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": "For pinned synthetic sample PX-01, return the - strand from px_core_A coor... | [
{
"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-2e45301df16d62fd3ffd",
"scenario_family_id": "fixture:v2:single:get_sequence:train:0:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For pinned synthetic sample PX-02, return the + strand from px_core_B coor... | [
{
"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-d6ebecc2f7dd9b60e418",
"scenario_family_id": "fixture:v2:single:get_sequence:train:1:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For pinned synthetic sample PX-03, return the + strand from px_core_A coor... | [
{
"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-835638216962d2b250a3",
"scenario_family_id": "fixture:v2:single:get_sequence:train:2:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For pinned synthetic sample PX-04, return the - strand from px_core_B coor... | [
{
"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-1859e74c5de078e87d0c",
"scenario_family_id": "fixture:v2:single:get_sequence:train:3:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For pinned synthetic sample PX-05, return the + strand from px_core_A coor... | [
{
"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-54504591dff2f24f72d4",
"scenario_family_id": "fixture:v2:single:get_sequence:train:4:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For pinned synthetic sample PX-06, return the + strand from px_core_B coor... | [
{
"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-f30f758048e7e92dca13",
"scenario_family_id": "fixture:v2:single:get_sequence:train:5:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For pinned synthetic sample PX-07, return the - strand from px_core_A coor... | [
{
"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-8ebcd724886ac23a5a73",
"scenario_family_id": "fixture:v2:single:get_sequence:train:6:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For pinned synthetic sample PX-08, return the + strand from px_core_B coor... | [
{
"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-0151a9a7f72a4fae4f35",
"scenario_family_id": "fixture:v2:single:get_sequence:train:7:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For synthetic neighborhood audit PX-156, find tRNA features within 1265 bp... | [
{
"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": "cx-17e4dabbf3eb35948e74",
"scenario_family_id": "fixture:v2:single:get_nearby_features:train:0:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For synthetic neighborhood audit PX-157, find CDS features within 1272 bp ... | [
{
"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": "cx-282313836707a5e138e6",
"scenario_family_id": "fixture:v2:single:get_nearby_features:train:1:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For synthetic neighborhood audit PX-158, find CDS features within 1279 bp ... | [
{
"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": "cx-e5e29335b7929955091e",
"scenario_family_id": "fixture:v2:single:get_nearby_features:train:2:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For synthetic neighborhood audit PX-159, find CDS features within 1286 bp ... | [
{
"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": "cx-1bce3224b2e5a3987fc6",
"scenario_family_id": "fixture:v2:single:get_nearby_features:train:3:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For synthetic neighborhood audit PX-160, find CDS features within 1293 bp ... | [
{
"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": "cx-ef2f45905984fe17cb02",
"scenario_family_id": "fixture:v2:single:get_nearby_features:train:4:1",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For synthetic neighborhood audit PX-161, find tRNA features within 1300 bp... | [
{
"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": "cx-1b1bf1ec91acabab4b0e",
"scenario_family_id": "fixture:v2:single:get_nearby_features:train:5:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For synthetic neighborhood audit PX-162, find CDS features within 1307 bp ... | [
{
"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": "cx-3754fbedb3bbc546bff9",
"scenario_family_id": "fixture:v2:single:get_nearby_features:train:6:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "For synthetic neighborhood audit PX-163, find CDS features within 1314 bp ... | [
{
"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": "cx-36d4ea4252dd122488c5",
"scenario_family_id": "fixture:v2:single:get_nearby_features:train:7:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Produce the validated reverse complement for synthetic oligo PX-187: CCGGG... | [
{
"type": "function",
"function": {
"name": "reverse_complement",
"description": "Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).",
"parameters": {
"type": "object",
"properties": {
... | {
"source_example_id": "cx-86af7c01bad43870cf9f",
"scenario_family_id": "fixture:v2:single:reverse_complement:train:0:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Produce the validated reverse complement for synthetic oligo PX-188: CGCAC... | [
{
"type": "function",
"function": {
"name": "reverse_complement",
"description": "Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).",
"parameters": {
"type": "object",
"properties": {
... | {
"source_example_id": "cx-73f247ff2a8ea9e5bac6",
"scenario_family_id": "fixture:v2:single:reverse_complement:train:1:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Produce the validated reverse complement for synthetic oligo PX-189: TTGGA... | [
{
"type": "function",
"function": {
"name": "reverse_complement",
"description": "Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).",
"parameters": {
"type": "object",
"properties": {
... | {
"source_example_id": "cx-555c98a5856297327546",
"scenario_family_id": "fixture:v2:single:reverse_complement:train:2:1",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Produce the validated reverse complement for synthetic oligo PX-190: CGTGT... | [
{
"type": "function",
"function": {
"name": "reverse_complement",
"description": "Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).",
"parameters": {
"type": "object",
"properties": {
... | {
"source_example_id": "cx-11e44c8188a4dfad10e4",
"scenario_family_id": "fixture:v2:single:reverse_complement:train:3:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Produce the validated reverse complement for synthetic oligo PX-191: CACAG... | [
{
"type": "function",
"function": {
"name": "reverse_complement",
"description": "Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).",
"parameters": {
"type": "object",
"properties": {
... | {
"source_example_id": "cx-3ba7fb8541a68accf8d4",
"scenario_family_id": "fixture:v2:single:reverse_complement:train:4:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Produce the validated reverse complement for synthetic oligo PX-192: GACTC... | [
{
"type": "function",
"function": {
"name": "reverse_complement",
"description": "Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).",
"parameters": {
"type": "object",
"properties": {
... | {
"source_example_id": "cx-296fa2a8f94955c427dd",
"scenario_family_id": "fixture:v2:single:reverse_complement:train:5:1",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Produce the validated reverse complement for synthetic oligo PX-193: ACCTT... | [
{
"type": "function",
"function": {
"name": "reverse_complement",
"description": "Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).",
"parameters": {
"type": "object",
"properties": {
... | {
"source_example_id": "cx-3626a1a67bf453d6baba",
"scenario_family_id": "fixture:v2:single:reverse_complement:train:6:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Produce the validated reverse complement for synthetic oligo PX-194: GTCTA... | [
{
"type": "function",
"function": {
"name": "reverse_complement",
"description": "Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).",
"parameters": {
"type": "object",
"properties": {
... | {
"source_example_id": "cx-6d406e770fb4c9e95419",
"scenario_family_id": "fixture:v2:single:reverse_complement:train:7:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Using the bacterial code, translate synthetic CDS PX-218 in frame 1 and re... | [
{
"type": "function",
"function": {
"name": "translate_dna",
"description": "Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.",
"parameters": {
"type": "object",
"properties": {
"dna": {
... | {
"source_example_id": "cx-ded50843cb42edcbe48d",
"scenario_family_id": "fixture:v2:single:translate_dna:train:0:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Using the standard code, translate synthetic CDS PX-219 in frame 1 and ret... | [
{
"type": "function",
"function": {
"name": "translate_dna",
"description": "Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.",
"parameters": {
"type": "object",
"properties": {
"dna": {
... | {
"source_example_id": "cx-2e3eef8d6107f762d62c",
"scenario_family_id": "fixture:v2:single:translate_dna:train:1:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Using the bacterial code, translate synthetic CDS PX-220 in frame 1 and om... | [
{
"type": "function",
"function": {
"name": "translate_dna",
"description": "Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.",
"parameters": {
"type": "object",
"properties": {
"dna": {
... | {
"source_example_id": "cx-0186cd36c5f20abeabe1",
"scenario_family_id": "fixture:v2:single:translate_dna:train:2:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Using the standard code, translate synthetic CDS PX-221 in frame 1 and ret... | [
{
"type": "function",
"function": {
"name": "translate_dna",
"description": "Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.",
"parameters": {
"type": "object",
"properties": {
"dna": {
... | {
"source_example_id": "cx-8b590d99e9caab95b7f5",
"scenario_family_id": "fixture:v2:single:translate_dna:train:3:1",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Using the bacterial code, translate synthetic CDS PX-222 in frame 1 and re... | [
{
"type": "function",
"function": {
"name": "translate_dna",
"description": "Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.",
"parameters": {
"type": "object",
"properties": {
"dna": {
... | {
"source_example_id": "cx-587910d549193a367e9e",
"scenario_family_id": "fixture:v2:single:translate_dna:train:4:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Using the standard code, translate synthetic CDS PX-223 in frame 1 and omi... | [
{
"type": "function",
"function": {
"name": "translate_dna",
"description": "Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.",
"parameters": {
"type": "object",
"properties": {
"dna": {
... | {
"source_example_id": "cx-6fba7abe6ae77ecb0afb",
"scenario_family_id": "fixture:v2:single:translate_dna:train:5:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Using the bacterial code, translate synthetic CDS PX-224 in frame 1 and re... | [
{
"type": "function",
"function": {
"name": "translate_dna",
"description": "Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.",
"parameters": {
"type": "object",
"properties": {
"dna": {
... | {
"source_example_id": "cx-da6f1fd855a9bb30ca5e",
"scenario_family_id": "fixture:v2:single:translate_dna:train:6:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Using the standard code, translate synthetic CDS PX-225 in frame 1 and ret... | [
{
"type": "function",
"function": {
"name": "translate_dna",
"description": "Translate DNA sequence to amino acid sequence using genetic code. Supports multiple reading frames and genetic code tables.",
"parameters": {
"type": "object",
"properties": {
"dna": {
... | {
"source_example_id": "cx-06e07ffc96b5ed56b411",
"scenario_family_id": "fixture:v2:single:translate_dna:train:7:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Measure Shannon sequence complexity for synthetic sample PX-280: ATAGAACAG... | [
{
"type": "function",
"function": {
"name": "calculate_entropy",
"description": "Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.",
... | {
"source_example_id": "cx-9c0a20b36e52cdb570a5",
"scenario_family_id": "fixture:v2:single:calculate_entropy:train:0:1",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Measure Shannon sequence complexity for synthetic sample PX-281: ACTCGAAAA... | [
{
"type": "function",
"function": {
"name": "calculate_entropy",
"description": "Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.",
... | {
"source_example_id": "cx-6433a99837676b70fb30",
"scenario_family_id": "fixture:v2:single:calculate_entropy:train:1:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Measure Shannon sequence complexity for synthetic sample PX-282: GGGTACACG... | [
{
"type": "function",
"function": {
"name": "calculate_entropy",
"description": "Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.",
... | {
"source_example_id": "cx-a36b17648bd31bf4b086",
"scenario_family_id": "fixture:v2:single:calculate_entropy:train:2:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Measure Shannon sequence complexity for synthetic sample PX-283: TGGGCTGAA... | [
{
"type": "function",
"function": {
"name": "calculate_entropy",
"description": "Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.",
... | {
"source_example_id": "cx-09a077281865609f16ac",
"scenario_family_id": "fixture:v2:single:calculate_entropy:train:3:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Measure Shannon sequence complexity for synthetic sample PX-284: CAAACGGAG... | [
{
"type": "function",
"function": {
"name": "calculate_entropy",
"description": "Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.",
... | {
"source_example_id": "cx-dbbbb4c6ef83b575e769",
"scenario_family_id": "fixture:v2:single:calculate_entropy:train:4:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Measure Shannon sequence complexity for synthetic sample PX-285: ATGCACAGT... | [
{
"type": "function",
"function": {
"name": "calculate_entropy",
"description": "Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.",
... | {
"source_example_id": "cx-c7adb9d872eed8487c4a",
"scenario_family_id": "fixture:v2:single:calculate_entropy:train:5:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Measure Shannon sequence complexity for synthetic sample PX-286: GTCTGAACA... | [
{
"type": "function",
"function": {
"name": "calculate_entropy",
"description": "Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.",
... | {
"source_example_id": "cx-04cf472afd9a0c3747c7",
"scenario_family_id": "fixture:v2:single:calculate_entropy:train:6:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Measure Shannon sequence complexity for synthetic sample PX-287: CGCTATGCC... | [
{
"type": "function",
"function": {
"name": "calculate_entropy",
"description": "Calculate Shannon entropy of a DNA or protein sequence as a measure of sequence complexity. Higher entropy indicates more random/complex sequences; lower entropy indicates more ordered/repetitive sequences.",
... | {
"source_example_id": "cx-dab9de8ae0616522696a",
"scenario_family_id": "fixture:v2:single:calculate_entropy:train:7:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
[
{
"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": "Calculate the dna molecular mass for pinned sample PX-311: GGTAAGCCGTGATAA... | [
{
"type": "function",
"function": {
"name": "calculate_molecular_weight",
"description": "Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. Supports DNA, RNA and Protein sequences with automatic type detection or explicit specification.",
"parameters": {
... | {
"source_example_id": "cx-730b9ffc8e6ac6ea3126",
"scenario_family_id": "fixture:v2:single:calculate_molecular_weight:train:0:0",
"supervised_target": "tool_call",
"turn_index": 2
} |
End of preview. Expand in Data Studio
CodeXomics-ToolCalling-v1
This dataset contains the supervised tool-calling trajectories used to fine-tune
CodeXomics-ToolAgent-4B-v1 (internally qwen3.5:4b-codexomics-tools-v5) for the CodeXomics
genomics workbench (an AI-native genome browser; source:
github.com/Scilence2022/CodeXomics). It is released
as the reproducibility artifact for the corresponding paper section and is licensed under
Apache-2.0.
Contents
train.jsonl— 373 supervised examplesvalid.jsonl— 123 validation examplestest.jsonl— 30 holdout examplesmanifest.json— dataset schema, eligibility metadata, registry hash, and leakage-control recordtoken-stats.json— render-length statistics per split (3,072-token budget)
Each line is an MLX-LM tool-calling example: a system prompt, a user instruction, and assistant
tool_calls in the OpenAI function-calling shape. Multi-step examples include the returned tool
results and use the cross-round reference syntax {tool_name.path}.
Composition
| Split | Single-call | Multi-step | Variants | Synthetic chains | Total |
|---|---|---|---|---|---|
| Train | 85 | 18 | 10 | 260 | 373 |
| Validation | 66 | 8 | 4 | 45 | 123 |
| Test | 21 | 8 | 1 | 0 | 30 |
Source trajectories (678 records) were admitted only after passing: (1) strong-model semantic
replay (DeepSeek V4 Flash), (2) fixture executability, (3) state verification for stateful
records, and (4) benchmark leakage control. All 172 CodeXomics Benchmark tests are fingerprinted
and excluded (benchmark_scope.use: leakage-gate-only).
Training schema
Six candidate tool schemas per request (gold tool always included), function descriptions truncated to 160 characters, parameter defaults preserved, semantically hard distractors, and a deterministic-randomized gold position.
Usage
huggingface-cli download <this-dataset> --local-dir codexomics-v5-data
Citation
@software{codexomics-toolagent-v1,
title = {CodeXomics-ToolCalling-v1},
author = {Song, Lifu},
year = {2026},
license = {Apache-2.0},
publisher = {Hugging Face}
}
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