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Releases: ModelSEED/modelseed-api

v0.1.0 — Initial Release

06 Apr 16:07
@jplfaria jplfaria
v0.1.0
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REST API backend for ModelSEED metabolic modeling, replacing the legacy Perl-based ProbModelSEED JSON-RPC service with a Python FastAPI application.

Live deployment: http://poplar.cels.anl.gov:8000/docs

Features

Models (11 endpoints)

  • List, view, copy, delete, export (JSON / SBML / CobraPy)
  • Atomic model editing: add/remove/modify reactions, compounds, biomass
  • Gapfill solution management: list, integrate, unintegrate, delete
  • FBA study listing and full flux result retrieval
  • Per-reaction and summary pathway data from ModelSEEDDatabase

Jobs (6 endpoints)

  • Model reconstruction from BV-BRC genome ID
  • Gapfilling against any media condition
  • Flux balance analysis
  • Model merging
  • Job status tracking and management

Biochemistry (4 endpoints, no auth required)

  • Search and query ModelSEED compounds and reactions
  • Database statistics

Additional

  • Media formulation listing (public + user custom)
  • Full PATRIC workspace proxy (8 endpoints)
  • Legacy RAST job listing (optional MySQL)
  • Demo dashboard at /demo/ for development testing

Architecture

  • Dual storage backends: PATRIC Workspace (production) or local filesystem (development/MCP) — selected via MODELSEED_STORAGE_BACKEND
  • Job dispatch: Subprocess scripts (default) or Celery+Redis (tasks at full parity, worker not yet deployed)
  • No KBase dependency: Runs entirely against BV-BRC/PATRIC APIs with local templates

Dependencies

Requires specific forks of upstream packages:

See README for full setup instructions.

Quick Start

# Clone all repos
git clone https://github.com/ModelSEED/modelseed-api.git
git clone -b main https://github.com/cshenry/ModelSEEDpy.git
git clone https://github.com/cshenry/KBUtilLib.git
git clone https://github.com/Fxe/cobrakbase.git
git clone -b dev https://github.com/ModelSEED/ModelSEEDDatabase.git
git clone https://github.com/ModelSEED/ModelSEEDTemplates.git
git clone https://github.com/kbaseapps/cb_annotation_ontology_api.git

# Docker (recommended)
docker compose -f modelseed-api/docker-compose.yml up --build
# Open http://localhost:8000/demo/
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