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{"messages":[{"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 read-only fixture PX-33, look up the exact synthetic gene identifier fxg13 without moving the genome view."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_gene_by_name","arguments":{"name":"fxg13","navigate_to_gene":false}}}]}],"tools":[{"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 tRNA\"), use search_features instead. 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{"messages":[{"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 read-only fixture PX-39, look up the exact synthetic gene identifier fxg19 without moving the genome view."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_gene_by_name","arguments":{"name":"fxg19","navigate_to_gene":false}}}]}],"tools":[{"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 tRNA\"), use search_features instead. 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{"messages":[{"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":"Validation card PX-40\nObjective: resolve an exact synthetic locus without changing the visible region.\nPinned inputs: {\"name\":\"fxg20\",\"navigate_to_gene\":false}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_gene_by_name","arguments":{"name":"fxg20","navigate_to_gene":false}}}]}],"tools":[{"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 tRNA\"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.","parameters":{"type":"object","properties":{"name":{"type":"string"},"exact_match":{"type":"boolean","default":false},"case_sensitive":{"type":"boolean","default":false},"navigate_to_gene":{"type":"boolean","default":true},"include_annotations":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["name"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"calc_region_gc","description":"Calculate GC content for a chromosome coordinate range from the currently loaded genome. 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{"messages":[{"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":"Audit fixture PX-63: list CDS records on px_core_A between 1470 and 1565, capped at 7."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_annotations","arguments":{"chromosome":"px_core_A","start":1470,"end":1565,"type":"CDS","limit":7}}}]}],"tools":[{"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 data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"type":{"type":"string"},"limit":{"type":"number","default":100},"offset":{"type":"number","default":0},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_highlights","description":"List all positional highlights currently shown for the active tab, including each highlight's id, chromosome, start/end coordinates (1-based inclusive), length, label, and color. Use this to review what is highlighted or to obtain an id before calling remove_highlight.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_loaded_files_list","description":"Get list of all currently loaded files in the genome browser with their complete paths and metadata","parameters":{"type":"object","properties":{"includeMetadata":{"type":"boolean","required":false,"default":true}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"export_cds_fasta","description":"Export coding sequences (CDS) in FASTA format","parameters":{"type":"object","properties":{"filename":{"type":"string","default":"cds_sequences.fasta"},"auto_save":{"type":"boolean","default":false},"include_gene_names":{"type":"boolean","default":true},"include_locus_tags":{"type":"boolean","default":true},"include_products":{"type":"boolean","default":true},"selection_type":{"type":"string","enum":["all","selected","current_view","by_gene_name","by_locus_tag"],"default":"all"},"gene_names":{"type":"array","items":{"type":"string"}},"locus_tags":{"type":"array","items":{"type":"string"}},"wrap_length":{"type":"integer","minimum":0,"maximum":200,"default":80}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_tasks","description":"List current tasks in the workspace task tracking system, optionally filtered by status.","parameters":{"type":"object","properties":{"status":{"type":"string","enum":["all","pending","in_progress","completed","failed"],"default":"all","required":false}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_available_tools","description":"List all available tools in the system, organized by category. Use this to discover what functionality is available or to get help with available commands.","parameters":{"type":"object","properties":{"category":{"type":"string","default":null},"include_details":{"type":"boolean","default":false},"format":{"type":"string","enum":["summary","detailed"],"default":"summary"}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-fa7dc74d7e697efc736e","scenario_family_id":"fixture:v2:single:list_annotations:train:0:0","supervised_target":"tool_call","turn_index":2}}
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{"messages":[{"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":"Audit fixture PX-65: list CDS records on px_core_A between 2570 and 2671, capped at 7."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_annotations","arguments":{"chromosome":"px_core_A","start":2570,"end":2671,"type":"CDS","limit":7}}}]}],"tools":[{"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 data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"type":{"type":"string"},"limit":{"type":"number","default":100},"offset":{"type":"number","default":0},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_loaded_files_list","description":"Get list of all currently loaded files in the genome browser with their complete paths and metadata","parameters":{"type":"object","properties":{"includeMetadata":{"type":"boolean","required":false,"default":true}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_highlights","description":"List all positional highlights currently shown for the active tab, including each highlight's id, chromosome, start/end coordinates (1-based inclusive), length, label, and color. Use this to review what is highlighted or to obtain an id before calling remove_highlight.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_tasks","description":"List current tasks in the workspace task tracking system, optionally filtered by status.","parameters":{"type":"object","properties":{"status":{"type":"string","enum":["all","pending","in_progress","completed","failed"],"default":"all","required":false}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_action_list","description":"Get the current sequence-editing Action queue. Actions are queued genome edit operations, not checklist Tasks.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"status":{"type":"string","enum":["all","pending","executing","completed","failed"],"default":"all"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_chromosome_list","description":"Get the list of all chromosomes (contigs/scaffolds) in the currently loaded genome, including their names, lengths, and which one is currently selected. Use this when the user asks about chromosome names, genome contigs, scaffold list, or wants to know what chromosomes are available.","parameters":{"type":"object","properties":{},"required":[],"additionalProperties":false},"strict":true}}],"metadata":{"source_example_id":"cx-51d57202003c6446cb7d","scenario_family_id":"fixture:v2:single:list_annotations:train:2:0","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Audit fixture PX-66: list tRNA records on px_core_B between 2707 and 2796, capped at 7."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_annotations","arguments":{"chromosome":"px_core_B","start":2707,"end":2796,"type":"tRNA","limit":7}}}]}],"tools":[{"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 data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"type":{"type":"string"},"limit":{"type":"number","default":100},"offset":{"type":"number","default":0},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_operons","description":"Get predicted operon structures for a chromosome from loaded annotations. Returns operon coordinates, strand, gene count, member genes, and length. Use this when the user asks to show, list, find, predict, or inspect operons in the current genome.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"show_action_list","description":"Display the Action List Manager interface for queued sequence-editing Actions. Actions are genome edit operations, not checklist Tasks.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_loaded_files_list","description":"Get list of all currently loaded files in the genome browser with their complete paths and metadata","parameters":{"type":"object","properties":{"includeMetadata":{"type":"boolean","required":false,"default":true}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_tasks","description":"List current tasks in the workspace task tracking system, optionally filtered by status.","parameters":{"type":"object","properties":{"status":{"type":"string","enum":["all","pending","in_progress","completed","failed"],"default":"all","required":false}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_highlights","description":"List all positional highlights currently shown for the active tab, including each highlight's id, chromosome, start/end coordinates (1-based inclusive), length, label, and color. Use this to review what is highlighted or to obtain an id before calling remove_highlight.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-b9a24fb75a908a7b553b","scenario_family_id":"fixture:v2:single:list_annotations:train:3:0","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Audit fixture PX-67: list CDS records on px_core_A between 3670 and 3762, capped at 7."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_annotations","arguments":{"chromosome":"px_core_A","start":3670,"end":3762,"type":"CDS","limit":7}}}]}],"tools":[{"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 data with position, type, strand, gene name, and product. NOT the same as search_annotations which searches by keyword.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"type":{"type":"string"},"limit":{"type":"number","default":100},"offset":{"type":"number","default":0},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_highlights","description":"List all positional highlights currently shown for the active tab, including each highlight's id, chromosome, start/end coordinates (1-based inclusive), length, label, and color. Use this to review what is highlighted or to obtain an id before calling remove_highlight.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_loaded_files_list","description":"Get list of all currently loaded files in the genome browser with their complete paths and metadata","parameters":{"type":"object","properties":{"includeMetadata":{"type":"boolean","required":false,"default":true}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_available_tools","description":"List all available tools in the system, organized by category. Use this to discover what functionality is available or to get help with available commands.","parameters":{"type":"object","properties":{"category":{"type":"string","default":null},"include_details":{"type":"boolean","default":false},"format":{"type":"string","enum":["summary","detailed"],"default":"summary"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"show_action_list","description":"Display the Action List Manager interface for queued sequence-editing Actions. Actions are genome edit operations, not checklist Tasks.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_tasks","description":"List current tasks in the workspace task tracking system, optionally filtered by status.","parameters":{"type":"object","properties":{"status":{"type":"string","enum":["all","pending","in_progress","completed","failed"],"default":"all","required":false}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-c5d95d641a7909c52239","scenario_family_id":"fixture:v2:single:list_annotations:train:4:0","supervised_target":"tool_call","turn_index":2}}
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{"messages":[{"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":"Validation card PX-133\nObjective: inspect the read-only details of one synthetic gene.\nPinned inputs: {\"geneName\":\"px013\",\"chromosome\":\"px_core_A\"}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"get_gene_details","arguments":{"geneName":"px013","chromosome":"px_core_A"}}}]}],"tools":[{"type":"function","function":{"name":"get_gene_details","description":"Get detailed information about a gene by its name or locus tag. This tool returns structured information including locus tag, product/function, coordinates, strand, length, and notes.","parameters":{"type":"object","properties":{"geneName":{"type":"string"},"chromosome":{"type":"string"},"clientId":{"type":"string","default":"default"}},"required":["geneName"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_chromosome_list","description":"Get the list of all chromosomes (contigs/scaffolds) in the currently loaded genome, including their names, lengths, and which one is currently selected. Use this when the user asks about chromosome names, genome contigs, scaffold list, or wants to know what chromosomes are available.","parameters":{"type":"object","properties":{},"required":[],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"get_annotation","description":"Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"chromosome":{"type":"string"},"full_details":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["identifier"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"search_annotations","description":"Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. NOT the same as search_features which searches for features by functional category/type, or find_gene_by_name which finds a specific gene by exact name.","parameters":{"type":"object","properties":{"query":{"type":"string"},"chromosome":{"type":"string"},"type":{"type":"string"},"fields":{"type":"array","items":{"type":"string"}},"limit":{"type":"number","default":50},"clientId":{"type":"string","default":"default"}},"required":["query"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"zoom_to_gene","description":"Zoom the genome browser view to fit a specific gene, centering on it with configurable padding. This changes the visible region to show the entire gene with surrounding context. Use this when the user asks to zoom to a gene, focus on a gene, center view on a gene, or fit a gene in view. NOT the same as select_gene which only highlights without zooming.","parameters":{"type":"object","properties":{"geneName":{"type":"string"},"chromosome":{"type":"string"},"padding":{"type":"integer","default":1000},"clientId":{"type":"string","default":"default"}},"required":["geneName"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"genome_codon_usage_analysis","description":"Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"featureType":{"type":"string","default":"CDS","enum":["CDS","gene","mRNA"]},"minLength":{"type":"integer","default":300,"minimum":1,"maximum":100000},"maxGenes":{"type":"integer","minimum":1},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-f693c86524be4b27013d","scenario_family_id":"fixture:v2:single:get_gene_details:dev:0:3","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Validation card PX-164\nObjective: collect typed features around a specified center coordinate.\nPinned inputs: {\"chromosome\":\"px_core_B\",\"position\":1641,\"distance\":1321,\"featureTypes\":[\"CDS\"]}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"get_nearby_features","arguments":{"chromosome":"px_core_B","position":1641,"distance":1321,"featureTypes":["CDS"]}}}]}],"tools":[{"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. 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Use this for genomic positions or the current browser region; use compute_gc only when the DNA sequence string is already provided.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_annotation","description":"Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. 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For gene-based navigation, use jump_to_gene instead. For retrieving raw sequence data, use get_sequence instead.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"position":{"type":"number","minimum":1},"clientId":{"type":"string","default":"default"}},"anyOf":[{"required":["start","end"]},{"required":["position"]},{"required":["start"]}],"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-b237d68471edea1f614d","scenario_family_id":"fixture:v2:single:get_nearby_features:dev:0:13","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Validation card PX-195\nObjective: derive the opposite-strand representation of the supplied oligo.\nPinned inputs: {\"sequence\":\"CGTTAGACTAGGAGGTAAAAACCGTATTG\"}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"reverse_complement","arguments":{"sequence":"CGTTAGACTAGGAGGTAAAAACCGTATTG"}}}]}],"tools":[{"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":{"sequence":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"preserve_case":{"type":"boolean","default":false},"validate_sequence":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_sequence_from_region","description":"Run BLAST on a sequence extracted directly from a loaded genome chromosome region.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"integer","minimum":1},"end":{"type":"integer","minimum":1},"blastType":{"type":"string","enum":["blastn","blastp","blastx","tblastn","tblastx"],"default":"blastn"},"database":{"type":"string","enum":["nt","nr","refseq_rna","refseq_genomic","refseq_protein","swissprot","pdb","est"],"default":"nt"},"evalue":{"type":"string","default":"0.01"},"maxTargets":{"type":"integer","default":50,"minimum":1,"maximum":1000},"service":{"type":"string","enum":["online","ncbi","remote","local","blast+"],"default":"online"}},"required":["chromosome","start","end","database"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_annotation","description":"Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"chromosome":{"type":"string"},"full_details":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["identifier"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"genome_codon_usage_analysis","description":"Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"featureType":{"type":"string","default":"CDS","enum":["CDS","gene","mRNA"]},"minLength":{"type":"integer","default":300,"minimum":1,"maximum":100000},"maxGenes":{"type":"integer","minimum":1},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_genome_file","description":"Load genome files (FASTA/GenBank) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","fasta","genbank"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"replace_sequence","description":"Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"sequence":{"type":"string"},"strand":{"type":"string","enum":["+","-"],"default":"+"}},"required":["chromosome","start","end","sequence"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-ad873a0c843b5a8b096b","scenario_family_id":"fixture:v2:single:reverse_complement:dev:0:0","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Validation card PX-226\nObjective: decode a coding fragment with the declared code-table options.\nPinned inputs: {\"dna\":\"ATGCAATATAAACTGACCTAA\",\"reading_frame\":1,\"genetic_code\":\"bacterial\",\"include_stop_codons\":false}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"translate_dna","arguments":{"dna":"ATGCAATATAAACTGACCTAA","reading_frame":1,"genetic_code":"bacterial","include_stop_codons":false}}}]}],"tools":[{"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":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"reading_frame":{"type":"number","enum":[1,2,3],"default":1},"genetic_code":{"type":"string","enum":["standard","vertebrate_mitochondrial","bacterial","archaeal"],"default":"standard"},"include_stop_codons":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["dna"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"stop_benchmark","description":"Stop the currently running benchmark. Gracefully terminates the benchmark execution and saves any partial results collected so far.","parameters":{"properties":{},"type":"object","required":[],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"blast_create_quick_db_for_current_genome","description":"Quickly create BLAST databases (both nucleotide and protein) for the entire currently loaded genome. Use this as the default/quick way to index the genome when no specific chromosome name is specified. Automatically associates databases with the genome for smart database selection.","parameters":{"type":"object","properties":{"createNucleotide":{"type":"boolean","default":true},"createProtein":{"type":"boolean","default":true},"genomeName":{"type":"string"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_create_protein_db_from_genome","description":"Create BLAST protein database from loaded genome using 6-frame translation","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"dbName":{"type":"string"}},"required":["chromosome"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"genome_codon_usage_analysis","description":"Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"featureType":{"type":"string","default":"CDS","enum":["CDS","gene","mRNA"]},"minLength":{"type":"integer","default":300,"minimum":1,"maximum":100000},"maxGenes":{"type":"integer","minimum":1},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_genome_file","description":"Load genome files (FASTA/GenBank) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","fasta","genbank"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-b32e3d8b44595beb786c","scenario_family_id":"fixture:v2:single:translate_dna:dev:0:19","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Validation card PX-257\nObjective: measure the G/C fraction of the explicit nucleotide sample.\nPinned inputs: {\"sequence\":\"AGCGGGTAAGTGCCGACACAGCACAGCC\",\"normalize_case\":true}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"compute_gc","arguments":{"sequence":"AGCGGGTAAGTGCCGACACAGCACAGCC","normalize_case":true}}}]}],"tools":[{"type":"function","function":{"name":"compute_gc","description":"Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"include_statistics":{"type":"boolean","default":true},"window_size":{"type":"number","default":0,"minimum":0,"maximum":1000},"step_size":{"type":"number","default":100,"minimum":1},"normalize_case":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"search_sequence_motif","description":"Search for specific sequence motifs or patterns within genomic regions. Supports exact matches, IUPAC ambiguity codes (N=any, R=A/G, Y=C/T, S=G/C, W=A/T, K=G/T, M=A/C, B=not A, D=not C, H=not G, V=not T), regular expressions, and mismatch tolerance.","parameters":{"type":"object","properties":{"motif":{"type":"string"},"pattern":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"strand":{"type":"string","enum":["+","-","both"],"default":"both"},"max_mismatches":{"type":"number","minimum":0,"default":0},"case_sensitive":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["motif"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"sequence":{"type":"string"},"reverse_complement":{"type":"boolean","default":false}},"required":["chromosome","position","sequence"],"additionalProperties":false},"strict":false}},{"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.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"genome_codon_usage_analysis","description":"Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"featureType":{"type":"string","default":"CDS","enum":["CDS","gene","mRNA"]},"minLength":{"type":"integer","default":300,"minimum":1,"maximum":100000},"maxGenes":{"type":"integer","minimum":1},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"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_position instead.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"strand":{"type":"string","enum":["+","-","both"],"default":"+"},"format":{"type":"string","enum":["raw","fasta","genbank"],"default":"raw"},"include_annotations":{"type":"boolean","default":false},"max_length":{"type":"number","default":1000000,"maximum":10000000},"clientId":{"type":"string","default":"default"}},"required":["start","end"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-36ef1c54baf284d15775","scenario_family_id":"fixture:v2:single:compute_gc:dev:0:5","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Validation card PX-288\nObjective: measure symbol-level Shannon complexity for the explicit sample.\nPinned inputs: {\"sequence\":\"GAGGTTTCACGATAGAAGTGATGAGGTTTGGG\"}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"calculate_entropy","arguments":{"sequence":"GAGGTTTCACGATAGAAGTGATGAGGTTTGGG"}}}]}],"tools":[{"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.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_reads_file","description":"Load sequencing reads files (SAM/BAM) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"sequence":{"type":"string"},"reverse_complement":{"type":"boolean","default":false}},"required":["chromosome","position","sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_genome_file","description":"Load genome files (FASTA/GenBank) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","fasta","genbank"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"replace_sequence","description":"Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"sequence":{"type":"string"},"strand":{"type":"string","enum":["+","-"],"default":"+"}},"required":["chromosome","start","end","sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_sequence_from_region","description":"Run BLAST on a sequence extracted directly from a loaded genome chromosome region.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"integer","minimum":1},"end":{"type":"integer","minimum":1},"blastType":{"type":"string","enum":["blastn","blastp","blastx","tblastn","tblastx"],"default":"blastn"},"database":{"type":"string","enum":["nt","nr","refseq_rna","refseq_genomic","refseq_protein","swissprot","pdb","est"],"default":"nt"},"evalue":{"type":"string","default":"0.01"},"maxTargets":{"type":"integer","default":50,"minimum":1,"maximum":1000},"service":{"type":"string","enum":["online","ncbi","remote","local","blast+"],"default":"online"}},"required":["chromosome","start","end","database"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-f944b8dc1f6b724cdd9e","scenario_family_id":"fixture:v2:single:calculate_entropy:dev:0:1","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Validation card PX-319\nObjective: derive molecular mass for the declared polymer type.\nPinned inputs: {\"sequence\":\"GCGCCGCCGATTGCGCTTCATGTTCTA\",\"type\":\"dna\"}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"calculate_molecular_weight","arguments":{"sequence":"GCGCCGCCGATTGCGCTTCATGTTCTA","type":"dna"}}}]}],"tools":[{"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":{"type":"object","properties":{"sequence":{"type":"string","pattern":"^[A-Za-z*-]+$"},"dna":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"protein":{"type":"string","pattern":"^[ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy*]+$"},"type":{"type":"string","enum":["dna","protein","auto"],"default":"auto"},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"reverse_complement","description":"Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).","parameters":{"type":"object","properties":{"sequence":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"preserve_case":{"type":"boolean","default":false},"validate_sequence":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"translate_sequence","description":"Translate DNA sequence to amino acid sequence. This is an alias for translate_dna — prefer using translate_dna instead, which supports additional options like reading frame and genetic code table selection.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"dna":{"type":"string"},"reading_frame":{"type":"number","enum":[1,2,3],"default":1}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_sequence_from_region","description":"Run BLAST on a sequence extracted directly from a loaded genome chromosome region.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"integer","minimum":1},"end":{"type":"integer","minimum":1},"blastType":{"type":"string","enum":["blastn","blastp","blastx","tblastn","tblastx"],"default":"blastn"},"database":{"type":"string","enum":["nt","nr","refseq_rna","refseq_genomic","refseq_protein","swissprot","pdb","est"],"default":"nt"},"evalue":{"type":"string","default":"0.01"},"maxTargets":{"type":"integer","default":50,"minimum":1,"maximum":1000},"service":{"type":"string","enum":["online","ncbi","remote","local","blast+"],"default":"online"}},"required":["chromosome","start","end","database"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"genome_codon_usage_analysis","description":"Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"featureType":{"type":"string","default":"CDS","enum":["CDS","gene","mRNA"]},"minLength":{"type":"integer","default":300,"minimum":1,"maximum":100000},"maxGenes":{"type":"integer","minimum":1},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"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":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"reading_frame":{"type":"number","enum":[1,2,3],"default":1},"genetic_code":{"type":"string","enum":["standard","vertebrate_mitochondrial","bacterial","archaeal"],"default":"standard"},"include_stop_codons":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["dna"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-2e13903bbdcd5c2f7c8d","scenario_family_id":"fixture:v2:single:calculate_molecular_weight:dev:0:12","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Validation card PX-350\nObjective: inspect length, composition, melting behavior, and hairpin risk of the oligo.\nPinned inputs: {\"sequence\":\"AGAAAAGCTCAGTGAGCTGTGA\"}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"calculate_primer_properties","arguments":{"sequence":"AGAAAAGCTCAGTGAGCTGTGA"}}}]}],"tools":[{"type":"function","function":{"name":"calculate_primer_properties","description":"Calculate biochemical properties like melting temperature (Tm), GC content, and length for a given DNA primer sequence (18-35 bp). Use this to check if a sequence is suitable as a PCR or sequencing primer.","parameters":{"type":"object","properties":{"sequence":{"type":"string"}},"required":["sequence"],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"load_genome_file","description":"Load genome files (FASTA/GenBank) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","fasta","genbank"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"sequence":{"type":"string"},"reverse_complement":{"type":"boolean","default":false}},"required":["chromosome","position","sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"genome_codon_usage_analysis","description":"Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"featureType":{"type":"string","default":"CDS","enum":["CDS","gene","mRNA"]},"minLength":{"type":"integer","default":300,"minimum":1,"maximum":100000},"maxGenes":{"type":"integer","minimum":1},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_sequence_from_region","description":"Run BLAST on a sequence extracted directly from a loaded genome chromosome region.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"integer","minimum":1},"end":{"type":"integer","minimum":1},"blastType":{"type":"string","enum":["blastn","blastp","blastx","tblastn","tblastx"],"default":"blastn"},"database":{"type":"string","enum":["nt","nr","refseq_rna","refseq_genomic","refseq_protein","swissprot","pdb","est"],"default":"nt"},"evalue":{"type":"string","default":"0.01"},"maxTargets":{"type":"integer","default":50,"minimum":1,"maximum":1000},"service":{"type":"string","enum":["online","ncbi","remote","local","blast+"],"default":"online"}},"required":["chromosome","start","end","database"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"compute_gc","description":"Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"include_statistics":{"type":"boolean","default":true},"window_size":{"type":"number","default":0,"minimum":0,"maximum":1000},"step_size":{"type":"number","default":100,"minimum":1},"normalize_case":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-a318ab4c9d9f94e69048","scenario_family_id":"fixture:v2:single:calculate_primer_properties:dev:0:10","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Validation card PX-381\nObjective: scan the explicit template for exact matches to the supplied primer.\nPinned inputs: {\"sequence\":\"GCACCGAGTGGTAGTCCC\",\"templateSequence\":\"CGATGGGGGACAACGTAACCCAGTGTAATGTATGAGCCGAGTAGGCCCAAGGGATTCGGTGCGTGCTATTGCCAGTATACGCAGGCGACCGTCCCTTCGTAACCAAGTACGTGATAACCGCTCGATGGTATGGCTACACTGGGATATCGAATGGTGGAGATGAAGTGTCCATGCTCGTAGTAGTAGGCAACAGGTTCATTAACGCGCTCCCCACCCCAAGCATAACGAAATTTCAAGCGGATTTGCTGAAACCGATTTATCGGCAAGTATTGCATTGAGGCTGTAACTGCGCGGCTTTAATTAGTAGAATGAGGCGTGCGGGGGGTAATTAGCGTACACTTTGTAAGAATTGTGCCGTATGCCTCCTTGAATGTAATGTCAACATTATTGGGCACCGAGTGGTAGTCCCTTGCGTAGCCTAAGG\",\"maxMismatches\":0,\"max3PrimeMismatches\":0}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_primer_binding_sites","arguments":{"sequence":"GCACCGAGTGGTAGTCCC","templateSequence":"CGATGGGGGACAACGTAACCCAGTGTAATGTATGAGCCGAGTAGGCCCAAGGGATTCGGTGCGTGCTATTGCCAGTATACGCAGGCGACCGTCCCTTCGTAACCAAGTACGTGATAACCGCTCGATGGTATGGCTACACTGGGATATCGAATGGTGGAGATGAAGTGTCCATGCTCGTAGTAGTAGGCAACAGGTTCATTAACGCGCTCCCCACCCCAAGCATAACGAAATTTCAAGCGGATTTGCTGAAACCGATTTATCGGCAAGTATTGCATTGAGGCTGTAACTGCGCGGCTTTAATTAGTAGAATGAGGCGTGCGGGGGGTAATTAGCGTACACTTTGTAAGAATTGTGCCGTATGCCTCCTTGAATGTAATGTCAACATTATTGGGCACCGAGTGGTAGTCCCTTGCGTAGCCTAAGG","maxMismatches":0,"max3PrimeMismatches":0}}}]}],"tools":[{"type":"function","function":{"name":"find_primer_binding_sites","description":"Search for binding sites of a primer sequence within a template, with scientific mismatch tolerance. Uses position-dependent scoring (3' end weighted), nearest-neighbor thermodynamic Tm estimation, and configurable filtering. Finds both forward and reverse-complement binding sites.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"templateSequence":{"type":"string"},"maxMismatches":{"type":"number"},"max3PrimeMismatches":{"type":"number","minimum":0},"minBindingTm":{"type":"number"},"scoringMode":{"type":"string","enum":["fast","thermodynamic"]},"naConcentration":{"type":"number","minimum":0},"primerConcentration":{"type":"number","minimum":0}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_annotation","description":"Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"chromosome":{"type":"string"},"full_details":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["identifier"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"genome_codon_usage_analysis","description":"Perform comprehensive genome-wide codon usage analysis across all CDS features to identify codon preferences and biases at the organism level. Analyzes synonymous codon preferences, calculates RSCU values, and provides detailed statistical analysis of codon bias strength including Effective Number of Codons (ENC) for each amino acid.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"featureType":{"type":"string","default":"CDS","enum":["CDS","gene","mRNA"]},"minLength":{"type":"integer","default":300,"minimum":1,"maximum":100000},"maxGenes":{"type":"integer","minimum":1},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_genome_file","description":"Load genome files (FASTA/GenBank) directly with file path specification or via file dialog","parameters":{"type":"object","properties":{"filePath":{"type":"string","required":false},"showFileDialog":{"type":"boolean","required":false,"default":false},"fileType":{"type":"string","required":false,"default":"auto","enum":["auto","fasta","genbank"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"save_primer","description":"Save a primer oligo to the primer library (stored separately from the genome, never written into the genome file). Binding sites are predicted automatically; provide chromosome/start/end only to pin a specific manual placement.","parameters":{"type":"object","properties":{"name":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"strand":{"type":"string"},"description":{"type":"string"},"sequence":{"type":"string"}},"required":["name","chromosome","start","end"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"replace_sequence","description":"Queue replacement of a sequence region with a new DNA sequence as a sequence-editing Action. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"sequence":{"type":"string"},"strand":{"type":"string","enum":["+","-"],"default":"+"}},"required":["chromosome","start","end","sequence"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-1f19640d03a49ac97494","scenario_family_id":"fixture:v2:single:find_primer_binding_sites:dev:0:1","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Locate BamHI sites in the explicit pinned DNA for digest check PX-404: CTCATTCGGTGCCGAACCTTTCCTGGGGAATTTTATATGATACATACCGCCCTGACCGAGTGTGGAGGCGCATCGTTGCATACGCAGAATTCTGCCGAATCACCCAAGCGCGGCAATATTCCTTCAATCTCCACAAATATGGATAGCGCTCGAGATTTCTACCCATCTTTTTAAATGAACACGCCGTTTAAAGCCCCAATCTCGTTCTCAATCTTACGCCTCGCTGAATCTCTCCCCAGAAAAAGCAGACTCAGCGGGCATTTTAATCCTCCATGTGACTTTAGGGAAGCCGTAAAAGCTGGGTTGGTATCCAACAGCGCTTGTATAATAGGCCAGTAACCAACTTAAGAATATCCTAACCGCCGGCGAAGCCTACTCGTCAAGTTATACAAATCATCGCTTGACTGTGATTGGGCGGGAGGATCCGTCATGTCTGCCTCAGCCAA."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_restriction_sites","arguments":{"enzyme":"BamHI","sequence":"CTCATTCGGTGCCGAACCTTTCCTGGGGAATTTTATATGATACATACCGCCCTGACCGAGTGTGGAGGCGCATCGTTGCATACGCAGAATTCTGCCGAATCACCCAAGCGCGGCAATATTCCTTCAATCTCCACAAATATGGATAGCGCTCGAGATTTCTACCCATCTTTTTAAATGAACACGCCGTTTAAAGCCCCAATCTCGTTCTCAATCTTACGCCTCGCTGAATCTCTCCCCAGAAAAAGCAGACTCAGCGGGCATTTTAATCCTCCATGTGACTTTAGGGAAGCCGTAAAAGCTGGGTTGGTATCCAACAGCGCTTGTATAATAGGCCAGTAACCAACTTAAGAATATCCTAACCGCCGGCGAAGCCTACTCGTCAAGTTATACAAATCATCGCTTGACTGTGATTGGGCGGGAGGATCCGTCATGTCTGCCTCAGCCAA"}}}]}],"tools":[{"type":"function","function":{"name":"find_restriction_sites","description":"Locates recognition and cleavage sites for restriction endonucleases in a genomic region. Supports 80+ enzymes with IUPAC ambiguity codes, staggered cut positions (5' overhang, 3' overhang, blunt end), and HF variants.","parameters":{"type":"object","properties":{"enzyme":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"integer"},"end":{"type":"integer"},"sequence":{"type":"string"}},"required":["enzyme"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_validate_database","description":"Validate a local BLAST database integrity and format","parameters":{"type":"object","properties":{"dbName":{"type":"string"}},"required":["dbName"],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"get_clipboard_content","description":"Get the current content of the sequence clipboard. The clipboard holds sequences that have been copied or cut from the genome using copy_sequence or cut_sequence. Use this to check what sequence is currently stored in the clipboard before pasting or to verify a copy/cut operation. NOT the same as get_action_list which lists pending editing actions.","parameters":{"type":"object","properties":{},"required":[],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"sequence":{"type":"string"},"reverse_complement":{"type":"boolean","default":false}},"required":["chromosome","position","sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_benchmark_status","description":"Get the current status of the benchmark system, including initialization state, whether a benchmark is currently running or paused, and how many test suites are loaded.","parameters":{"properties":{},"type":"object","required":[],"additionalProperties":false},"strict":true}},{"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":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"reading_frame":{"type":"number","enum":[1,2,3],"default":1},"genetic_code":{"type":"string","enum":["standard","vertebrate_mitochondrial","bacterial","archaeal"],"default":"standard"},"include_stop_codons":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["dna"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-74e5fd0115a5330e0d08","scenario_family_id":"fixture:v2:single:find_restriction_sites:train:0:0","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Locate HindIII sites in the explicit pinned DNA for digest check PX-405: GGTGTTGACTTCGCAGCTGCGCGAAAGTACCTGCATAGGGCCGTAGCCTCATTGCTTGCTCATGTTACGCTCATGGAAGTAAAAGACGCCAAATGAGCGAGATATGGGAACGTACATTACGGTGTAGGCCCCCTACAGTTATGTGTACTCCCTACCCTAACTAGGGCTGCGAGGAGCCTGCAGATACTCACGGGTTGAGAGCTACTTTCGAAGTGGGCTCCGAGTAAGGAAAACCTGTCCGCTGTTTAGGGGGTTCATATATGGCCCCTCAGTAACATCAAGGCATTAGTCGGTTGCTCTAGTGTTGGTGTACGACATCCGGGCATTTGGGACGAGCCTCCTTCAGGTCACGCTCCTCAACCGCGGAGATATTAGCGTTAGTAAACGTCAGCACAAGAGGCTACCTCCCTAGCGACTTCCCAAGCTTGCGTCTCAAAATAATAGTAGA."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_restriction_sites","arguments":{"enzyme":"HindIII","sequence":"GGTGTTGACTTCGCAGCTGCGCGAAAGTACCTGCATAGGGCCGTAGCCTCATTGCTTGCTCATGTTACGCTCATGGAAGTAAAAGACGCCAAATGAGCGAGATATGGGAACGTACATTACGGTGTAGGCCCCCTACAGTTATGTGTACTCCCTACCCTAACTAGGGCTGCGAGGAGCCTGCAGATACTCACGGGTTGAGAGCTACTTTCGAAGTGGGCTCCGAGTAAGGAAAACCTGTCCGCTGTTTAGGGGGTTCATATATGGCCCCTCAGTAACATCAAGGCATTAGTCGGTTGCTCTAGTGTTGGTGTACGACATCCGGGCATTTGGGACGAGCCTCCTTCAGGTCACGCTCCTCAACCGCGGAGATATTAGCGTTAGTAAACGTCAGCACAAGAGGCTACCTCCCTAGCGACTTCCCAAGCTTGCGTCTCAAAATAATAGTAGA"}}}]}],"tools":[{"type":"function","function":{"name":"find_restriction_sites","description":"Locates recognition and cleavage sites for restriction endonucleases in a genomic region. Supports 80+ enzymes with IUPAC ambiguity codes, staggered cut positions (5' overhang, 3' overhang, blunt end), and HF variants.","parameters":{"type":"object","properties":{"enzyme":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"integer"},"end":{"type":"integer"},"sequence":{"type":"string"}},"required":["enzyme"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"sequence":{"type":"string"},"reverse_complement":{"type":"boolean","default":false}},"required":["chromosome","position","sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_benchmark_status","description":"Get the current status of the benchmark system, including initialization state, whether a benchmark is currently running or paused, and how many test suites are loaded.","parameters":{"properties":{},"type":"object","required":[],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"get_clipboard_content","description":"Get the current content of the sequence clipboard. The clipboard holds sequences that have been copied or cut from the genome using copy_sequence or cut_sequence. Use this to check what sequence is currently stored in the clipboard before pasting or to verify a copy/cut operation. NOT the same as get_action_list which lists pending editing actions.","parameters":{"type":"object","properties":{},"required":[],"additionalProperties":false},"strict":true}},{"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 tRNA\"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.","parameters":{"type":"object","properties":{"name":{"type":"string"},"exact_match":{"type":"boolean","default":false},"case_sensitive":{"type":"boolean","default":false},"navigate_to_gene":{"type":"boolean","default":true},"include_annotations":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["name"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_detect_sequence_type","description":"Detect whether a sequence is DNA, RNA, or protein","parameters":{"type":"object","properties":{"sequence":{"type":"string"}},"required":["sequence"],"additionalProperties":false},"strict":true}}],"metadata":{"source_example_id":"cx-9c55205fa94adfa70417","scenario_family_id":"fixture:v2:single:find_restriction_sites:train:1:0","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. 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{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. 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{"messages":[{"role":"system","content":"Use only the supplied CodeXomics tools. Ground every argument in the request or tool results. 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{"messages":[{"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":"Locate BamHI sites in the explicit pinned DNA for digest check PX-410: GTCTTTAGACACCCCGTGCTGCCCCTATTGGTCTCCATCGGAGAGAGGTGCGAATTCCTAAGTTGAGTGCGGCCCTGTCGAAGTTTTTAGATGAGGTCGTCGTGAGTCGGGGTGCAGAGGTACAATCCTATGTCTCGGGCGGATTTGCACCGAAGTCTTCTTACCTTGCCAAGGTCGGTTGGCTTGGATAGCTTCGAAGTGGGCAACGCTCGGTTGCGTCAAAGCTAACCGACGCGTTTACGAGTACAATCAAATGTGCCGCAAGTACATACGCGGTCCACGTCGTTCGGATAGCGGCTTGACGAAGGTGGATCTAACTATTCCGGAAGGGATAAGCGAGGCTTGGCGAATAGGACCGAAGGGGAGGCTCTCTGCGAGAGTATCATTTTGAGACGAGGAGGATCGGTAACAGGCACCGCGCTCGCTGGATCCATTTCCTTTGTCAGAGGGTA."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_restriction_sites","arguments":{"enzyme":"BamHI","sequence":"GTCTTTAGACACCCCGTGCTGCCCCTATTGGTCTCCATCGGAGAGAGGTGCGAATTCCTAAGTTGAGTGCGGCCCTGTCGAAGTTTTTAGATGAGGTCGTCGTGAGTCGGGGTGCAGAGGTACAATCCTATGTCTCGGGCGGATTTGCACCGAAGTCTTCTTACCTTGCCAAGGTCGGTTGGCTTGGATAGCTTCGAAGTGGGCAACGCTCGGTTGCGTCAAAGCTAACCGACGCGTTTACGAGTACAATCAAATGTGCCGCAAGTACATACGCGGTCCACGTCGTTCGGATAGCGGCTTGACGAAGGTGGATCTAACTATTCCGGAAGGGATAAGCGAGGCTTGGCGAATAGGACCGAAGGGGAGGCTCTCTGCGAGAGTATCATTTTGAGACGAGGAGGATCGGTAACAGGCACCGCGCTCGCTGGATCCATTTCCTTTGTCAGAGGGTA"}}}]}],"tools":[{"type":"function","function":{"name":"find_restriction_sites","description":"Locates recognition and cleavage sites for restriction endonucleases in a genomic region. Supports 80+ enzymes with IUPAC ambiguity codes, staggered cut positions (5' overhang, 3' overhang, blunt end), and HF variants.","parameters":{"type":"object","properties":{"enzyme":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"integer"},"end":{"type":"integer"},"sequence":{"type":"string"}},"required":["enzyme"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. Call execute_actions(auto_save=true) to apply queued sequence-editing Actions.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"chromosome":{"type":"string"},"position":{"type":"number","minimum":1},"sequence":{"type":"string"},"reverse_complement":{"type":"boolean","default":false}},"required":["chromosome","position","sequence"],"additionalProperties":false},"strict":false}},{"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":{"type":"object","properties":{"sequence":{"type":"string","pattern":"^[A-Za-z*-]+$"},"dna":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"protein":{"type":"string","pattern":"^[ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy*]+$"},"type":{"type":"string","enum":["dna","protein","auto"],"default":"auto"},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_benchmark_status","description":"Get the current status of the benchmark system, including initialization state, whether a benchmark is currently running or paused, and how many test suites are loaded.","parameters":{"properties":{},"type":"object","required":[],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"reverse_complement","description":"Generate the reverse complement of a DNA sequence. Reverses the sequence order and converts each base to its complement (A↔T, G↔C).","parameters":{"type":"object","properties":{"sequence":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"preserve_case":{"type":"boolean","default":false},"validate_sequence":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_validate_database","description":"Validate a local BLAST database integrity and format","parameters":{"type":"object","properties":{"dbName":{"type":"string"}},"required":["dbName"],"additionalProperties":false},"strict":true}}],"metadata":{"source_example_id":"cx-b2d5f8cbbae0ad332dc3","scenario_family_id":"fixture:v2:single:find_restriction_sites:train:6:0","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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":"Locate HindIII sites in the explicit pinned DNA for digest check PX-411: ATTACAGAACCAATAAATGTTGATTGAGTCAAAGTACATCCGACAGTCAACTTAAAGCGGAGATAGAGGATAAACGCGATGTTCGTCTAATTACTAAACAAGGATTTAGTGAGGTCGGGATTTTACACCTACCTTGTTGGAGAGTTTGCAATACGCCTGGGGATCCCGGTATCGCACTTTCGTACAATTCCTCACCACTCGAGCATTCGAAGGTTCTCCGAGTAGTGCCTCGTATGAATCGCTTAAGCTCGATCTATATTTTACTCAAGTAGTCTCTGTCTATTCCCAGGTCAACTTAATGTGTCAACTCCGTCACCCCAACGGAAGTACGTGCTAGTTCGTCTCGGGCTACCGATGCACACTCCCCTCGTTTATACAAAACTCTAAATATGCTCATTATGCGTCAAACCTTCTCATCGGCAGGTTGAAGCTTGCTCGAGGGGCCCAATATAAT."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_restriction_sites","arguments":{"enzyme":"HindIII","sequence":"ATTACAGAACCAATAAATGTTGATTGAGTCAAAGTACATCCGACAGTCAACTTAAAGCGGAGATAGAGGATAAACGCGATGTTCGTCTAATTACTAAACAAGGATTTAGTGAGGTCGGGATTTTACACCTACCTTGTTGGAGAGTTTGCAATACGCCTGGGGATCCCGGTATCGCACTTTCGTACAATTCCTCACCACTCGAGCATTCGAAGGTTCTCCGAGTAGTGCCTCGTATGAATCGCTTAAGCTCGATCTATATTTTACTCAAGTAGTCTCTGTCTATTCCCAGGTCAACTTAATGTGTCAACTCCGTCACCCCAACGGAAGTACGTGCTAGTTCGTCTCGGGCTACCGATGCACACTCCCCTCGTTTATACAAAACTCTAAATATGCTCATTATGCGTCAAACCTTCTCATCGGCAGGTTGAAGCTTGCTCGAGGGGCCCAATATAAT"}}}]}],"tools":[{"type":"function","function":{"name":"find_restriction_sites","description":"Locates recognition and cleavage sites for restriction endonucleases in a genomic region. 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For direct navigation to a known gene, try jump_to_gene first.","parameters":{"type":"object","properties":{"name":{"type":"string"},"exact_match":{"type":"boolean","default":false},"case_sensitive":{"type":"boolean","default":false},"navigate_to_gene":{"type":"boolean","default":true},"include_annotations":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["name"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_validate_database","description":"Validate a local BLAST database integrity and format","parameters":{"type":"object","properties":{"dbName":{"type":"string"}},"required":["dbName"],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"calculate_molecular_weight","description":"Calculate the molecular weight of a DNA, RNA, or protein sequence in Daltons. 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NOT the same as get_action_list which lists pending editing actions.","parameters":{"type":"object","properties":{},"required":[],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. Set reverse_complement=true to reverse-complement the provided sequence before it is inserted. This is not a checklist Task. 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{"messages":[{"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":"Validation card PX-412\nObjective: scan explicit DNA for recognition sites of the declared enzyme.\nPinned inputs: {\"enzyme\":\"XhoI\",\"sequence\":\"AGCCCGCATCTCTTTACTCTGTGTTCCCATAATTCTTGTGGCATCGTCTGACAGATATAGCCACGATCCTAGTTGCGTGGTATTTTGAAGCCGTTCCTTAAAGGATCTGTGCTAATAACCAGTCTAACCTGCGCCGTTGTAGCGGGCGTACGAATCCCAGCCGCAGCCCTATTGTAGGGCACCTGACTCGTCAGGCAAGACTTTCGACGTGACACCGCAAACCTCGAGCCGATAATTCTTCTCTCCTCCCTTGCGTTGGAGCTCGCAATTAAAGGTGAGCATTTGTCTTAACCGCCCTCCCGCGATTGTGGGACATGTAAGGTCCCAGCTCATGATGCATGCCTTTCGGCAACTTAAGCAACTCACGGGGACTCAATAGAACACTAGGACGCAAACTCATTGTCGTGGACGTTTGTGCAATCTTAAGCCTCGAGTGTTTACTGCATGTTAGGGGTT\"}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"find_restriction_sites","arguments":{"enzyme":"XhoI","sequence":"AGCCCGCATCTCTTTACTCTGTGTTCCCATAATTCTTGTGGCATCGTCTGACAGATATAGCCACGATCCTAGTTGCGTGGTATTTTGAAGCCGTTCCTTAAAGGATCTGTGCTAATAACCAGTCTAACCTGCGCCGTTGTAGCGGGCGTACGAATCCCAGCCGCAGCCCTATTGTAGGGCACCTGACTCGTCAGGCAAGACTTTCGACGTGACACCGCAAACCTCGAGCCGATAATTCTTCTCTCCTCCCTTGCGTTGGAGCTCGCAATTAAAGGTGAGCATTTGTCTTAACCGCCCTCCCGCGATTGTGGGACATGTAAGGTCCCAGCTCATGATGCATGCCTTTCGGCAACTTAAGCAACTCACGGGGACTCAATAGAACACTAGGACGCAAACTCATTGTCGTGGACGTTTGTGCAATCTTAAGCCTCGAGTGTTTACTGCATGTTAGGGGTT"}}}]}],"tools":[{"type":"function","function":{"name":"find_restriction_sites","description":"Locates recognition and cleavage sites for restriction endonucleases in a genomic region. 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Supports multiple reading frames and genetic code tables.","parameters":{"type":"object","properties":{"dna":{"type":"string","pattern":"^[ATGCNatgcn]+$"},"reading_frame":{"type":"number","enum":[1,2,3],"default":1},"genetic_code":{"type":"string","enum":["standard","vertebrate_mitochondrial","bacterial","archaeal"],"default":"standard"},"include_stop_codons":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["dna"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_detect_sequence_type","description":"Detect whether a sequence is DNA, RNA, or protein","parameters":{"type":"object","properties":{"sequence":{"type":"string"}},"required":["sequence"],"additionalProperties":false},"strict":true}},{"type":"function","function":{"name":"insert_sequence","description":"Queue insertion of a DNA sequence at a specified position as a sequence-editing Action. 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{"messages":[{"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":"Validation card PX-443\nObjective: compute fragment boundaries after the declared enzyme combination.\nPinned inputs: {\"enzymes\":[\"PstI\",\"EcoRI\"],\"sequence\":\"ATTGCTGACCTGATGTGTTCTAGTCGAGTGTGTTATCGTGCCGTGCAGCTAGCGCGGAAATTAGGGGACCGACCCGGTACCAAGGTGATGCCAGGATGTATGGCACGGAATTTTGTTCCCAGTAGGCGATGGACACGAGCCTGAAATGCAAGCGACGTCGAGATGGGGCCCGCGTTACTTATGGTAGGAGCTTTAAGTGTCAGGCTTGAGCTATGTTCCCGTTGATTGTAACCTAACTGTACGTGTATATCAGCGTAATATGTTAATATACCGACCCGCTGGCATATGGTTAGGGAATTTCGCTCTCACGCTTGACCGCCATTGTTCTTCTACCGACCCACGGTAGTAATTGTGCCCTGCCTCGGTCAGATGAGCTATTCCGGAGCACATCCTTATCCTATCGGACAAACCAGAGGTAAATAAAAATGTAAAACCGACCCTCGTTAGTATACCATTTCACTGCAGGCTACTATATTCTACGAATTCGACTTAAGGCTAGGTACTCACAC\"}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"virtual_digest","arguments":{"enzymes":["PstI","EcoRI"],"sequence":"ATTGCTGACCTGATGTGTTCTAGTCGAGTGTGTTATCGTGCCGTGCAGCTAGCGCGGAAATTAGGGGACCGACCCGGTACCAAGGTGATGCCAGGATGTATGGCACGGAATTTTGTTCCCAGTAGGCGATGGACACGAGCCTGAAATGCAAGCGACGTCGAGATGGGGCCCGCGTTACTTATGGTAGGAGCTTTAAGTGTCAGGCTTGAGCTATGTTCCCGTTGATTGTAACCTAACTGTACGTGTATATCAGCGTAATATGTTAATATACCGACCCGCTGGCATATGGTTAGGGAATTTCGCTCTCACGCTTGACCGCCATTGTTCTTCTACCGACCCACGGTAGTAATTGTGCCCTGCCTCGGTCAGATGAGCTATTCCGGAGCACATCCTTATCCTATCGGACAAACCAGAGGTAAATAAAAATGTAAAACCGACCCTCGTTAGTATACCATTTCACTGCAGGCTACTATATTCTACGAATTCGACTTAAGGCTAGGTACTCACAC"}}}]}],"tools":[{"type":"function","function":{"name":"virtual_digest","description":"Performs an in-silico restriction digest of a chromosome or sequence using one or more restriction enzymes. 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Use this when the user asks for details about one specific gene/annotation by name or identifier. Returns the complete annotation record with all available fields. NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"chromosome":{"type":"string"},"full_details":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["identifier"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"compute_gc","description":"Calculate GC content percentage and other nucleotide composition statistics for a DNA sequence.","parameters":{"type":"object","properties":{"sequence":{"type":"string"},"include_statistics":{"type":"boolean","default":true},"window_size":{"type":"number","default":0,"minimum":0,"maximum":1000},"step_size":{"type":"number","default":100,"minimum":1},"normalize_case":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["sequence"],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-6d9a3dbbc3f44a748ae4","scenario_family_id":"fixture:v2:single:virtual_digest:dev:0:10","supervised_target":"tool_call","turn_index":2}}
{"messages":[{"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 protein snapshot for the synthetic protein record pcf017 in Synthetic bacterium Beta, limiting the audit PX-497 to 4 entries. This is a UniProt lookup, not a genome-gene search."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"search_uniprot_database","arguments":{"search_query":"pcf017","organism":"Synthetic bacterium Beta","max_results":4}}}]}],"tools":[{"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":{"search_query":{"type":"string"},"search_type":{"type":"string","enum":["protein_name","gene_name","organism","keyword","uniprot_id","sequence","all_fields"],"default":"all_fields"},"organism":{"type":"string"},"reviewed_only":{"type":"boolean","default":false},"evidence_filter":{"type":"array","items":{"type":"string","enum":["experimental","homology","predicted","uncertain"]},"default":[]},"length_range":{"type":"object","properties":{"min":{"type":"number","minimum":1},"max":{"type":"number","minimum":1}}},"max_results":{"type":"number","minimum":1,"maximum":1000,"default":100},"sort_by":{"type":"string","enum":["relevance","protein_name","organism","length","date_modified"],"default":"relevance"},"include_isoforms":{"type":"boolean","default":false},"output_fields":{"type":"array","items":{"type":"string","enum":["accession","protein_name","gene_name","organism","length","sequence","function","go_terms"]},"default":["accession","protein_name","gene_name","organism","length"]},"clientId":{"type":"string","default":"default"}},"required":["search_query"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"get_annotation","description":"Get detailed information about a specific annotation by locus_tag, gene name, or protein_id. 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NOT the same as list_annotations which returns multiple annotations in a region, or search_annotations which searches by keyword pattern.","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"chromosome":{"type":"string"},"full_details":{"type":"boolean","default":false},"clientId":{"type":"string","default":"default"}},"required":["identifier"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"uniprot_get_protein","description":"Get detailed protein information from UniProt","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"sequence":{"type":"string"},"blastType":{"type":"string","enum":["blastn","blastp","blastx","tblastn","tblastx"]},"database":{"type":"string","default":"nr"}},"required":["sequence","blastType","database"],"additionalProperties":false},"strict":false}},{"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 tRNA\"), use search_features instead. For direct navigation to a known gene, try jump_to_gene first.","parameters":{"type":"object","properties":{"name":{"type":"string"},"exact_match":{"type":"boolean","default":false},"case_sensitive":{"type":"boolean","default":false},"navigate_to_gene":{"type":"boolean","default":true},"include_annotations":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":["name"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"search_pdb_structures","description":"Search PDB database for experimental protein structures by gene name. Returns available X-ray crystallography, NMR, cryo-EM, and other experimental structure data.","parameters":{"type":"object","properties":{"geneName":{"type":"string"},"organism":{"type":"string","default":"Homo sapiens"},"max_resolution":{"type":"number","minimum":0.5,"maximum":10,"default":5},"structure_methods":{"type":"array","items":{"type":"string","enum":["x-ray","nmr","cryo-em","neutron","fiber diffraction"]},"default":["x-ray","nmr","cryo-em"]},"max_results":{"type":"number","minimum":1,"maximum":50,"default":10},"clientId":{"type":"string","default":"default"}},"required":["geneName"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"search_annotations","description":"Full-text search across annotation fields (product, gene, note, locus_tag, etc.) to find annotations matching a query string. Use this when the user asks to search annotations by keyword, find genes by product description, or look up annotations by name pattern. 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