Question
I have a counts matrix of transcriptomic reads from a murine multi-tissue fibroblast atlas, tissue.fibroblast.q1.rds. I want to know what tissue the fibroblast corresponding to barcode Cell_11249_MCI is from, and what tissue the fibroblast corresponding to the barcode Cell_10369_WXV is. Please provide an answer in a string format with each answer separated by a comma, and select each answer from "Lymph node", "Pancreas", "Muscle", "Tendon", "Mesentery", "Omentum" , 'Adipose", "Artery", "Bone", "Heart", "Intestine", "Skin", "Lung", "Liver", or "Spleen". Expected output format example: Pancreas,Omentum.
- Inferred answer
Lung,BoneUniquely inferred from submitted scores.- Domain
- Single-cell
- Question style
- Routine Analysis
An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.
Galaxy
12/12 terminal item results
UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.
Codex GPT-5.5
3 replicates
Codex GPT-5.5
Replicate 1
IncorrectUDT-only
AnswerOmentum,Bone
WorkflowLookup fibroblast tissue from RDS→Inspect RDS structure for barcode metadata→Target barcode marker scores→Inspect reference fibroblast RDS→Inspect reference fibroblast Seurat RDS→2 more tools
Codex GPT-5.5
Replicate 2
IncorrectUDT-only
AnswerOmentum,Bone
WorkflowRDS tissue lookup diagnostic→RDS marker diagnostic→RDS source match tissue→RDS source match tissue Seurat→RDS source match tissue Seurat v2→3 more tools
- Total tokens
- 3.5M
- Output
- 21.0K
Codex GPT-5.5
Replicate 3
CorrectUDT + standard tools
AnswerLung,Bone
WorkflowInspect fibroblast RDS metadata→Inspect fibroblast RDS metadata v2→Inspect fibroblast RDS metadata v3→UDT probe cat
- Total tokens
- 6.6M
- Output
- 28.6K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
CorrectUDT-only
AnswerLung,Bone
WorkflowInspect fibroblast RDS structure→Inspect fibroblast barcode conventions→Inspect fibroblast target barcodes→Inspect authoritative fibroblast atlas
- Total tokens
- 22.6M
- Output
- 21.4K
Codex GPT-5.6 Sol
Replicate 2
IncorrectUDT-only
AnswerOmentum,Bone
WorkflowInspect fibroblast atlas RDS structure→Inspect target fibroblast cells→Upload1→Inspect authoritative steady-state Seurat object→Match fibroblast cells to authoritative tissue labels
- Total tokens
- 4.4M
- Output
- 11.9K
Codex GPT-5.6 Sol
Replicate 3
IncorrectUDT-only
AnswerOmentum,Bone
WorkflowInspect RDS structure for fibroblast atlas→Inspect target fibroblast barcodes and suffix groups→Inspect authoritative fibroblast source atlas→Inspect authoritative fibroblast source atlas with Seurat→Exact match fibroblast tissues to authoritative atlas→1 more tools
- Total tokens
- 35.5M
- Output
- 27.4K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
IncorrectUDT + standard tools
AnswerOmentum,Bone
WorkflowRds To Tabular→Seurat Data→Inspect RDS Structure→Match Q1 Reference Diagnostic→Seurat Export Cellbrowser→3 more tools
- Total tokens
- 10.5M
- Output
- 42.3K
Codex + DeepSeek-v4-pro-0813
Replicate 2
IncorrectUDT + standard tools
AnswerOmentum,Bone
WorkflowRds To Tabular→Inspect RDS→Inspect Matrix→Inspect Attrs→Inspect Seurat Min→3 more tools
- Total tokens
- 15.4M
- Output
- 40.8K
Codex + DeepSeek-v4-pro-0813
Replicate 3
RerunCorrectUDT + standard tools
AnswerLung,Bone
WorkflowRDS to tabular→SCEasy convert→Inspect RDS→Inspect Colnames→Profile Cells→1 more tools
- Total tokens
- 5.1M
- Output
- 57.8K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
RerunCorrectUDT + standard tools
AnswerLung,Bone
WorkflowRDS to tabular→RDS structure inspection→Target cell expression profiles→Excel to Tabular→RDS tissue marker scoring→4 more tools
- Total tokens
- 45.6M
- Output
- 61.0K
Codex GPT-5.6 Luna
Replicate 2
RerunIncorrectUDT-only
AnswerLung,Lymph node
WorkflowUser-defined tool
- Total tokens
- 20.9M
- Output
- 65.8K
Codex GPT-5.6 Luna
Replicate 3
CorrectUDT + standard tools
AnswerLung,Bone
WorkflowRDS Structure Report→Inspect Target Cells→Target Expression Neighbors→Score Tissue Marker Panels→Xlsx2Tsv→3 more tools
- Total tokens
- 20.2M
- Output
- 64.7K