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Overview

GEMs MAP is a desktop-style web application for working with genome-scale metabolic models (GEMs). It runs on your own computer: one command, gemsmap, starts a local Python server that holds the models, runs COBRApy and serves the interface to your browser.

Three workspaces

The switcher at the top left of the window moves between three workspaces. They share the same model and data.

Workspace In this documentation What you do there
COBRAGUI COBRAGUI Import, explore, edit and simulate a model; compare and export results.
Map Builder Maps Draw pathway figures, bind them to the model, map results onto them, export figures.
Templates Templates Design and review model-independent pathway templates and apply them to a model.

COBRAGUI stands for COBRA graphical user interface. It has its own logo and name because it is meant to grow into a front end for more of the COBRA ecosystem, while it ships inside GEMs MAP. In the source code it lives in src/lab/ and backend/cobragui/.

Where things run

flowchart LR
    subgraph Browser["Your browser"]
        UI["GEMs MAP interface<br/>(COBRAGUI · Map Builder · Templates)"]
        ST[("Browser storage<br/>autosave, sessions,<br/>your templates")]
    end
    subgraph Local["Your computer"]
        BE["GEMs MAP server (gemsmap)<br/>COBRApy · FastAPI · 127.0.0.1:8765"]
        CA[("Model cache<br/>MetaNetX cache<br/>BiGG tables")]
    end
    BE -->|"serves the interface"| UI
    UI <-->|"HTTP /api"| BE
    UI --- ST
    BE --- CA
    BE -.->|"only for identifier lookups"| NET["MetaNetX · KEGG · ChEBI<br/>(internet)"]
  • All flux computations run in Python, on your computer. The browser never computes fluxes. The backend listens on 127.0.0.1 only.
  • The Map Builder and the template matcher run in the browser. Drawing maps and applying templates happen there; the server's COBRApy part is needed for COBRAGUI and for online identity searches.
  • Network access is limited to identifier services. The metabolite analysis queries MetaNetX, and the template identity search queries KEGG and ChEBI (resolved through MetaNetX). Answers are cached locally. The BiGG tables are downloaded once with an explicit command and then used offline; GEMs MAP does not call the BiGG API.
  • Imported model files are copied to a local cache (%LOCALAPPDATA%\cobragui\models on Windows, ~/.cache/cobragui/models on macOS and Linux), so a restarted server reloads them. The original file is never modified.

What you need to know first

You do not need to program to use GEMs MAP, but the analyses are standard constraint-based methods and their results only make sense with their assumptions in mind. If terms such as flux, bounds or objective are new, start with the Glossary and the explanation of constraint-based analysis.

Next: Install and start GEMs MAP · then take the first look at the window.