EcoSeek

Scientific Agent Environment for Ecology

EcoSeek is an open-source scientific agent environment for ecological and computational biology workflows. It combines domain-specialized language models, ecological tool pipelines, and a secure gateway to help researchers run species distribution models, analyze biodiversity data, and build knowledge graphs from their laptop or an HPC cluster.

View on GitHub AgenticSeek Fork EcoAgent Tools

Three ways to use EcoSeek

FREE

DIY / Community

Run everything locally with EcoCoder and EcoAgent. Free, reproducible, and fully open. Uses local Ollama inference and 30+ ecological tools. No API keys needed.

BYOK

Bring Your Own Key

Use your DeepSeek API key for stronger reasoning when you lack local GPU hardware. Keys are stored locally and never leave your machine. Combine with EcoAgent tools for hybrid workflows.

LAB

Lab / Managed

Connect to lab servers, workstations, and HPC clusters through AgenticPlug. Audit trails, approval gates for compute operations, and persistent sessions. Designed for multi-user research environments.

Architecture

EcoSeek client (UI / CLI / agent runtime) | v AgenticPlug gateway (auth, sessions, policy, approvals, audit) | v Compute backends EcoCoder local ---- domain-specialized ecological LLM EcoCoder cluster -- remote HPC inference via tunnel EcoAgent tools ---- 30+ ecological analysis tools DeepSeek BYOK ----- user-provided API key HPC / OpenClaw ---- lab servers and clusters

GitHub proves who the user is. AgenticPlug decides what the user can do.

Components

AgenticSeek User-facing client foundation. Provides the agent runtime, CLI, and web UI. EcoSeek adds ecological providers (EcoCoder local, EcoCoder cluster, DeepSeek BYOK) and connector discovery.
AgenticPlug Secure gateway and connector layer. Handles authentication (GitHub identity), scoped sessions, role-based authorization, approval workflows for risky operations, and audit logging.
EcoCoder Domain-adapted QLoRA fine-tune of Qwen2.5-Coder-7B-Instruct on ~80K lines of ecological computing code. Exposes an OpenAI-compatible inference endpoint. Runs on Ollama locally or on HPC clusters.
EcoAgent Ecological workflow and tool layer. 30+ tools including species queries (GBIF), literature search, diversity analysis, species distribution modeling (MaxEnt, SDM), triplet extraction, taxonomy resolution, and knowledge graph construction.

Ecological Tools

EcoAgent exposes 30+ tools via an HTTP API with risk classification and AgenticPlug approval gating:

query_species
query_papers
compute_diversity
fit_sdm
fit_maxent
extract_triplets
resolve_taxonomy
build_knowledge_graph
compute_bioclim
classify_abstract
query_gbif_parquet
evaluate_niche
predict_susceptibility
compute_effort_bias

Read-only tools run freely. Compute-intensive tools (SDM, MaxEnt, niche evaluation) carry risk metadata and can require approval through AgenticPlug before execution.

Getting Started

DIY / Community mode

Run the EcoAgent tool server locally:

pip install ecoagent[full]
python -m ecoagent.tool_server --port 8200

# Or with Docker
docker run -p 8200:8200 -e ECOAGENT_PROFILE=ci ghcr.io/alrobles/ecoagent:0.1.0

BYOK mode

Store your DeepSeek API key locally, then configure EcoSeek:

python -m sources.keystore set deepseek YOUR_KEY
# Key stored in OS keychain or ~/.config/ecoseek/keys.json
# Never committed, logged, or sent to GitHub

Lab / Managed mode

Deploy AgenticPlug as the gateway, connect to your HPC cluster:

cd agenticplug && npm start
# Configure connectors, sessions, and approval policies
# See docs/approval-workflow.md for risky operation gates

Attribution: EcoSeek is built on a fork of AgenticSeek. We gratefully acknowledge the AgenticSeek project and contributors as the foundation for this work. EcoSeek is an independent downstream adaptation focused on scientific and ecological computing. AgenticSeek is licensed under GPLv3.

Contact

github.com/alrobles · a.l.robles.fernandez@gmail.com

EcoSeek is developed at the Reuman Lab, University of Kansas.