Video Tutorials¶

This section provides several video tutorials exemplifying a number of different functionalities present in SAMMI.

Upload Maps¶

Upload SBML and BioPAX annotated models as well as metabolic pathways from KEGG.

Download Maps¶

Download SAMMI maps in SAMMI specific format, as well as formats compatible with other platforms and static images.

Shelving Metabolites¶

This tutorial covers different ways to shelve, or temporarily remove nodes from the map, as well as how to put them back.

Positioning Nodes and Edges¶

How to fix nodes in positions, arrange them in different shapes, and curve edges.

Adding, Removing and Editing Nodes¶

How to split, duplicate, and join nodes, and how to add new or existing nodes.

Navigating Graph¶

How to navigate between different subgraphs, search for nodes, see which reactions nodes participate in, and track metabolic pathways between different subgraphs.

Visualizing Data¶

How to plot data onto the model and change color and size scales.

Selecting Paths and Components¶

How to automatically select relevant pathways and components within your map.

Combining Subgraphs¶

How to combine and rename subgraphs.

Changing Default Settings¶

Change default look node and edge settings as well as simulation parameters to change the map appearance and automated node positioning.

Undo Map Edits¶

How to save different map states and return to different iterations of your visualization.

Annotating Text and Shapes¶

Add annotation text and rectangular shapes to your graph.

COBRA Plugins¶

Introduction to COBRA plugins. Load SAMMI models directly from within the Python and MATLAB command lines.