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Welcome to the ToxPipe wiki! Below are a few helpful links for getting started. These links may also be accessed at the main ToxPipe Dashboard.

ToxPipe Components

Manuscript on Overleaf (current)
Manuscript on Word
ToxPipe Evaluations Documentation - Documentation for model evaluation including scores, tests ran, and methodology

ToxPipe LiteLLM - API for programmatic access to ToxPipe models
ToxPipe LibreChat - ChatGPT-like interface for conversing with ToxPipe models
ToxPipe Langflow - Tracking and debugging model behavior and expenses (will eventually be moved to https://flows.toxpipe.niehs.nih.gov/)
ToxPipe Langfuse - Utility for logging, auditing, and management of queries
ToxPipe API - API for creating and running AI agents with tool support and for performing AI-driven RAG/literature searches
ToxPipe Evaluations - Application for running and evaluating ToxPipe models and agents

GPU server (ehsdttlp30.niehs.nih.gov) - must be on NIEHS VPN to access. Hosts: Dashy, LiteLLM, LibreChat, MongoDB, ChromaDB
- MongoDB - Stores LibreChat history, Dockerized
- ChromaDB - Stores text embeddings for RAG search, Dockerized
NIEHS Posit Connect server - Hosts: ToxPipe API, ToxPipe Evaluations app, ChemBioTox API
Postgres server (ehsdtt031535.niehs.nih.gov) - Hosts: ChemBioTox, history for ToxPipe agents

ChemBioTox API - API for programmatic access to the ChemBioTox database, accessed by ToxPipe agents
ChemCrow - LangChain-based package for LLM-based chemical work, ToxPipe was based on this
ChEMBL - Database of chemical, bioactivity, and genomic data, used in ToxPipe's RAG search
FastAPI - RESTful API framework for Python
GELI - LLM tool for interpreting gene expression data generated by Sciome's BMDExpress
InterCiteR - AI tool for getting citations
Langflow - Visual tool for AI model workflow creation
Langfuse - Management interface for viewing LLM request traces, evals, metrics, and prompts
LBAT - REST API for querying BioC PubMed article data
LibreChat - OpenAI-like interface for providing open source AI model conversation access
LiteLLM - API for unified AI model access and budgeting/tracking
NTP publications - Toxicity/technical/research reports from the NTP, used in ToxPipe's RAG search
ToxPipe evaluations - Repository for ToxPipe model evaluation code