Codex GPT-5.5
replicate 1
passUDT + standard tools
Answer
downregulationWorkflow
Galaxy UDTGprofiler GostDESeq2clusterProfilerg:Profilerfold-change calculation
- Total tokens
- 1.32M
- Output
- 9.9K
New token-optimization experiment
Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.
Question
Using differential expression analysis (padj < 0.05, |log2FC| > 0.5) and GO Biological Process enrichment analysis, determine whether upregulation or downregulation of genes primarily drives the metabolic effects of CBD treatment in CRC cells.
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 4.38M total | 3/3 replicate 1 replicate 2 replicate 3 3.19M total |
| Codex GPT-5.6 Sol | 3/3 replicate 1 replicate 2 replicate 3 11.04M total | 2/3 replicate 1 replicate 2 replicate 3 4.57M total |
| Codex GPT-5.6 Luna | 2/3 replicate 1 replicate 2 replicate 3 47.29M total | 3/3 replicate 1 replicate 2 replicate 3 6.79M total |
| DeepSeek V4 Pro via Codex | 3/3 replicate 1 replicate 2 replicate 3 35.12M total | 3/3 replicate 1 replicate 2 replicate 3 13.44M total |
| DeepSeek V4 Pro via Claude Codesuperseded | 3/3 replicate 1 replicate 2 replicate 3 13.55M total | 3/3 replicate 1 replicate 2 replicate 3 4.76M total |
Execution condition
Galaxy-API code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 2
passUDT + standard tools
Answer
downregulationWorkflow
Galaxy UDTGprofiler GostDESeq2clusterProfilerg:Profiler
- Total tokens
- 1.69M
- Output
- 15.3K
Codex GPT-5.5
replicate 3
passUDT + standard tools
Answer
downregulationWorkflow
Galaxy UDTGprofiler GostDESeq2g:ProfilerclusterProfiler
- Total tokens
- 1.37M
- Output
- 9.2K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
passUDT + standard tools
Answer
DownregulationWorkflow
Convert Characters1Select columnsDESeq2Galaxy UDTGprofiler Gost
- Total tokens
- 3.64M
- Output
- 15.8K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
downregulationWorkflow
Select columnsDESeq2Filter rowsGprofiler Gost
- Total tokens
- 4.81M
- Output
- 17.0K
Codex GPT-5.6 Sol
replicate 3
passUDT + standard tools
Answer
downregulationWorkflow
Select columnsDESeq2Galaxy UDTGprofiler Gost
- Total tokens
- 2.59M
- Output
- 14.9K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
passUDT + standard tools
Answer
downregulationWorkflow
Csv To TabularSelect columnsDESeq2Galaxy UDTFilter rowsGprofiler Gost
- Total tokens
- 10.24M
- Output
- 45.1K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
downregulationWorkflow
Csv To TabularSelect columnsEdgerFilter rowsGprofiler Gost
- Total tokens
- 13.71M
- Output
- 43.9K
Codex GPT-5.6 Luna
replicate 3
fail
Why it missed
Model and enrichment scope changedThis run fit all ten treatment groups with edgeR, used the live GO_Biological_Process_2023 library, and chose the direction by counting significant metabolic terms. That broader route returned upregulation; the matched CBD-versus-DMSO analysis supporting the accepted answer returns downregulation.
Answer
upregulationWorkflow
Csv To TabularConvert Characters1Edgermore stepsAnnotatemyidsGSEApy Enrichr
- Total tokens
- 23.34M
- Output
- 66.2K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
pass
Answer
downregulationWorkflow
Galaxy via BioBlendDESeq2clusterProfilerg:Profiler
- Total tokens
- 4.88M
- Output
- 37.3K
DeepSeek V4 Pro via Codex
replicate 2
pass
Answer
downregulationWorkflow
Galaxy via BioBlendSciPyDESeq2clusterProfilerg:Profilerfold-change calculation
- Total tokens
- 8.58M
- Output
- 32.0K
DeepSeek V4 Pro via Codex
replicate 3
pass
Answer
downregulationWorkflow
Galaxy via BioBlendDESeq2clusterProfilerg:Profiler
- Total tokens
- 21.66M
- Output
- 71.7K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
pass
Answer
downregulationWorkflow
DESeq2Gprofiler Gostfold-change calculation
- Total tokens
- 2.70M
- Output
- 25.8K
DeepSeek V4 Pro via Claude Code
replicate 2
passUDT + standard tools
Answer
downregulationWorkflow
DESeq2fold-change calculationg:ProfilerKEGGReactome
- Total tokens
- 5.71M
- Output
- 47.0K
DeepSeek V4 Pro via Claude Code
replicate 3
passUDT + standard tools
Answer
downregulationWorkflow
Select columnsDESeq2Gprofiler Gostfold-change calculationg:Profiler
- Total tokens
- 5.15M
- Output
- 41.1K
Execution condition
Open-ended code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 1
pass
Answer
downregulationWorkflow
Local analysisclusterProfilerPyDESeq2GSEApyg:Profiler
- Total tokens
- 1.37M
- Output
- 10.2K
Codex GPT-5.5
replicate 2
pass
Answer
downregulationWorkflow
Local analysisDESeq2clusterProfilerapeglmedgeRSciPy
- Total tokens
- 747.7K
- Output
- 9.8K
Codex GPT-5.5
replicate 3
pass
Answer
downregulationWorkflow
Local analysisSciPystatsmodelsGSEApyDESeq2edgeR
- Total tokens
- 1.08M
- Output
- 11.9K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
fail
Why it missed
Model scope changed the enrichment directionThe direct CBD-versus-DMSO fit pointed to downregulation, but this run chose a ten-level, all-30-sample dispersion model and counted live GO terms to select upregulation. Expanding the model beyond the matched six-sample comparison changed the requested direction.
Answer
UpregulationWorkflow
Local analysis
- Total tokens
- 1.13M
- Output
- 12.5K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
downregulationWorkflow
Local analysis
- Total tokens
- 1.51M
- Output
- 11.6K
Codex GPT-5.6 Sol
replicate 3
pass
Answer
DownregulationWorkflow
Local analysis
- Total tokens
- 1.93M
- Output
- 12.0K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
downregulationWorkflow
Local analysis
- Total tokens
- 1.58M
- Output
- 13.4K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
downregulationWorkflow
Local analysis
- Total tokens
- 1.99M
- Output
- 18.8K
Codex GPT-5.6 Luna
replicate 3
pass
Answer
downregulationWorkflow
Local analysis
- Total tokens
- 3.23M
- Output
- 15.3K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
pass
Answer
downregulationWorkflow
Local analysisDESeq2clusterProfilerSciPystatsmodelsGSEApy
- Total tokens
- 3.31M
- Output
- 28.0K
DeepSeek V4 Pro via Codex
replicate 2
pass
Answer
downregulationWorkflow
Local analysisDESeq2clusterProfilerstatsmodelsGSEApyedgeR
- Total tokens
- 6.69M
- Output
- 43.8K
DeepSeek V4 Pro via Codex
replicate 3
pass
Answer
downregulationWorkflow
Local analysisSciPystatsmodelsGSEApyReactomeDESeq2
- Total tokens
- 3.43M
- Output
- 23.4K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
pass
Answer
downregulationWorkflow
Local analysisclusterProfilerPyDESeq2SciPyGSEApy
- Total tokens
- 1.26M
- Output
- 23.8K
DeepSeek V4 Pro via Claude Code
replicate 2
pass
Answer
downregulationWorkflow
Local analysisDESeq2clusterProfilerstatsmodelsSciPyGSEApy
- Total tokens
- 2.42M
- Output
- 25.6K
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
downregulationWorkflow
Local analysisSciPyPyDESeq2GSEApystatsmodels
- Total tokens
- 1.09M
- Output
- 19.2K
bix-24-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
Downregulation- Total tokens
- 1.46M
- Input
- 1.45M
- Cached input
- 1.37M
- Output
- 11.0K
Galaxy-API code · October 2026
replicate 2
Correct
Answer
downregulation- Total tokens
- 3.31M
- Input
- 3.30M
- Cached input
- 3.18M
- Output
- 14.7K
Galaxy-API code · October 2026
replicate 3
Correct
Answer
Downregulation- Total tokens
- 1.30M
- Input
- 1.29M
- Cached input
- 1.21M
- Output
- 10.5K
Open-ended code averaged 1.52M tokens; previous website Galaxy averaged 3.68M; the new Galaxy runs averaged 2.02M, or 1.33× 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.