messages listlengths 3 11 | tools listlengths 6 6 | metadata unknown |
|---|---|---|
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Retrieve the coding fragment at fixture_contig_A positions 301 to 315, the... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "cx-296ffd91b2306ab29bfe",
"scenario_family_id": "workflow:translation_check",
"trajectory": true,
"synthetic": false,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Search the pinned UniProt snapshot for reviewed bacterial ribosomal protei... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "cx-dbefff4e3be2fceff7a9",
"scenario_family_id": "workflow:protein_lookup",
"trajectory": true,
"synthetic": false,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Search the pinned UniProt snapshot for reviewed bacterial ribosomal protei... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "cx-dbefff4e3be2fceff7a9",
"scenario_family_id": "workflow:protein_lookup",
"trajectory": true,
"synthetic": false,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Analyze domains in this protein sequence"
},
{
"role": "assistant"... | [
{
"type": "function",
"function": {
"name": "analyze_interpro_domains",
"description": "Analyze protein domains, families, and functional sites using InterPro database. Provides comprehensive domain architecture, functional annotations, and evolutionary relationships.",
"parameters": {
... | {
"source_example_id": "cx-2709f01bece9beebcc6d",
"scenario_family_id": "registry:analyze_interpro_domains:0",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Create a BLAST database from the loaded chromosome"
},
{
"role": "... | [
{
"type": "function",
"function": {
"name": "blast_create_db_from_genome",
"description": "Create BLAST nucleotide database from a specific chromosome of the currently loaded genome. Use this ONLY when you want to index a single chromosome and have its exact name from the loaded genome (e.g. U00... | {
"source_example_id": "cx-3f6ef8d22106f673e8a1",
"scenario_family_id": "registry:blast_create_db_from_genome:0",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Make a searchable database for E. coli K-12 genome"
},
{
"role": "... | [
{
"type": "function",
"function": {
"name": "blast_create_db_from_genome",
"description": "Create BLAST nucleotide database from a specific chromosome of the currently loaded genome. Use this ONLY when you want to index a single chromosome and have its exact name from the loaded genome (e.g. U00... | {
"source_example_id": "cx-de751040340af25048a1",
"scenario_family_id": "registry:blast_create_db_from_genome:1",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Search this DNA sequence against NCBI nucleotide database"
},
{
"r... | [
{
"type": "function",
"function": {
"name": "blast_search_online",
"description": "Perform BLAST sequence similarity search using NCBI online databases",
"parameters": {
"type": "object",
"properties": {
"sequence": {
"type": "string"
},
... | {
"source_example_id": "cx-9e82c11ce3a6af29ed03",
"scenario_family_id": "registry:blast_search_online:0",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "BLAST this protein sequence against SwissProt"
},
{
"role": "assis... | [
{
"type": "function",
"function": {
"name": "blast_search_online",
"description": "Perform BLAST sequence similarity search using NCBI online databases",
"parameters": {
"type": "object",
"properties": {
"sequence": {
"type": "string"
},
... | {
"source_example_id": "cx-a2967a1e8e508fc15617",
"scenario_family_id": "registry:blast_search_online:1",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Hide the gene track"
},
{
"role": "assistant",
"content": null... | [
{
"type": "function",
"function": {
"name": "toggle_track",
"description": "Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.",
"parameters": {
"type": "object",
"properties": {... | {
"source_example_id": "cx-ac779b3a0b1d3917f872",
"scenario_family_id": "registry:toggle_track:0",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Show GC content"
},
{
"role": "assistant",
"content": null,
... | [
{
"type": "function",
"function": {
"name": "toggle_track",
"description": "Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.",
"parameters": {
"type": "object",
"properties": {... | {
"source_example_id": "cx-e267c57abfe8a7918f7c",
"scenario_family_id": "registry:toggle_track:1",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Attach the note curated independently to the annotation identified as gene... | [
{
"type": "function",
"function": {
"name": "update_annotation",
"description": "Legacy compatibility tool that creates a reviewable annotation ChangeSet; it does not mutate an annotation directly.",
"parameters": {
"type": "object",
"properties": {
"identifier": ... | {
"source_example_id": "cx-690008a7ba510c7cdd39",
"scenario_family_id": "coverage:update_annotation:v1",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Attach the note curated independently to the annotation identified as gene... | [
{
"type": "function",
"function": {
"name": "update_annotation",
"description": "Legacy compatibility tool that creates a reviewable annotation ChangeSet; it does not mutate an annotation directly.",
"parameters": {
"type": "object",
"properties": {
"identifier": ... | {
"source_example_id": "cx-690008a7ba510c7cdd39",
"scenario_family_id": "coverage:update_annotation:v1",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Show at most ten edit-history entries for annotation geneX."
},
{
... | [
{
"type": "function",
"function": {
"name": "get_annotation_history",
"description": "Retrieve change history for a specific annotation or the entire genome",
"parameters": {
"type": "object",
"properties": {
"identifier": {
"type": "string"
... | {
"source_example_id": "cx-381ffddc84238eb78adc",
"scenario_family_id": "coverage:get_annotation_history:v1",
"trajectory": false,
"synthetic": false,
"variant": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg01 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-1f23194884cb028b",
"scenario_family_id": "synthetic:find",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg01 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-1f23194884cb028b",
"scenario_family_id": "synthetic:find",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-7d7e2684ed06bb13",
"scenario_family_id": "synthetic:seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-7d7e2684ed06bb13",
"scenario_family_id": "synthetic:seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-3d54d3420c3d07b0",
"scenario_family_id": "synthetic:seq_revcomp",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-3d54d3420c3d07b0",
"scenario_family_id": "synthetic:seq_revcomp",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-b5bc9fe8d262f125",
"scenario_family_id": "synthetic:seq_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-b5bc9fe8d262f125",
"scenario_family_id": "synthetic:seq_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，查找 BamHI 酶切位点，然后对整段序列做虚拟酶切。"
}... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-3d08f98177eb41e2",
"scenario_family_id": "synthetic:seq_digest",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，查找 BamHI 酶切位点，然后对整段序列做虚拟酶切。"
}... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-3d08f98177eb41e2",
"scenario_family_id": "synthetic:seq_digest",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，查找 BamHI 酶切位点，然后对整段序列做虚拟酶切。"
}... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-3d08f98177eb41e2",
"scenario_family_id": "synthetic:seq_digest",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, list the annotations on px_core_A, then ... | [
{
"type": "function",
"function": {
"name": "list_annotations",
"description": "List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation ... | {
"source_example_id": "v3-syn-1ef2228c55fe7c0e",
"scenario_family_id": "synthetic:ann_list",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, list the annotations on px_core_A, then ... | [
{
"type": "function",
"function": {
"name": "list_annotations",
"description": "List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation ... | {
"source_example_id": "v3-syn-1ef2228c55fe7c0e",
"scenario_family_id": "synthetic:ann_list",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，查看 px_core_B:525 附近 5000bp 内的特征，并取出第一个特征的完整注释。"
},
{
... | [
{
"type": "function",
"function": {
"name": "get_nearby_features",
"description": "Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position... | {
"source_example_id": "v3-syn-b499166c326b72a7",
"scenario_family_id": "synthetic:ann_nearby",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，查看 px_core_B:525 附近 5000bp 内的特征，并取出第一个特征的完整注释。"
},
{
... | [
{
"type": "function",
"function": {
"name": "get_nearby_features",
"description": "Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position... | {
"source_example_id": "v3-syn-b499166c326b72a7",
"scenario_family_id": "synthetic:ann_nearby",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In the pinned UniProt fixture corpus, search for \"pinned catalytic\", the... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-03204345b46b95d3",
"scenario_family_id": "synthetic:uniprot",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In the pinned UniProt fixture corpus, search for \"pinned catalytic\", the... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-03204345b46b95d3",
"scenario_family_id": "synthetic:uniprot",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，精确查找基因 fxg12（不要跳转视图），取出其返回区间的序列，并计算该序列的 GC 含量。"
},
{
... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-48b422b013592de8",
"scenario_family_id": "synthetic:find_seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，精确查找基因 fxg12（不要跳转视图），取出其返回区间的序列，并计算该序列的 GC 含量。"
},
{
... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-48b422b013592de8",
"scenario_family_id": "synthetic:find_seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，精确查找基因 fxg12（不要跳转视图），取出其返回区间的序列，并计算该序列的 GC 含量。"
},
{
... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-48b422b013592de8",
"scenario_family_id": "synthetic:find_seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-b04c6f813ad2eefa",
"scenario_family_id": "synthetic:seq_translate_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-b04c6f813ad2eefa",
"scenario_family_id": "synthetic:seq_translate_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-b04c6f813ad2eefa",
"scenario_family_id": "synthetic:seq_translate_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "先列出已加载浏览器中所有轨道的可见性，然后打开蛋白质轨道。"
},
{
"role": "assistant",
"cont... | [
{
"type": "function",
"function": {
"name": "get_track_status",
"description": "Get the current visibility status of all tracks in the genome browser. Returns which tracks (genes, sequence, gc, variants, reads, proteins) are currently visible and their descriptions. Use this when the user asks a... | {
"source_example_id": "v3-syn-2b6fc9516f25072f",
"scenario_family_id": "synthetic:track_verify_a",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "先列出已加载浏览器中所有轨道的可见性，然后打开蛋白质轨道。"
},
{
"role": "assistant",
"cont... | [
{
"type": "function",
"function": {
"name": "get_track_status",
"description": "Get the current visibility status of all tracks in the genome browser. Returns which tracks (genes, sequence, gc, variants, reads, proteins) are currently visible and their descriptions. Use this when the user asks a... | {
"source_example_id": "v3-syn-2b6fc9516f25072f",
"scenario_family_id": "synthetic:track_verify_a",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Close the reads track in the genome browser, then re-check the current tra... | [
{
"type": "function",
"function": {
"name": "toggle_track",
"description": "Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.",
"parameters": {
"type": "object",
"properties": {... | {
"source_example_id": "v3-syn-c01c101c24b8c781",
"scenario_family_id": "synthetic:track_verify_b",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Close the reads track in the genome browser, then re-check the current tra... | [
{
"type": "function",
"function": {
"name": "toggle_track",
"description": "Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.",
"parameters": {
"type": "object",
"properties": {... | {
"source_example_id": "v3-syn-c01c101c24b8c781",
"scenario_family_id": "synthetic:track_verify_b",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Create a regulatory annotation named px_reg_A on U00096 at 200000-200600, ... | [
{
"type": "function",
"function": {
"name": "create_annotation",
"description": "Create a new user-defined annotation",
"parameters": {
"type": "object",
"properties": {
"type": {
"type": "string",
"enum": [
"gene",
... | {
"source_example_id": "v3-syn-57298e47ec1c56b5",
"scenario_family_id": "synthetic:annotation_crud",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Create a regulatory annotation named px_reg_A on U00096 at 200000-200600, ... | [
{
"type": "function",
"function": {
"name": "create_annotation",
"description": "Create a new user-defined annotation",
"parameters": {
"type": "object",
"properties": {
"type": {
"type": "string",
"enum": [
"gene",
... | {
"source_example_id": "v3-syn-57298e47ec1c56b5",
"scenario_family_id": "synthetic:annotation_crud",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Create a regulatory annotation named px_reg_A on U00096 at 200000-200600, ... | [
{
"type": "function",
"function": {
"name": "create_annotation",
"description": "Create a new user-defined annotation",
"parameters": {
"type": "object",
"properties": {
"type": {
"type": "string",
"enum": [
"gene",
... | {
"source_example_id": "v3-syn-57298e47ec1c56b5",
"scenario_family_id": "synthetic:annotation_crud",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在固定 UniProt 语料中搜索催化蛋白，获取第一条条目，然后对该条目进行结构域分析。"
},
{
"role": "assist... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-708b988103bcc268",
"scenario_family_id": "synthetic:protein_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在固定 UniProt 语料中搜索催化蛋白，获取第一条条目，然后对该条目进行结构域分析。"
},
{
"role": "assist... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-708b988103bcc268",
"scenario_family_id": "synthetic:protein_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在固定 UniProt 语料中搜索催化蛋白，获取第一条条目，然后对该条目进行结构域分析。"
},
{
"role": "assist... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-708b988103bcc268",
"scenario_family_id": "synthetic:protein_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Export the current view to /tmp/px_blast.fasta, build a nucleotide databas... | [
{
"type": "function",
"function": {
"name": "export_current_view_fasta",
"description": "Export sequences from the current genome view in FASTA format",
"parameters": {
"type": "object",
"properties": {
"filename": {
"type": "string",
"defa... | {
"source_example_id": "v3-syn-09155844bb787fb0",
"scenario_family_id": "synthetic:blast_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Export the current view to /tmp/px_blast.fasta, build a nucleotide databas... | [
{
"type": "function",
"function": {
"name": "export_current_view_fasta",
"description": "Export sequences from the current genome view in FASTA format",
"parameters": {
"type": "object",
"properties": {
"filename": {
"type": "string",
"defa... | {
"source_example_id": "v3-syn-09155844bb787fb0",
"scenario_family_id": "synthetic:blast_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Export the current view to /tmp/px_blast.fasta, build a nucleotide databas... | [
{
"type": "function",
"function": {
"name": "export_current_view_fasta",
"description": "Export sequences from the current genome view in FASTA format",
"parameters": {
"type": "object",
"properties": {
"filename": {
"type": "string",
"defa... | {
"source_example_id": "v3-syn-09155844bb787fb0",
"scenario_family_id": "synthetic:blast_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Export the current view to /tmp/px_blast.fasta, build a nucleotide databas... | [
{
"type": "function",
"function": {
"name": "export_current_view_fasta",
"description": "Export sequences from the current genome view in FASTA format",
"parameters": {
"type": "object",
"properties": {
"filename": {
"type": "string",
"defa... | {
"source_example_id": "v3-syn-09155844bb787fb0",
"scenario_family_id": "synthetic:blast_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 8,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，精确查找基因 fxg20（不要跳转视图），然后取出其返回区间的序列。"
},
{
"role": "as... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-8ec084e268adcb1e",
"scenario_family_id": "synthetic:find",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，精确查找基因 fxg20（不要跳转视图），然后取出其返回区间的序列。"
},
{
"role": "as... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-8ec084e268adcb1e",
"scenario_family_id": "synthetic:find",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg01 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-64cfdae446939bca",
"scenario_family_id": "synthetic:find_details",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg01 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-64cfdae446939bca",
"scenario_family_id": "synthetic:find_details",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg01 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-64cfdae446939bca",
"scenario_family_id": "synthetic:find_details",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-536 - 链的序列，并计算该序列的 GC 含量。"
},
{
"ro... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-011a18922d316ac9",
"scenario_family_id": "synthetic:seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-536 - 链的序列，并计算该序列的 GC 含量。"
},
{
"ro... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-011a18922d316ac9",
"scenario_family_id": "synthetic:seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-c6287c2af888ea6b",
"scenario_family_id": "synthetic:seq_entropy",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-c6287c2af888ea6b",
"scenario_family_id": "synthetic:seq_entropy",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并返回它的反向互补序列。"
},
{
"role... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-531acca58f177b75",
"scenario_family_id": "synthetic:seq_revcomp",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-548 - 链的序列，并返回它的反向互补序列。"
},
{
"role... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-531acca58f177b75",
"scenario_family_id": "synthetic:seq_revcomp",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-aa9b2a9cb6dea0d9",
"scenario_family_id": "synthetic:seq_translate",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-aa9b2a9cb6dea0d9",
"scenario_family_id": "synthetic:seq_translate",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，并计算其分子量。"
},
{
"role": "... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-2d214281badef782",
"scenario_family_id": "synthetic:seq_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，并计算其分子量。"
},
{
"role": "... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-2d214281badef782",
"scenario_family_id": "synthetic:seq_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-6dad2012cf49b883",
"scenario_family_id": "synthetic:seq_digest",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-6dad2012cf49b883",
"scenario_family_id": "synthetic:seq_digest",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, retrieve the + strand of px_core_A:500-5... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-6dad2012cf49b883",
"scenario_family_id": "synthetic:seq_digest",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，列出 px_core_B 上的注释，并取出第一条注释的完整信息。"
},
{
"role": "assi... | [
{
"type": "function",
"function": {
"name": "list_annotations",
"description": "List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation ... | {
"source_example_id": "v3-syn-09daa97e8c385813",
"scenario_family_id": "synthetic:ann_list",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，列出 px_core_B 上的注释，并取出第一条注释的完整信息。"
},
{
"role": "assi... | [
{
"type": "function",
"function": {
"name": "list_annotations",
"description": "List genome annotations in a specified region or chromosome with filtering by feature type. Use this when the user asks to list, show, or display annotations/genes/features in a region. Returns structured annotation ... | {
"source_example_id": "v3-syn-09daa97e8c385813",
"scenario_family_id": "synthetic:ann_list",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find features near px_core_A:525 within ... | [
{
"type": "function",
"function": {
"name": "get_nearby_features",
"description": "Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position... | {
"source_example_id": "v3-syn-741d5ba82e18b2db",
"scenario_family_id": "synthetic:ann_nearby",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find features near px_core_A:525 within ... | [
{
"type": "function",
"function": {
"name": "get_nearby_features",
"description": "Get genomic features (genes, CDS, etc.) near a specific position within a given distance range. Returns features sorted by proximity to the target position. Use this when the user asks for features near a position... | {
"source_example_id": "v3-syn-741d5ba82e18b2db",
"scenario_family_id": "synthetic:ann_nearby",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具的 UniProt 语料中搜索 \"pinned catalytic\"，并取出第一条结果条目的完整信息。"
},
{
"... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-740fff1748032115",
"scenario_family_id": "synthetic:uniprot",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具的 UniProt 语料中搜索 \"pinned catalytic\"，并取出第一条结果条目的完整信息。"
},
{
"... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-740fff1748032115",
"scenario_family_id": "synthetic:uniprot",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg11 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-d867e937265d8fb6",
"scenario_family_id": "synthetic:find_seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg11 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-d867e937265d8fb6",
"scenario_family_id": "synthetic:find_seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg11 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-d867e937265d8fb6",
"scenario_family_id": "synthetic:find_seq_gc",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，按阅读框 2 翻译，并计算所得蛋白的分子量。"
},
{... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-c24470b273ccbab8",
"scenario_family_id": "synthetic:seq_translate_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，按阅读框 2 翻译，并计算所得蛋白的分子量。"
},
{... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-c24470b273ccbab8",
"scenario_family_id": "synthetic:seq_translate_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，取出 px_core_B:500-542 - 链的序列，按阅读框 2 翻译，并计算所得蛋白的分子量。"
},
{... | [
{
"type": "function",
"function": {
"name": "get_sequence",
"description": "Retrieve DNA sequence for a specific genomic region. Returns the raw sequence data and basic statistics. USE THIS TOOL ONLY WHEN THE PROMPT CONTAINS THE WORD \"sequence\". For visualizing genomic regions, use navigate_to... | {
"source_example_id": "v3-syn-c24470b273ccbab8",
"scenario_family_id": "synthetic:seq_translate_mw",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "关闭基因组浏览器中的读段轨道，然后重新检查当前轨道可见性。"
},
{
"role": "assistant",
"cont... | [
{
"type": "function",
"function": {
"name": "toggle_track",
"description": "Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.",
"parameters": {
"type": "object",
"properties": {... | {
"source_example_id": "v3-syn-cfa021b9178c5231",
"scenario_family_id": "synthetic:track_verify_b",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "关闭基因组浏览器中的读段轨道，然后重新检查当前轨道可见性。"
},
{
"role": "assistant",
"cont... | [
{
"type": "function",
"function": {
"name": "toggle_track",
"description": "Show or hide specific tracks in the genome browser (genes, GC content, sequence, etc.). Use this to control which genomic data layers are visible.",
"parameters": {
"type": "object",
"properties": {... | {
"source_example_id": "v3-syn-cfa021b9178c5231",
"scenario_family_id": "synthetic:track_verify_b",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Clear the pending task list, create a task named PX-verify with status in_... | [
{
"type": "function",
"function": {
"name": "clear_tasks",
"description": "Remove all tasks from the workspace task tracking system.",
"parameters": {
"type": "object",
"properties": {
"confirm": {
"type": "boolean",
"default": true,
... | {
"source_example_id": "v3-syn-d6d5b2e094d61654",
"scenario_family_id": "synthetic:task_lifecycle",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Clear the pending task list, create a task named PX-verify with status in_... | [
{
"type": "function",
"function": {
"name": "clear_tasks",
"description": "Remove all tasks from the workspace task tracking system.",
"parameters": {
"type": "object",
"properties": {
"confirm": {
"type": "boolean",
"default": true,
... | {
"source_example_id": "v3-syn-d6d5b2e094d61654",
"scenario_family_id": "synthetic:task_lifecycle",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Clear the pending task list, create a task named PX-verify with status in_... | [
{
"type": "function",
"function": {
"name": "clear_tasks",
"description": "Remove all tasks from the workspace task tracking system.",
"parameters": {
"type": "object",
"properties": {
"confirm": {
"type": "boolean",
"default": true,
... | {
"source_example_id": "v3-syn-d6d5b2e094d61654",
"scenario_family_id": "synthetic:task_lifecycle",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Clear the pending task list, create a task named PX-verify with status in_... | [
{
"type": "function",
"function": {
"name": "clear_tasks",
"description": "Remove all tasks from the workspace task tracking system.",
"parameters": {
"type": "object",
"properties": {
"confirm": {
"type": "boolean",
"default": true,
... | {
"source_example_id": "v3-syn-d6d5b2e094d61654",
"scenario_family_id": "synthetic:task_lifecycle",
"trajectory": true,
"synthetic": true,
"turn_index": 8,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Clear the pending task list, create a task named PX-verify with status in_... | [
{
"type": "function",
"function": {
"name": "clear_tasks",
"description": "Remove all tasks from the workspace task tracking system.",
"parameters": {
"type": "object",
"properties": {
"confirm": {
"type": "boolean",
"default": true,
... | {
"source_example_id": "v3-syn-d6d5b2e094d61654",
"scenario_family_id": "synthetic:task_lifecycle",
"trajectory": true,
"synthetic": true,
"turn_index": 10,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在 U00096 上创建名为 px_reg_A 的调控注释（200000-200600），将其 note 更新为 px conserved regi... | [
{
"type": "function",
"function": {
"name": "create_annotation",
"description": "Create a new user-defined annotation",
"parameters": {
"type": "object",
"properties": {
"type": {
"type": "string",
"enum": [
"gene",
... | {
"source_example_id": "v3-syn-9fd5caec7917ffe7",
"scenario_family_id": "synthetic:annotation_crud",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在 U00096 上创建名为 px_reg_A 的调控注释（200000-200600），将其 note 更新为 px conserved regi... | [
{
"type": "function",
"function": {
"name": "create_annotation",
"description": "Create a new user-defined annotation",
"parameters": {
"type": "object",
"properties": {
"type": {
"type": "string",
"enum": [
"gene",
... | {
"source_example_id": "v3-syn-9fd5caec7917ffe7",
"scenario_family_id": "synthetic:annotation_crud",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在 U00096 上创建名为 px_reg_A 的调控注释（200000-200600），将其 note 更新为 px conserved regi... | [
{
"type": "function",
"function": {
"name": "create_annotation",
"description": "Create a new user-defined annotation",
"parameters": {
"type": "object",
"properties": {
"type": {
"type": "string",
"enum": [
"gene",
... | {
"source_example_id": "v3-syn-9fd5caec7917ffe7",
"scenario_family_id": "synthetic:annotation_crud",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Search the pinned UniProt corpus for a catalytic protein, fetch the first ... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-c0b4b806780ad01f",
"scenario_family_id": "synthetic:protein_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Search the pinned UniProt corpus for a catalytic protein, fetch the first ... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-c0b4b806780ad01f",
"scenario_family_id": "synthetic:protein_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "Search the pinned UniProt corpus for a catalytic protein, fetch the first ... | [
{
"type": "function",
"function": {
"name": "search_uniprot_database",
"description": "Search UniProt database with various search types including protein names, gene names, organisms, and functional keywords.",
"parameters": {
"type": "object",
"properties": {
"s... | {
"source_example_id": "v3-syn-c0b4b806780ad01f",
"scenario_family_id": "synthetic:protein_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。"
},... | [
{
"type": "function",
"function": {
"name": "export_current_view_fasta",
"description": "Export sequences from the current genome view in FASTA format",
"parameters": {
"type": "object",
"properties": {
"filename": {
"type": "string",
"defa... | {
"source_example_id": "v3-syn-a485d06c2081a674",
"scenario_family_id": "synthetic:blast_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。"
},... | [
{
"type": "function",
"function": {
"name": "export_current_view_fasta",
"description": "Export sequences from the current genome view in FASTA format",
"parameters": {
"type": "object",
"properties": {
"filename": {
"type": "string",
"defa... | {
"source_example_id": "v3-syn-a485d06c2081a674",
"scenario_family_id": "synthetic:blast_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。"
},... | [
{
"type": "function",
"function": {
"name": "export_current_view_fasta",
"description": "Export sequences from the current genome view in FASTA format",
"parameters": {
"type": "object",
"properties": {
"filename": {
"type": "string",
"defa... | {
"source_example_id": "v3-syn-a485d06c2081a674",
"scenario_family_id": "synthetic:blast_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 6,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "将当前视图导出到 /tmp/px_blast.fasta，用它构建名为 px_nucl 的核酸数据库，校验该数据库，然后列出全部数据库。"
},... | [
{
"type": "function",
"function": {
"name": "export_current_view_fasta",
"description": "Export sequences from the current genome view in FASTA format",
"parameters": {
"type": "object",
"properties": {
"filename": {
"type": "string",
"defa... | {
"source_example_id": "v3-syn-a485d06c2081a674",
"scenario_family_id": "synthetic:blast_chain",
"trajectory": true,
"synthetic": true,
"turn_index": 8,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg19 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-1805a211f56a3fa6",
"scenario_family_id": "synthetic:find",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "In pinned synthetic sample PX-01, find gene fxg19 exactly (do not navigate... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-1805a211f56a3fa6",
"scenario_family_id": "synthetic:find",
"trajectory": true,
"synthetic": true,
"turn_index": 4,
"supervised_target": "tool_call"
} |
[
{
"role": "system",
"content": "Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. Ask for missing required information instead of inventing it."
},
{
"role": "user",
"content": "在只读夹具 PX-01 中，精确查找基因 fxg20（不要跳转视图），再获取该基因的详细信息，然后取出其返回区间的序列。"
},
{
... | [
{
"type": "function",
"function": {
"name": "find_gene_by_name",
"description": "Search for a SPECIFIC GENE by its name or locus tag (e.g., lacZ, b0062, dnaA). Use this when you know the gene identifier. For searching by functional annotation or feature type (e.g., \"all kinase genes\", \"all tR... | {
"source_example_id": "v3-syn-577d1114b49fa8b2",
"scenario_family_id": "synthetic:find_details",
"trajectory": true,
"synthetic": true,
"turn_index": 2,
"supervised_target": "tool_call"
} |
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