biome/env.sample at main · jataware/biome · GitHub

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# API Keys
OPENAI_API_KEY=
GEMINI_API_KEY=
ANTHROPIC_API_KEY=

# docker -- will be set with docker-compose if nothing is set
# BIOME_LIT_REVIEW_DIR=/jupyter/_literature_review

# local -- uncomment the below two lines if not running in docker
# BIOME_LIT_REVIEW_DIR=./_literature_review

LANGSMITH_TRACING=true
LANGSMITH_ENDPOINT="https://api.smith.langchain.com"
LANGSMITH_API_KEY=
LANGSMITH_PROJECT=


# Server Mode LLM Selection Options
LLM_PROVIDER_IMPORT_PATH=archytas.models.openai.OpenAIModel
LLM_SERVICE_MODEL=gpt-4.1
LLM_SERVICE_TOKEN=${OPENAI_API_KEY}

# LLM for PaperQA2
PAPERQA_LLM_MODEL="gpt-4.1-mini"

#
# API Keys for specific (optional) integrations
## EPA Air Quality System API credentialsa (email, key)
API_EPA_AQS_EMAIL=
API_EPA_AQS=
## FDA openFDA API credentials, which includes access to FAERS, and other data (key)
API_OPENFDA=
## USDA FoodData Central API credentials (key)
API_USDA_FDC=
## Census API credentials (key)
API_CENSUS=
## CDC Tracking Network API credentials (key)
API_CDC_TRACKING_NETWORK=
## Synapse API credentials (http bearer token), for use in nf.synapse.org and other *.synapse.org portals
API_SYNAPSE=
## Netrias API credentials (key)
NETRIAS_KEY=
## Alphagenome API key
ALPHAGENOME_KEY=
# ImmPort Username and Password
IMMPORT_USERNAME=
IMMPORT_PASSWORD=

# [OPTIONAL API KEYS] for literature review
# Entrez
ENTREZ_API_KEY=
ENTREZ_EMAIL=
SEMANTIC_SCHOLAR_API_KEY=
#
# Deployment Specific
# -- only change below this line if you have special requirements for environment!
#

# Jupyter
JUPYTER_SERVER=http://jupyter:8888
JUPYTER_TOKEN=89f73481102c46c0bc13b2998f9a4fce
PYTHONPATH=/jupyter
ENABLE_CHECKPOINTS=true
TOOL_ENABLED_ASK_USER=true
TOOL_ENABLED_RUN_CODE=true
SEND_KERNEL_STATE=false