No. Every analysis in COBRAGUI runs through the interface. COBRApy does the work in the background, and results can be exported as JSON or CSV for your own scripts.
Is my model uploaded anywhere?
No. The backend runs on your computer (127.0.0.1) and keeps a copy of imported files in a local cache. Network access is used only for identifier lookups (MetaNetX, KEGG, ChEBI) and for the one-time download of the BiGG tables. See Overview.
Which model formats are supported?
SBML (with FBC), COBRA JSON and MATLAB .mat in COBRAGUI; COBRA JSON and SBML in the Map Builder alone. See Importing models.
Why does FBA give a different flux distribution than another tool, or than last time?
Most models have many optimal flux distributions. FBA and even pFBA return one of them, and which one can depend on the solver and its state. The optimal objective value is reproducible; individual fluxes may not be. Use FVA to see how much a flux can vary at the optimum. This happened while these pages were being prepared: see the warning in Metabolite analysis.
Why is the pFBA "objective" not the minimised total flux?
GEMs MAP reports the biological objective (for example growth) as the objective value, and the minimised Σ|flux| separately as Total flux (pFBA). See pFBA.
Can I choose the solver?
Not yet. GEMs MAP uses COBRApy's default solver in the backend environment (GLPK in a standard installation) and records it in every result. Solver selection is on the Roadmap.
Can I run flux sampling or gene knockouts?
Not yet; both are planned. Sampling results made with other tools can be imported into the Map Builder and shown as density or box plots. To explore a knockout by hand, block the gene's reactions in a duplicated model state.
My model has no Subsystems tab.
The model has no subsystem annotations. The export of iML1515 from the new BiGG site (iML1515.biggr.sbml), for example, carries none, while the classic BiGG JSON has a subsystem for every reaction. See About the examples.
The template coverage badge says 25/25. Does that mean the pathway is active?
No. Coverage says how much of the template exists in the model's structure. Whether it carries flux depends on a simulation.
Why is a template slot left open instead of matched?
Because the evidence was insufficient or contradictory, for example two equally plausible anomers. GEMs MAP prefers an open slot to a wrong one; you decide in the review dialog. See Identity and matching.
Can the same metabolite appear several times on a map?
Yes. Repeated drawings, typical for cofactors, are visual copies of one model metabolite and always show the same data. See Maps.
Where is my work saved?
COBRAGUI sessions (states, results) and the Map Builder's autosave live in the browser; structural edits and curation in the backend cache. Save projects (.gemsmap) and export models and results to keep them safely. See Saving and exporting.
Is GEMs MAP affiliated with COBRApy, BiGG, MetaNetX or KEGG?
No. It uses their software or data and cites them; it is an independent project.