Codex GPT-5.5
replicate 1
passUDT-only
Answer
5.812405901836796Workflow
Galaxy UDTPyDESeq2GSEApyReactomeEnrichr
- Total tokens
- 1.63M
- Output
- 20.1K
New token-optimization experiment
Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.
Question
What is the odds ratio for p53-mediated cell cycle gene regulation in an enrichment analysis using gseapy with Reactome_2022 using all statistically differentially expressed genes from a pydeseq2 analysis that includes all related treatment groups (DMSO, DMSO_Serum_starvation, Cisplatin_IC50_CBD_IC50, Cisplatin_IC50_CBD_IC50_Serum_starvation_16h) for proper dispersion estimation, after pre-filtering to keep only genes with counts greater than 10 in at least one of all 30 samples, (padj<=0.05, absolute lfc>=0.5, baseMean>=10) between CBD/cisplatin combination treatment and DMSO?
Comparison
Pass counts and token totals across the same three replicates.
| Agent | Galaxy-API code | Open-ended code |
|---|---|---|
| Codex GPT-5.5 | 3/3 replicate 1 replicate 2 replicate 3 3.92M total | 1/3 replicate 1 replicate 2 replicate 3 1.29M total |
| Codex GPT-5.6 Sol | 3/3 replicate 1 replicate 2 replicate 3 3.95M total | 2/3 replicate 1 replicate 2 replicate 3 4.32M total |
| Codex GPT-5.6 Luna | 1/3 replicate 1 replicate 2 replicate 3 12.94M total | 2/3 replicate 1 replicate 2 replicate 3 6.07M total |
| DeepSeek V4 Pro via Codex | 0/3 replicate 1 replicate 2 replicate 3 131.17M total | 0/3 replicate 1 replicate 2 replicate 3 5.47M total |
| DeepSeek V4 Pro via Claude Codesuperseded | 2/3 replicate 1 replicate 2 replicate 3 10.89M total | 0/3 replicate 1 replicate 2 replicate 3 2.40M total |
Execution condition
Galaxy-API code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 2
passUDT + standard tools
Answer
5.812405901836796Workflow
Galaxy UDTGSEApy EnrichrPyDESeq2Reactome
- Total tokens
- 1.29M
- Output
- 20.5K
Codex GPT-5.5
replicate 3
passUDT-only
Answer
5.8124059018368Workflow
Galaxy UDTPyDESeq2GSEApyReactomeEnrichr
- Total tokens
- 999.4K
- Output
- 26.7K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
passUDT + standard tools
Answer
5.812405901836796Workflow
Galaxy UDTGSEApy EnrichrPyDESeq2
- Total tokens
- 1.33M
- Output
- 14.3K
Codex GPT-5.6 Sol
replicate 2
passUDT + standard tools
Answer
5.812405901836796Workflow
Galaxy UDTGSEApy EnrichrPyDESeq2
- Total tokens
- 1.45M
- Output
- 13.4K
Codex GPT-5.6 Sol
replicate 3
passUDT + standard tools
Answer
5.812405901836796Workflow
Galaxy UDTGSEApy EnrichrPyDESeq2Reactome
- Total tokens
- 1.17M
- Output
- 12.1K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
passUDT + standard tools
Answer
5.812405901836796Workflow
Galaxy UDTGSEApy EnrichrReactomePyDESeq2
- Total tokens
- 2.57M
- Output
- 23.8K
Codex GPT-5.6 Luna
replicate 2
failUDT + standard tools
Why it missed
Unrequested custom enrichment universeThis run supplied a custom 19,073/19,074-gene background to GSEApy and obtained 5.817980. The task does not request a custom universe; the standard amd64 route returns 5.812406, which rounds to the accepted 5.81.
Answer
5.817980373535929Workflow
Galaxy UDTGSEApy EnrichrReactomePyDESeq2
- Total tokens
- 4.81M
- Output
- 35.9K
Scoring review: Re-scored under the published two-decimal rule. The observed 5.817980 rounds to 5.82, not the accepted amd64 result 5.81.
Codex GPT-5.6 Luna
replicate 3
failUDT + standard tools
Why it missed
Unrequested custom enrichment universeThis run supplied a custom 19,073/19,074-gene background to GSEApy and obtained 5.817980. The task does not request a custom universe; the standard amd64 route returns 5.812406, which rounds to the accepted 5.81.
Answer
5.817980373535929Workflow
Upload datasetGalaxy UDTGSEApy EnrichrPyDESeq2
- Total tokens
- 5.56M
- Output
- 33.9K
Scoring review: Re-scored under the published two-decimal rule. The observed 5.817980 rounds to 5.82, not the accepted amd64 result 5.81.
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
fail
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
7.172895157772285Workflow
Galaxy via BioBlendGSEApyPyDESeq2EnrichrReactome
- Total tokens
- 65.84M
- Output
- 146.0K
DeepSeek V4 Pro via Codex
replicate 2
failUDT + standard tools
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
5.8591207373971095Workflow
Galaxy via BioBlendSciPystatsmodelsGSEApyPyDESeq2
- Total tokens
- 63.43M
- Output
- 199.3K
DeepSeek V4 Pro via Codex
replicate 3
fail
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
not producedWorkflow
Galaxy via BioBlendGSEApyPyDESeq2EnrichrReactome
- Total tokens
- 1.90M
- Output
- 17.9K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
passUDT + standard tools
Answer
5.812405901836796Workflow
Galaxy UDTGSEApy EnrichrPyDESeq2
- Total tokens
- 2.45M
- Output
- 35.3K
DeepSeek V4 Pro via Claude Code
replicate 2
failUDT + standard tools
Why it missed
Identifier and background scope changedThis run used 679 foreground symbols and a 20,090-gene background instead of 656 unique mapped symbols and a 19,074-gene universe. The larger contingency table changed the odds ratio from 5.812 to 5.922.
Answer
5.922121594252742Workflow
Galaxy UDTGSEApy EnrichrPyDESeq2Reactome
- Total tokens
- 6.12M
- Output
- 67.0K
DeepSeek V4 Pro via Claude Code
replicate 3
passUDT + standard tools
Answer
5.812405901836796Workflow
DESeq2GSEApy EnrichrPyDESeq2
- Total tokens
- 2.32M
- Output
- 30.5K
Execution condition
Open-ended code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 1
fail
Why it missed
Identifier and background scope changedThis run's Ensembl mapping and enrichment background produced an odds ratio of 5.846. The stable mapped foreground and universe produce 5.840 on this architecture.
Answer
5.8459948320413435Workflow
Local analysisPyDESeq2GSEApySciPyEnrichr
- Total tokens
- 396.6K
- Output
- 8.5K
Codex GPT-5.5
replicate 2
fail
Why it missed
Identifier and background scope changedThis run changed which mapped genes entered the foreground or Reactome universe, producing an odds ratio of 6.128 instead of the accepted 5.81/5.84 result.
Answer
6.12816088009Workflow
Local analysisPyDESeq2GSEApySciPystatsmodels
- Total tokens
- 433.9K
- Output
- 7.0K
Codex GPT-5.5
replicate 3
pass
Answer
5.84034789185101Workflow
Local analysisPyDESeq2GSEApySciPystatsmodels
- Total tokens
- 462.4K
- Output
- 7.5K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
fail
Why it missed
DE gene set changedThis run selected 654 unique mapped DE genes rather than the stable 653-gene arm64 foreground and reported 5.831005. Under the published exact two-decimal rule, 5.83 is neither accepted platform result, 5.81 or 5.84.
Answer
5.831005059276599Workflow
Local analysis
- Total tokens
- 2.53M
- Output
- 11.3K
Scoring review: Re-scored under the published two-decimal rule. The observed 5.831005 rounds to 5.83, which is neither accepted platform result, 5.81 or 5.84.
Codex GPT-5.6 Sol
replicate 2
pass
Answer
5.840347891851011Workflow
Local analysis
- Total tokens
- 1.04M
- Output
- 7.9K
Scoring review: Re-scored under the published platform-aware rule. The observed 5.840348 rounds to the accepted arm64 result, 5.84.
Codex GPT-5.6 Sol
replicate 3
pass
Answer
5.840347891851011Workflow
Local analysis
- Total tokens
- 739.2K
- Output
- 6.7K
Scoring review: Re-scored under the published platform-aware rule. The observed 5.840348 rounds to the accepted arm64 result, 5.84.
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
5.840348Workflow
Local analysis
- Total tokens
- 1.13M
- Output
- 13.4K
Scoring review: Re-scored under the published platform-aware rule. The observed 5.840348 rounds to the accepted arm64 result, 5.84.
Codex GPT-5.6 Luna
replicate 2
fail
Why it missed
DE gene set changedThis run selected 654 unique mapped DE genes rather than the stable 653-gene arm64 foreground and reported 5.831005. It rounds to 5.83, outside the accepted platform values 5.81 and 5.84.
Answer
5.831005059276599Workflow
Local analysis
- Total tokens
- 2.54M
- Output
- 19.8K
Scoring review: Re-scored under the published two-decimal rule. The observed 5.831005 rounds to 5.83, which is neither accepted platform result, 5.81 or 5.84.
Codex GPT-5.6 Luna
replicate 3
pass
Answer
5.840348Workflow
Local analysis
- Total tokens
- 2.41M
- Output
- 17.0K
Scoring review: Re-scored under the published platform-aware rule. The observed 5.840348 rounds to the accepted arm64 result, 5.84.
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
fail
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
5.831005059276599Workflow
Local analysisGSEApyPyDESeq2SciPyEnrichr
- Total tokens
- 2.65M
- Output
- 28.4K
DeepSeek V4 Pro via Codex
replicate 2
fail
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
5.831005059276599Workflow
Local analysisPyDESeq2GSEApySciPyscikit-learn
- Total tokens
- 999.8K
- Output
- 16.5K
DeepSeek V4 Pro via Codex
replicate 3
fail
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
5.831005059276599Workflow
Local analysisGSEApySciPystatsmodelsPyDESeq2
- Total tokens
- 1.83M
- Output
- 27.7K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
fail
Why it missed
Identifier and background scope changedThis run used a different identifier mapping, foreground, or enrichment universe from the stable route. Because the odds ratio depends on the full background table, that scope change moved the result outside the accepted 5.81/5.84 values.
Answer
5.8459948320413435Workflow
Local analysisPyDESeq2GSEApySciPyReactome
- Total tokens
- 1.10M
- Output
- 18.2K
DeepSeek V4 Pro via Claude Code
replicate 2
fail
Why it missed
Identifier and background scope changedThis run used a different identifier mapping, foreground, or enrichment universe from the stable route. Because the odds ratio depends on the full background table, that scope change moved the result outside the accepted 5.81/5.84 values.
Answer
5.623828794341755Workflow
Local analysisGSEApyPyDESeq2EnrichrReactome
- Total tokens
- 619.0K
- Output
- 7.4K
DeepSeek V4 Pro via Claude Code
replicate 3
fail
Why it missed
Identifier and background scope changedThis run used a different identifier mapping, foreground, or enrichment universe from the stable route. Because the odds ratio depends on the full background table, that scope change moved the result outside the accepted 5.81/5.84 values.
Answer
6.159561800428674Workflow
Local analysisPyDESeq2GSEApySciPy
- Total tokens
- 680.6K
- Output
- 11.1K
bix-43-q2 · October 2026 · three additional replicates
GPT-5.6 Sol · token optimization
Galaxy-API code, high reasoning, Fast service. Previous runs are retained above.
Galaxy-API code · October 2026
replicate 1
Correct
Answer
5.812405901836796- Total tokens
- 917.7K
- Input
- 905.8K
- Cached input
- 860.8K
- Output
- 11.8K
Galaxy-API code · October 2026
replicate 2
Correct
Answer
5.812405901836796- Total tokens
- 864.3K
- Input
- 852.2K
- Cached input
- 794.9K
- Output
- 12.1K
Galaxy-API code · October 2026
replicate 3
Correct
Answer
5.812405901836796- Total tokens
- 894.5K
- Input
- 883.0K
- Cached input
- 823.3K
- Output
- 11.5K
Open-ended code averaged 1.44M tokens; previous website Galaxy averaged 1.32M; the new Galaxy runs averaged 0.89M, or 0.62× Open-ended code. Each mean covers three replicates of this same task with GPT-5.6 Sol.
Cached input is already included in input tokens. Full nested tool/job evidence is in each HF run's galaxy_execution_records.tar.gz, with an accompanying member index.