | Model evidence |
| --- | --- | --- | --- | --- |
| ena-drr037765-first-500 | sequence | DRR037765, DRR037765.fastq.gz@md5:81735432a6f578b332aae58cdbd95231 | 500 reads; 235,490 total bases; 469-471 bp read length; 28.8462355% GC; 95.3976814% Q30. The first 500 complete parsed FASTQ records were selected deterministically from 967 source records. | [viewer](https://drive.google.com/file/d/1rxnnNrCWyNVYL6chy22eRu9Vc1jX8Wsq/view?usp=drivesdk) / [trace archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) (`lsc109-final5-share/model/ena/trace.jsonl`) |
| uniprot-human-ras-sv1 | alignment | P01116@SV1, P01111@SV1, P01112@SV1 | KRAS P01116 was the active reference; all three RAS rows preserved the four pinned core motifs. Live p-distances were 0.1315789474, 0.1368421053, and 0.1578947368; the exact three-leaf neighbor-joining Newick was reproduced. The Newick and provenance sidecar round-tripped by SHA-256; an exact collision failed without changing either file; remount retained the same session. | [viewer](https://drive.google.com/file/d/1idnFKeWlOk0UkKh6h_Nlbw8JOA6DRWl5/view?usp=drivesdk) / [trace archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) (`lsc109-final5-share/model/ras/trace.jsonl`) |
| ncbi-nc-001416-1 | sequence | NC_001416.1, NP_040628.1 | The 48,502-base record mapped cI at complement(37227..37940) and OR3/OR2/OR1 at 37951..37967, 37974..37990, and 37998..38014. Genetic code 11 translation produced the pinned 237-aa NP_040628.1 protein and SHA-256 ec5d954fd10be8c19c920e78badc5d9e9cc281f6801e2c5fde3803c9f133f580. | [viewer](https://drive.google.com/file/d/1rdSNs6nqK9Abpfo4LfTMd1w-HQ9ok3De/view?usp=drivesdk) / [trace archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) (`lsc109-final5-share/model/ncbi/trace.jsonl`) |
The submitted prompts were the exact ordered marketplace prompts recorded below. Optional Life Science Research skills were unavailable, so every successful run qualified the official-database endpoint fallback. The RAS workflow saved a provenance-bearing Newick file, verified create-new/no-overwrite behavior, reopened it by digest, and retained the viewer session across remount.
The NCBI model run also exercised the formerly over-envelope cI feature query followed by later OR1-OR3 queries, controls, and translation in the same session; bounded pagination kept the full completion request below the installed-host envelope without stalling command revision advancement.
## Installed-host failure matrix
| Requirement | Result | Scenario-specific evidence |
| --- | --- | --- |
| network-unavailable | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| rate-limit | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| malformed-database-response | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| accession-missing | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| payload-format-mismatch | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| oversized-source-or-analysis-budget | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| deterministic-subset-failure | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| optional-skill-unavailable-fallback | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| output-collision | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| output-quota-failure | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
| viewer-retry-remount | passed | [scenario evidence archive](https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk) |
Every failure was actionable and left no misleading viewer or newly published artifact. No scenario used bundled, synthetic, or pre-existing biological data.
Reference workflows: https://linear.app/openai/issue/LSC-79/validate-the-v1-sequence-viewer-reference-workflow and https://linear.app/openai/issue/LSC-82/validate-the-v1-alignment-viewer-reference-workflow.
## Synchronized qualification record
```json
{
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"contractSchemaVersion": 1,
"issue": "LSC-109",
"status": "passed",
"qualifiedAt": "2026-07-02T14:57:33.986Z",
"pluginVersion": "0.1.26",
"manifestName": "sequence-viewer",
"environment": {
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"treeSha": "7690b55352fc38cccf2e97bbb1ee37e51cfbcc44"
},
"submittedSourceSnapshot": {
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"digestAlgorithm": "sha256(sorted tracked relativePath NUL byteLength NUL fileSha256 LF)",
"excludedEvidenceFiles": [
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],
"fileCount": 316,
"kind": "tracked-plugin-source",
"sha256": "815303ec54a02acec897d262b1aeba5997f1ccb724606a97e8b7910d507046ca"
},
"runtimeBundleSha256": "2d9e8b8cbf24b3ad07fb94fd2816bc83c7a21f00e30fa2ab1a14338b0267db8c",
"qualificationRun": {
"url": "https://drive.google.com/file/d/13UwN-CT7_kGkWqAiCR8dZxJK6aRSUr-Y/view?usp=drivesdk",
"sha256": "a79ff9202229bfdc2c39f1a28624d03205d447801e7d47c0ea14f69a740f0816"
},
"evidenceManifest": {
"url": "https://drive.google.com/file/d/1HJmyJeBFtDrhWYczcA1OT8J4HKbckZuK/view?usp=drivesdk",
"sha256": "643c76608cb4068bda74cc313231d09180bccd5ad06c3d84e1c9938a2bbc279c"
},
"evidenceArchive": {
"url": "https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk",
"sha256": "9561b6557faf616d2a6dc91da87f5f09f6b5874c6e46becb6aa3631474aefbc1"
}
},
"bundle": {
"kind": "marketplace-bundle",
"sha256": "2d9e8b8cbf24b3ad07fb94fd2816bc83c7a21f00e30fa2ab1a14338b0267db8c",
"manifestSha256": "e251955505f5b3c4c65b55d79ff24c051260c094d6dcc47bca6dd686e6c26848",
"starterContractSha256": "cdfebb95e15ffad58710d9183c7fd850e51b04e72500c6ca1413dfaa557bfb8d",
"fileCount": 13,
"byteLength": 3002439
},
"plugin": {
"name": "sequence-viewer",
"version": "0.1.26"
},
"server": {
"name": "biological-sequence-viewer",
"version": "0.1.26"
},
"host": {
"name": "Codex model host plus Playwright installed marketplace host",
"version": "Codex 0.143.0-alpha.33 / qualification host 1",
"build": "LSC-109 exact marketplace bundle model and visible browser host"
},
"os": {
"platform": "linux",
"release": "5.15.0-1110-azure",
"architecture": "x64"
},
"model": {
"name": "GPT-5.6 SOL",
"configuration": {
"entryPoint": "codex exec with mounted MCP App",
"marketplaceBundleCount": 1,
"optionalSkillLane": "unavailable"
}
},
"reasoning": {
"level": "Ultra",
"description": "literal Ultra reasoning"
},
"optionalLifeScienceSkills": {
"available": [],
"unavailable": [
"NCBI Entrez skill",
"UniProt skill",
"ENA/SRA skill"
],
"inventoryRecorded": true,
"unavailableFallbackQualified": true
}
},
"examples": [
{
"id": "ena-drr037765-first-500",
"prompt": "Fetch ENA DRR037765 first 500 reads to active workspace; open and report live length range, GC, Q30, and subset provenance",
"status": "passed",
"workspace": {
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"initialEntries": [],
"preexistingBiologicalFiles": 0,
"preexistingOutputs": 0
},
"viewer": {
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"contributionCount": 1,
"sessionCount": 1,
"activeSessionIds": [
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],
"mode": "sequence",
"singleOpenVerified": true,
"stateAssertions": [
"FASTQ overview",
"500 reads",
"read length, GC, and Q30 values from live viewer context"
]
},
"source": {
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"identifiers": [
"DRR037765",
"DRR037765.fastq.gz@md5:81735432a6f578b332aae58cdbd95231"
],
"officialEndpoints": [
"https://www.ebi.ac.uk/ena/portal/api/filereport",
"https://ftp.sra.ebi.ac.uk/vol1/fastq/DRR037/DRR037765/DRR037765.fastq.gz"
],
"route": "official-database-endpoint",
"bytesTransferred": 127687,
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"retrievedAt": "2026-07-02T14:57:04.080Z",
"subsetRule": "first 500 complete parsed FASTQ records in source order, canonical four-line FASTQ",
"identityValidated": true,
"formatValidated": true,
"nonEmptyValidated": true,
"boundedPayloadValidated": true,
"provenanceValidated": true,
"usedBundledFixture": false,
"usedPreexistingFile": false
},
"science": {
"status": "passed",
"liveViewerState": true,
"expectedResults": {
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"totalBases": 235490,
"readLengthMin": 469,
"readLengthMax": 471,
"gcPercent": 28.8462355,
"q30Percent": 95.3976814,
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},
"observations": [
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"The first 500 complete parsed FASTQ records were selected deterministically from 967 source records."
],
"operations": [
"read the mounted FASTQ summary from live viewer state"
]
},
"artifacts": {
"source": {
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},
"derived": null
},
"evidence": {
"screenshot": {
"url": "https://drive.google.com/file/d/11gjz67tpeyubOEd1Pnixmjf0e1RsQ1TU/view?usp=drivesdk",
"sha256": "8f45e0e71781243bf1fe4f522d65dafd9c7d6cf8ab53256d3718a954520060db"
},
"trace": {
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"archiveSha256": "9561b6557faf616d2a6dc91da87f5f09f6b5874c6e46becb6aa3631474aefbc1",
"memberPath": "lsc109-final5-share/installed-host/traces/ena-drr037765-first-500.json",
"sha256": "f0db23454e2e3f0b736ede7ed4bc361271d01c895952e4877e724b9372e9d4b1"
},
"log": {
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"archiveSha256": "9561b6557faf616d2a6dc91da87f5f09f6b5874c6e46becb6aa3631474aefbc1",
"memberPath": "lsc109-final5-share/installed-host/playwright.log",
"sha256": "7295cf3273358825f8bc836552530d2c3b74717e3697cad2004ff04c09a6ca0d"
},
"completeArchive": {
"url": "https://drive.google.com/file/d/15RF7MSatf_zpj97v5Zo0pV2sk2r_R8Po/view?usp=drivesdk",
"sha256": "9561b6557faf616d2a6dc91da87f5f09f6b5874c6e46becb6aa3631474aefbc1"
}
},
"timing": {
"startedAt": "2026-07-02T14:57:03.675Z",
"completedAt": "2026-07-02T14:57:07.656Z",
"durationMs": 3981
},
"bytes": {
"transferred": 127687,
"written": 482468
},
"acceptableNondeterminism": [
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"collision-safe source filename suffix on a non-clean workspace"
],
"modelRun": {
"entryPoint": "codex-chat",
"status": "passed",
"prompt": "Fetch ENA DRR037765 first 500 reads to active workspace; open and report live length range, GC, Q30, and subset provenance",
"model": "GPT-5.6 SOL",
"reasoning": "Ultra",
"installedBundleSha256": "2d9e8b8cbf24b3ad07fb94fd2816bc83c7a21f00e30fa2ab1a14338b0267db8c",
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"viewerMounted": true,
"optionalSkillAvailable": false,
"officialEndpointFallbackUsed": true,
"threadId": "019f235a-37b2-7041-a157-f829bc0bfcc6",
"toolSequence": [
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"sequence.query_viewer"
],
"evidence": {
"screenshot": {
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},
"log": {
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}
},
{
"id": "uniprot-human-ras-sv1",
"prompt": "Fetch UniProt P01116/P01111/P01112 alignment; map conserved motifs to KRAS, compute distances/tree, publish Newick to workspace",
"status": "passed",
"workspace": {
"fresh": true,
"initialEntries": [],
"preexistingBiologicalFiles": 0,
"preexistingOutputs": 0
},
"viewer": {
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"activeSessionIds": [
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],
"mode": "alignment",
"singleOpenVerified": true,
"stateAssertions": [
"three-row, 191-column aligned FASTA",
"P01116 KRAS as active reference",
"reference-coordinate mapping and conservation",
"distance matrix and graphical neighbor-joining tree"
]
},
"source": {
"database": "UniProtKB",
"identifiers": [
"P01116@SV1",
"P01111@SV1",
"P01112@SV1"
],
"officialEndpoints": [
"https://rest.uniprot.org/uniprotkb/P01116.fasta",
"https://rest.uniprot.org/uniprotkb/P01111.fasta",
"https://rest.uniprot.org/uniprotkb/P01112.fasta"
],
"route": "official-database-endpoint",
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"subsetRule": null,
"identityValidated": true,
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"nonEmptyValidated": true,
"boundedPayloadValidated": true,
"provenanceValidated": true,
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},
"science": {
"status": "passed",
"liveViewerState": true,
"expectedResults": {
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"artifactSha256": "cb32dd89ca7855f7666fbdf3f2ff926f935b1dbc9e7f57573f884dda7e59c68f",
"reference": "P01116",
"motifs": [
"P-loop KRAS 10-17 GAGGVGKS",
"switch I KRAS 30-38 DEYDPTIED",
"switch II KRAS 60-76 GQEEYSAMRDQYMRTGE",
"NKXD region KRAS 116-119 NKCD"
],
"caaxTails": {
"P01116": "CIIM",
"P01111": "CVVM",
"P01112": "CVLS"
},
"pDistances": {
"P01116/P01111": 0.1315789474,
"P01116/P01112": 0.1368421053,
"P01111/P01112": 0.1578947368
},
"treeLeaves": [
"P01116",
"P01111",
"P01112"
],
"treeNewick": "('P01116':0.027632,('P01111':0.076316,'P01112':0.081579):0.027632);",
"treeInterpretation": "exploratory uncorrected p-distance guide tree; do not interpret the three-leaf topology as a publication phylogeny"
},
"observations": [
"KRAS P01116 was the active reference; all three RAS rows preserved the four pinned core motifs.",
"Live p-distances were 0.1315789474, 0.1368421053, and 0.1578947368; the exact three-leaf neighbor-joining Newick was reproduced.",
"The Newick and provenance sidecar round-tripped by SHA-256; an exact collision failed without changing either file; remount retained the same session."
],
"operations": [
"sequence.control_viewer set_alignment_reference P01116",
"map KRAS reference residues 10-17, 30-38, 60-76, and 116-119",
"sequence.run_analysis distance-matrix",
"sequence.run_analysis build-tree neighbor-joining",
"sequence.export_artifact newick to workspace"
]
},
"artifacts": {
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},
"derived": {
"format": "newick",
"destination": {
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"base": "opened-source",
"relativePath": "RAS-P01116-P01111-P01112-NJ.nwk"
},
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},
"observedError": "ENA file metadata did not uniquely match the pinned run and FASTQ file."
},
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"evidence": {
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},
"observedError": "The authoritative response exceeded the starter byte budget."
},
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"noMisleadingArtifact": true,
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}
},
"observedError": "The pinned ENA run did not contain 500 complete, identity-matched FASTQ reads."
},
{
"requirement": "optional-skill-unavailable-fallback",
"status": "passed",
"actionableResult": true,
"noMisleadingViewer": true,
"noMisleadingArtifact": true,
"noBundledFallback": true,
"testRef": "visible ENA starter acquires through MCP and reports live FASTQ QC",
"evidence": {
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"trace": {
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},
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},
"requirement": "optional-skill-unavailable-fallback",
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}
},
"optionalSkillAvailable": false,
"officialEndpointFallbackSucceeded": true
},
{
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"status": "passed",
"actionableResult": true,
"noMisleadingViewer": true,
"noMisleadingArtifact": true,
"noBundledFallback": true,
"testRef": "visible UniProt RAS starter maps a reference, computes distances/tree, and publishes provenance Newick",
"evidence": {
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},
"trace": {
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},
"observedError": "The viewer could not persist the requested workbench payload: The workspace export or provenance sidecar already exists."
},
{
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"status": "passed",
"actionableResult": true,
"noMisleadingViewer": true,
"noMisleadingArtifact": true,
"noBundledFallback": true,
"testRef": "bundle-backed output quota failure preserves the mounted source and publishes no derived artifact",
"evidence": {
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},
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},
"observedError": "The viewer could not persist the requested workbench payload: The workspace destination does not have enough free disk space for this chunk."
},
{
"requirement": "viewer-retry-remount",
"status": "passed",
"actionableResult": true,
"noMisleadingViewer": true,
"noMisleadingArtifact": true,
"noBundledFallback": true,
"testRef": "visible UniProt RAS starter maps a reference, computes distances/tree, and publishes provenance Newick",
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},
"trace": {
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}
},
"retryOrRemountSucceeded": true,
"sessionContinuityVerified": true
}
],
"relatedIssues": [
{
"id": "LSC-79",
"url": "https://linear.app/openai/issue/LSC-79/validate-the-v1-sequence-viewer-reference-workflow",
"workflow": "Qualified annotated lambda Sequence reference workflow"
},
{
"id": "LSC-82",
"url": "https://linear.app/openai/issue/LSC-82/validate-the-v1-alignment-viewer-reference-workflow",
"workflow": "Qualified multi-record human RAS Alignment reference workflow"
}
],
"knownLimits": [
"The three-leaf RAS tree is an exploratory guide tree, not a publication phylogeny.",
"Authoritative endpoints remain externally operated and can rate-limit or become temporarily unavailable.",
"The installed-host harness records the optional-skill-disabled official-endpoint lane; optional skills are not required for success."
],
"acceptableNondeterminism": [
"retrieval timestamp and HTTP cache metadata",
"collision-safe source filename suffix on a non-clean workspace",
"collision-safe acquired-source filename suffix on a non-clean workspace",
"equivalent Newick child ordering and display layout with the same leaf set and distances",
"retrieval timestamp, HTTP cache metadata, and GenBank annotation serialization"
]
}
```
SHA-256: a793a8d98137e0b110b3bf669d3c77b9505a4aecafc54d92e76956db69d79f7d