Index

_

__init__() (BRAD.agent.Agent method) (BRAD.agent.AgentFactory method)

_call() (in module BRAD.bradllm) _llm_type() (in module BRAD.bradllm)

A

add_output_file_path_to_string() (in module BRAD.utils) add_sentence() (in module BRAD.router) adj_matrix_builder() (in module BRAD.rag) Agent (class in BRAD.agent) AgentFactory (class in BRAD.agent)

annotations() (in module BRAD.gene_ontology) arxiv() (in module BRAD.scraper) arxiv_scrape() (in module BRAD.scraper) arxiv_search() (in module BRAD.scraper) arxivStageOne() (in module BRAD.scraper) arxivStageTwo() (in module BRAD.scraper)

B

best_match() (in module BRAD.rag) biorxiv() (in module BRAD.scraper) biorxiv_real_search() (in module BRAD.scraper) bot (in module BRAD.bradllm) BRAD.agent module BRAD.bradllm module BRAD.chat module BRAD.coder module BRAD.endpoints module BRAD.enrichr module BRAD.gene_ontology module BRAD.geneDatabaseCaller module

BRAD.llms module BRAD.log module BRAD.planner module BRAD.promptTemplates module BRAD.pythonCaller module BRAD.rag module BRAD.router module BRAD.scraper module BRAD.utils module buildRoutes() (in module BRAD.router)

C

callPython() (in module BRAD.pythonCaller) chartGO() (in module BRAD.gene_ontology) chat() (BRAD.agent.Agent method) (in module BRAD.chat) chatbotHelp() (BRAD.agent.Agent method) code_caller() (in module BRAD.coder) compile_latex_to_pdf() (in module BRAD.utils)

configure_RAG_contextualCompression() (in module BRAD.endpoints) configure_RAG_numberArticles() (in module BRAD.endpoints) configure_RAG_searchMechanism() (in module BRAD.endpoints) contextual_compression() (in module BRAD.rag) create_database() (in module BRAD.rag) create_db() (in module BRAD.scraper) cut() (in module BRAD.rag)

D

databases_available() (in module BRAD.endpoints) databases_create() (in module BRAD.endpoints) databases_set() (in module BRAD.endpoints)

debugLog() (in module BRAD.log) delete_dirs_without_log() (in module BRAD.utils) displayPipeline2User() (in module BRAD.planner) documentEnrichment() (in module BRAD.rag)

E

editPythonCode() (in module BRAD.pythonCaller) ensure_directory_exists() (in module BRAD.utils) errorLog() (in module BRAD.log)

execute_python_code() (in module BRAD.pythonCaller) executeCode() (in module BRAD.coder) extract_python_code() (in module BRAD.pythonCaller)

F

fetch_annotation() (in module BRAD.gene_ontology) fieldChooserTemplate() (in module BRAD.promptTemplates) fieldSelectorFromDataFrame() (in module BRAD.utils)

fileChooserTemplate() (in module BRAD.promptTemplates) find_closest_function() (in module BRAD.pythonCaller) find_integer_in_string() (in module BRAD.utils) find_py_files() (in module BRAD.pythonCaller)

G

geneDatabaseCallerTemplate() (in module BRAD.promptTemplates) geneDatabaseLLMreply() (in module BRAD.promptTemplates) geneDBRetriever() (in module BRAD.geneDatabaseCaller) geneOntology() (in module BRAD.gene_ontology) get_agent() (BRAD.agent.AgentFactory method) get_all_sources() (in module BRAD.rag) get_arguments_from_code() (in module BRAD.pythonCaller) get_default_context() (in module BRAD.promptTemplates) get_display() (BRAD.agent.Agent method) get_py_description() (in module BRAD.pythonCaller) get_wordnet_pos() (in module BRAD.rag)

getDocumentSimilarity() (in module BRAD.rag) getInputDocumentJSONs() (in module BRAD.rag) getKnownPipelines() (in module BRAD.planner) getLLMcalls() (BRAD.agent.Agent method) getModules() (BRAD.agent.Agent method) getPreviousInput() (in module BRAD.rag) getPythonEditingTemplate() (in module BRAD.promptTemplates) getRouter() (in module BRAD.router) getRouterPath() (in module BRAD.router) getTablesFormatting() (in module BRAD.geneDatabaseCaller) goSearch() (in module BRAD.gene_ontology)

H

has_unclosed_symbols() (in module BRAD.pythonCaller)

history_chat_template() (in module BRAD.promptTemplates)

I

initiate_start() (in module BRAD.endpoints) invoke() (BRAD.agent.Agent method) (in module BRAD.endpoints)

is_json_serializable() (in module BRAD.log)

L

llm (BRAD.agent.Agent property) llm_apikey() (in module BRAD.endpoints) llm_get() (in module BRAD.endpoints) llm_set() (in module BRAD.endpoints) llm_switcher() (in module BRAD.llms) llmCallLog() (in module BRAD.log) load_config() (BRAD.agent.Agent method) load_file_to_dataframe() (in module BRAD.utils)

load_literature_db() (BRAD.agent.Agent method) load_llama() (in module BRAD.llms) load_nvidia() (in module BRAD.llms) load_openai() (in module BRAD.llms) load_state() (BRAD.agent.Agent method) loadFileLog() (in module BRAD.log) loadFromFile() (in module BRAD.utils) logger() (in module BRAD.log)

M

makeNamesConsistent() (in module BRAD.utils) matlabPromptTemplate() (in module BRAD.promptTemplates) module BRAD.agent BRAD.bradllm BRAD.chat BRAD.coder BRAD.endpoints BRAD.enrichr BRAD.gene_ontology BRAD.geneDatabaseCaller BRAD.llms BRAD.log BRAD.planner BRAD.promptTemplates BRAD.pythonCaller BRAD.rag BRAD.router BRAD.scraper BRAD.utils

N

normalize_adjacency_matrix() (in module BRAD.rag)

O

outputFiles() (in module BRAD.utils)

outputFromPriorStep() (in module BRAD.utils)

P

pagerank_rerank() (in module BRAD.rag) pagerank_weighted() (in module BRAD.rag) parse_llm_response() (in module BRAD.geneDatabaseCaller) (in module BRAD.scraper) pdfDownloadPath() (in module BRAD.utils) planner() (in module BRAD.planner)

plannerEditingTemplate() (in module BRAD.promptTemplates) plannerTemplate() (in module BRAD.promptTemplates) plannerTemplateForLibrarySelection() (in module BRAD.promptTemplates) pubmed() (in module BRAD.scraper) pubmedPaper() (in module BRAD.gene_ontology) pythonPromptTemplate() (in module BRAD.promptTemplates) pythonPromptTemplateWithFiles() (in module BRAD.promptTemplates)

Q

queryDocs() (in module BRAD.rag)

queryEnrichr() (in module BRAD.enrichr)

R

read_prompts() (in module BRAD.router) read_python_docstrings() (in module BRAD.pythonCaller) reconfig() (BRAD.agent.Agent method) relative_frequency_of_char() (in module BRAD.rag) remove_repeats() (in module BRAD.rag)

reroute() (in module BRAD.router) rerouteTemplate() (in module BRAD.promptTemplates) resetMemory() (BRAD.agent.Agent method) response2processes() (in module BRAD.planner) result_set_to_string() (in module BRAD.scraper) retrieval() (in module BRAD.rag)

S

save() (in module BRAD.utils) save_config() (BRAD.agent.Agent method) save_state() (BRAD.agent.Agent method) savefig() (in module BRAD.utils) scrapeTemplate() (in module BRAD.promptTemplates) scriptSelectorTemplate() (in module BRAD.promptTemplates) search_pubmed_article() (in module BRAD.scraper) sessions_change() (in module BRAD.endpoints) sessions_create() (in module BRAD.endpoints) sessions_open() (in module BRAD.endpoints) sessions_remove() (in module BRAD.endpoints)

sessions_rename() (in module BRAD.endpoints) set_arxiv_df_display() (in module BRAD.scraper) set_global_output_path() (in module BRAD.endpoints) set_llm() (BRAD.agent.Agent method) setReportTitleTemplate() (in module BRAD.promptTemplates) strip_root_path() (in module BRAD.utils) summarize_code_execution_results() (in module BRAD.coder) summarize_code_template() (in module BRAD.promptTemplates) summarize_document_template() (in module BRAD.promptTemplates) summarizeAnalysisPipelineTemplate() (in module BRAD.promptTemplates) summarizeDatabaseCallerTemplate() (in module BRAD.promptTemplates) summarizeRAGTemplate() (in module BRAD.promptTemplates)

T

textGO() (in module BRAD.gene_ontology)

to_langchain() (BRAD.agent.Agent method)

U

updateDatabase() (in module BRAD.scraper)

updateMemory() (BRAD.agent.Agent method) userOutput() (in module BRAD.log)

V

validate_database_name() (in module BRAD.endpoints)

W

webScraping() (in module BRAD.scraper) webScrapingStageOne() (in module BRAD.scraper)

webScrapingStageTwo() (in module BRAD.scraper) word_similarity() (in module BRAD.utils)