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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":"Produce the validated reverse complement for synthetic oligo PX-193: ACCTTGGAAGGGTAAGACCTGCTTCCG."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"reverse_complement","arguments":{"sequence":"ACCTTGGAAGGGTAAGACCTGCTTCCG"}}}]}],"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":"execute_actions","description":"Execute all pending sequence-editing Actions and generate a modified GenBank file. This executes queued genome edits only; it does not run checklist Tasks. Reverse-complement paste_sequence and insert_sequence Actions are converted before they are applied.","parameters":{"type":"object","properties":{"auto_save":{"type":"boolean","default":false},"filename":{"type":"string"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"predict_promoter","description":"Predict promoter regions in DNA sequence","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"sequence":{"type":"string"}},"required":["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":"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}}],"metadata":{"source_example_id":"cx-3626a1a67bf453d6baba","scenario_family_id":"fixture:v2:single:reverse_complement: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":"Produce the validated reverse complement for synthetic oligo PX-194: GTCTAGCCTCATCGGCAACGGACCCTAT."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"reverse_complement","arguments":{"sequence":"GTCTAGCCTCATCGGCAACGGACCCTAT"}}}]}],"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":"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":"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_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":"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":"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}}],"metadata":{"source_example_id":"cx-6d406e770fb4c9e95419","scenario_family_id":"fixture:v2:single:reverse_complement:train:7:0","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. 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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":"From the pinned enzyme catalog for audit PX-470, list commercial entries matching BamHI with recognition lengths 4-10."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_restriction_enzymes","arguments":{"query":"BamHI","minRecognitionLength":4,"maxRecognitionLength":10,"commercialOnly":true}}}]}],"tools":[{"type":"function","function":{"name":"list_restriction_enzymes","description":"List available restriction enzymes from the built-in database (80+ enzymes). Supports filtering by name query, recognition sequence length, overhang type (5' overhang, 3' overhang, blunt), and commercial availability. Also shows isoschizomers and HF variants.","parameters":{"type":"object","properties":{"query":{"type":"string"},"minRecognitionLength":{"type":"integer"},"maxRecognitionLength":{"type":"integer"},"overhangType":{"type":"string","enum":["5''_overhang","3''_overhang","blunt"]},"commercialOnly":{"type":"boolean","default":true}},"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":"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":"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":"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_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}}],"metadata":{"source_example_id":"cx-308e3e97772ede1bd99c","scenario_family_id":"fixture:v2:single:list_restriction_enzymes: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":"From the pinned enzyme catalog for audit PX-472, list commercial entries matching XhoI with recognition lengths 4-10."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_restriction_enzymes","arguments":{"query":"XhoI","minRecognitionLength":4,"maxRecognitionLength":10,"commercialOnly":true}}}]}],"tools":[{"type":"function","function":{"name":"list_restriction_enzymes","description":"List available restriction enzymes from the built-in database (80+ enzymes). Supports filtering by name query, recognition sequence length, overhang type (5' overhang, 3' overhang, blunt), and commercial availability. Also shows isoschizomers and HF variants.","parameters":{"type":"object","properties":{"query":{"type":"string"},"minRecognitionLength":{"type":"integer"},"maxRecognitionLength":{"type":"integer"},"overhangType":{"type":"string","enum":["5''_overhang","3''_overhang","blunt"]},"commercialOnly":{"type":"boolean","default":true}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_primers","description":"List primers in the library and their binding sites (pinned + predicted) for the current chromosome, optionally filtered by genomic interval.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"}},"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":"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":"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_plugins","description":"List all available plugins in the system, including installed, enabled, and marketplace plugins. Provides comprehensive plugin information and status.","parameters":{"type":"object","properties":{"status":{"type":"string","enum":["all","installed","enabled","disabled","available","outdated"],"default":"all"},"category":{"type":"string","default":null},"search_term":{"type":"string","default":null},"include_functions":{"type":"boolean","default":true},"include_metadata":{"type":"boolean","default":true},"sort_by":{"type":"string","enum":["name","version","status","last_used","popularity"],"default":"name"},"limit":{"type":"number","default":50,"minimum":1,"maximum":200},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-9179c11eaa3fd7010e9e","scenario_family_id":"fixture:v2:single:list_restriction_enzymes:train:6:1","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":"From the pinned enzyme catalog for audit PX-473, list commercial entries matching PstI with recognition lengths 4-10."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_restriction_enzymes","arguments":{"query":"PstI","minRecognitionLength":4,"maxRecognitionLength":10,"commercialOnly":true}}}]}],"tools":[{"type":"function","function":{"name":"list_restriction_enzymes","description":"List available restriction enzymes from the built-in database (80+ enzymes). Supports filtering by name query, recognition sequence length, overhang type (5' overhang, 3' overhang, blunt), and commercial availability. Also shows isoschizomers and HF variants.","parameters":{"type":"object","properties":{"query":{"type":"string"},"minRecognitionLength":{"type":"integer"},"maxRecognitionLength":{"type":"integer"},"overhangType":{"type":"string","enum":["5''_overhang","3''_overhang","blunt"]},"commercialOnly":{"type":"boolean","default":true}},"required":[],"additionalProperties":false},"strict":false}},{"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":"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":"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_primers","description":"List primers in the library and their binding sites (pinned + predicted) for the current chromosome, optionally filtered by genomic interval.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"list_dna_markers","description":"List available DNA markers/ladders from the built-in commercial marker database. Covers NEB, Thermo Fisher, Takara, and common Chinese domestic brands (TransGen, Vazyme, BioMaded, Sangon). Supports filtering by brand, category, and text search.","parameters":{"type":"object","properties":{"query":{"type":"string"},"brand":{"type":"string"},"category":{"type":"string","enum":["ladder","digest_marker"]}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-de7b70cbd7a8af04fbf3","scenario_family_id":"fixture:v2:single:list_restriction_enzymes:train:7:0","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-474\nObjective: filter the pinned enzyme index by the supplied catalog constraints.\nPinned inputs: {\"query\":\"NotI\",\"minRecognitionLength\":4,\"maxRecognitionLength\":10,\"commercialOnly\":true}.\nDo not substitute values from another genome or external service."},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_restriction_enzymes","arguments":{"query":"NotI","minRecognitionLength":4,"maxRecognitionLength":10,"commercialOnly":true}}}]}],"tools":[{"type":"function","function":{"name":"list_restriction_enzymes","description":"List available restriction enzymes from the built-in database (80+ enzymes). Supports filtering by name query, recognition sequence length, overhang type (5' overhang, 3' overhang, blunt), and commercial availability. Also shows isoschizomers and HF variants.","parameters":{"type":"object","properties":{"query":{"type":"string"},"minRecognitionLength":{"type":"integer"},"maxRecognitionLength":{"type":"integer"},"overhangType":{"type":"string","enum":["5''_overhang","3''_overhang","blunt"]},"commercialOnly":{"type":"boolean","default":true}},"required":[],"additionalProperties":false},"strict":false}},{"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":"get_genome_info","description":"Get comprehensive information about the loaded genome including chromosomes, annotations, statistics, and metadata. Use this to understand the available genomic data.","parameters":{"type":"object","properties":{"include_statistics":{"type":"boolean","default":true},"include_annotations":{"type":"boolean","default":true},"include_chromosomes":{"type":"boolean","default":true},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"blast_filter_results","description":"Filter BLAST search results by identity, E-value, coverage, or hit count. Defaults to the most recent BLAST search, so the filter criteria are usually the only arguments needed.","parameters":{"type":"object","properties":{"searchId":{"type":"string"},"results":{"type":"object"},"minIdentity":{"type":"number"},"maxEvalue":{"type":"number"},"minCoverage":{"type":"number"},"maxHits":{"type":"integer"}},"required":[],"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}}],"metadata":{"source_example_id":"cx-fe2159104fcbd4e7eede","scenario_family_id":"fixture:v2:single:list_restriction_enzymes: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":"从固定酶目录中筛选名称匹配 EcoRI、识别长度为 4-10 且可商购的条目（PX-475）。"},{"role":"assistant","content":null,"tool_calls":[{"id":"call_1","type":"function","function":{"name":"list_restriction_enzymes","arguments":{"query":"EcoRI","minRecognitionLength":4,"maxRecognitionLength":10,"commercialOnly":true}}}]}],"tools":[{"type":"function","function":{"name":"list_restriction_enzymes","description":"List available restriction enzymes from the built-in database (80+ enzymes). Supports filtering by name query, recognition sequence length, overhang type (5' overhang, 3' overhang, blunt), and commercial availability. Also shows isoschizomers and HF variants.","parameters":{"type":"object","properties":{"query":{"type":"string"},"minRecognitionLength":{"type":"integer"},"maxRecognitionLength":{"type":"integer"},"overhangType":{"type":"string","enum":["5''_overhang","3''_overhang","blunt"]},"commercialOnly":{"type":"boolean","default":true}},"required":[],"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}},{"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":"navigate_to_position","description":"Navigate to specific genomic coordinates in the genome browser to VISUALIZE the region. Use this when users ask to \"show\", \"display\", or \"view\" a genomic region by coordinates. Coordinates are 1-based base pairs; the chromosome defaults to the one currently displayed, so pass chromosome only when the user names a sequence that is actually loaded. 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}},{"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":"get_current_state","description":"Get the current state of the genome browser including position, visible tracks, loaded data, and session information. Use this to understand the current context before making other operations.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"include_tracks":{"type":"boolean","default":true},"include_data_summary":{"type":"boolean","default":true}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-9292d302c851da59a403","scenario_family_id":"fixture:v2:single:list_restriction_enzymes:holdout:0:26","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":"Explain what GC content means without running any analysis."},{"role":"assistant","content":"GC content is the percentage of guanine and cytosine bases in a DNA sequence."}],"tools":[{"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":"list_plugins","description":"List all available plugins in the system, including installed, enabled, and marketplace plugins. Provides comprehensive plugin information and status.","parameters":{"type":"object","properties":{"status":{"type":"string","enum":["all","installed","enabled","disabled","available","outdated"],"default":"all"},"category":{"type":"string","default":null},"search_term":{"type":"string","default":null},"include_functions":{"type":"boolean","default":true},"include_metadata":{"type":"boolean","default":true},"sort_by":{"type":"string","enum":["name","version","status","last_used","popularity"],"default":"name"},"limit":{"type":"number","default":50,"minimum":1,"maximum":200},"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":"codon_usage_analysis","description":"Analyze codon usage patterns in DNA coding sequence with comprehensive statistics and visualization. Supports analysis by direct sequence input, gene name, or locus tag.","parameters":{"type":"object","properties":{"sequence":{"type":"string","minLength":3,"pattern":"^[ATGC]+$"},"geneName":{"type":"string"},"locusTag":{"type":"string"},"chromosome":{"type":"string","default":"current"},"clientId":{"type":"string","default":"default"},"include_statistics":{"type":"boolean","default":true},"normalize_sequence":{"type":"boolean","default":true},"genetic_code":{"type":"string","enum":["standard","vertebrate_mitochondrial","yeast_mitochondrial","mold_mitochondrial"],"default":"standard"},"window_size":{"type":"integer","minimum":0,"default":0},"step_size":{"type":"integer","minimum":1,"default":1}},"required":[],"anyOf":[{"required":["sequence"]},{"required":["geneName"]},{"required":["locusTag"]}],"additionalProperties":false},"strict":false}},{"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":"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}}],"metadata":{"source_example_id":"cx-90f46435481f1784933a","scenario_family_id":"decision:no_tool:concept","supervised_target":"no_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":"Show me an example of how a region navigation request could be phrased, but do not navigate."},{"role":"assistant","content":"For example: Navigate to positions 1000 through 2000 on the active chromosome."}],"tools":[{"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":"calc_region_gc","description":"Calculate GC content for a chromosome coordinate range from the currently loaded genome. 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":"bookmark_position","description":"Save a named genomic position or region bookmark for quick navigation later. Use this when the user asks to bookmark, pin, flag, or save a specific coordinate range. This stores only the genomic interval, not track visibility or full workspace layout.","parameters":{"type":"object","properties":{"name":{"type":"string"},"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"notes":{"type":"string","default":""},"clientId":{"type":"string","default":"default"}},"required":["name"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"highlight_region","description":"Add a persistent visual highlight (a colored box) over a genomic region, spanning the full height of the ruler and tracks. Unlike select_sequence_region (which sets a single active selection for copy/extract), this supports MULTIPLE and OVERLAPPING highlights that stay visible while panning and zooming. Use when the user asks to \"highlight\", \"mark\", or \"box\" a region so it stands out. Each call adds one more highlight; use clear_highlights to remove them all or remove_highlight to remove one.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"label":{"type":"string"},"color":{"type":"string"},"clientId":{"type":"string","default":"default"}},"anyOf":[{"required":["start"]},{"required":["end"]}],"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"select_sequence_region","description":"Select a specific sequence region by genomic coordinates (start-end position), highlighting it in the genome view. This sets the region as the active sequence selection, useful for subsequent operations like copy, extract, or analysis.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"clientId":{"type":"string","default":"default"}},"required":["start","end"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"switch_to_tab","description":"Switch to a specific tab in the browser interface by tab ID, name, or index position","parameters":{"anyOf":[{"required":["tab_id"]},{"required":["tab_name"]},{"required":["tab_index"]}],"properties":{"tab_id":{"type":"string"},"tab_name":{"type":"string"},"tab_index":{"type":"integer","minimum":0},"clientId":{"type":"string"}},"type":"object","required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-ad6f951e0229003bc572","scenario_family_id":"decision:no_tool:syntax","supervised_target":"no_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":"Go to the gene."},{"role":"assistant","content":"Which gene name or locus tag should I navigate to?"}],"tools":[{"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":"delete_annotation","description":"Delete a genome annotation by identifier (locus_tag, gene name, or protein_id) with change tracking. Use this when the user explicitly asks to delete or remove a specific annotation. NOT the same as delete_sequence which removes sequence data.","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"chromosome":{"type":"string"},"agent":{"type":"string","default":"mcp-agent"},"clientId":{"type":"string","default":"default"}},"required":["identifier"],"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":"get_coding_sequence","description":"Extract the coding DNA sequence (CDS) for a specific gene by name or locus tag. Returns the actual coding nucleotide sequence without introns.","parameters":{"type":"object","properties":{"gene_name":{"type":"string"},"include_upstream":{"type":"number","default":0,"minimum":0},"include_downstream":{"type":"number","default":0,"minimum":0},"format":{"type":"string","enum":["raw","fasta","genbank"],"default":"raw"},"clientId":{"type":"string","default":"default"}},"required":["gene_name"],"additionalProperties":false},"strict":false}},{"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}}],"metadata":{"source_example_id":"cx-fda0fc2f8cf079266102","scenario_family_id":"decision:clarify:gene","supervised_target":"ask_clarification","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":"Extract the sequence from that region."},{"role":"assistant","content":"Please provide the chromosome and start/end coordinates, or select a region first."}],"tools":[{"type":"function","function":{"name":"delete_sequence","description":"Queue deletion of a sequence region 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}},"required":["chromosome","start","end"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"select_sequence_region","description":"Select a specific sequence region by genomic coordinates (start-end position), highlighting it in the genome view. This sets the region as the active sequence selection, useful for subsequent operations like copy, extract, or analysis.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number"},"end":{"type":"number"},"clientId":{"type":"string","default":"default"}},"required":["start","end"],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"highlight_region","description":"Add a persistent visual highlight (a colored box) over a genomic region, spanning the full height of the ruler and tracks. Unlike select_sequence_region (which sets a single active selection for copy/extract), this supports MULTIPLE and OVERLAPPING highlights that stay visible while panning and zooming. Use when the user asks to \"highlight\", \"mark\", or \"box\" a region so it stands out. Each call adds one more highlight; use clear_highlights to remove them all or remove_highlight to remove one.","parameters":{"type":"object","properties":{"chromosome":{"type":"string"},"start":{"type":"number","minimum":1},"end":{"type":"number","minimum":1},"label":{"type":"string"},"color":{"type":"string"},"clientId":{"type":"string","default":"default"}},"anyOf":[{"required":["start"]},{"required":["end"]}],"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":"calc_region_gc","description":"Calculate GC content for a chromosome coordinate range from the currently loaded genome. 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_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-ecfa56b25b652ec407b7","scenario_family_id":"decision:clarify:coordinates","supervised_target":"ask_clarification","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":"Infer a maximum-likelihood phylogenetic tree with IQ-TREE."},{"role":"assistant","content":"No IQ-TREE execution tool is available in the current CodeXomics tool catalog."}],"tools":[{"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":"jump_to_gene","description":"Jump directly to a gene location by gene name or locus tag. This is the PRIMARY tool for navigating to genes when you know the gene name.","parameters":{"type":"object","properties":{"geneName":{"type":"string"},"clientId":{"type":"string","default":"default"}},"required":["geneName"],"additionalProperties":false},"strict":false}},{"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":"delete_annotation","description":"Delete a genome annotation by identifier (locus_tag, gene name, or protein_id) with change tracking. Use this when the user explicitly asks to delete or remove a specific annotation. NOT the same as delete_sequence which removes sequence data.","parameters":{"type":"object","properties":{"identifier":{"type":"string"},"chromosome":{"type":"string"},"agent":{"type":"string","default":"mcp-agent"},"clientId":{"type":"string","default":"default"}},"required":["identifier"],"additionalProperties":false},"strict":false}},{"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}}],"metadata":{"source_example_id":"cx-2abcbfdc229647108d3c","scenario_family_id":"decision:unavailable:phylogeny","supervised_target":"unavailable_tool","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":"只解释什么是反向互补序列，不要调用工具。"},{"role":"assistant","content":"反向互补序列是先将碱基替换为互补碱基，再反转序列方向得到的序列。"}],"tools":[{"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":"get_benchmark_results","description":"Get the benchmark results history. Returns statistics from all previous benchmark runs, including success rates, test counts, durations, and the latest run details.","parameters":{"properties":{"index":{"type":"number"}},"type":"object","required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"load_annotation_file","description":"Load annotation files (GFF/BED/GTF) 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","gff","bed","gtf"]},"clientId":{"type":"string","default":"default"}},"required":[],"additionalProperties":false},"strict":false}},{"type":"function","function":{"name":"jump_to_gene","description":"Jump directly to a gene location by gene name or locus tag. This is the PRIMARY tool for navigating to genes when you know the gene name.","parameters":{"type":"object","properties":{"geneName":{"type":"string"},"clientId":{"type":"string","default":"default"}},"required":["geneName"],"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}},{"type":"function","function":{"name":"get_current_state","description":"Get the current state of the genome browser including position, visible tracks, loaded data, and session information. Use this to understand the current context before making other operations.","parameters":{"type":"object","properties":{"clientId":{"type":"string","default":"default"},"include_tracks":{"type":"boolean","default":true},"include_data_summary":{"type":"boolean","default":true}},"required":[],"additionalProperties":false},"strict":false}}],"metadata":{"source_example_id":"cx-5203541387423ff89958","scenario_family_id":"decision:no_tool:zh_concept","supervised_target":"no_call","turn_index":2}}
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