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Learn > User Guide

User Guide

An Introduction to Network Science Using the ‘Atoms to Eve’, v1 2016.

EQNI, LLC.

v1, 2016

v2, 2020

Chapter 0

Table of Contents (Entire Featureset)

  1. Preface
  2. Overview
    1. Purpose
    2. Goals
    3. Advantages over desktop software
    4. Limitations
  3. Creating a Network
    1. Drawing in Canvas
    2. Using Interactive Spreadsheet
      1. Copy/Pasting
    3. Saving .a2e Projects
    4. Importing Excel Files
    5. Starting from Seed Networks
      1. Basic geometries
      2. Simple topologies
    6. Types of Networks
      1. Freeform
      2. Circular
      3. Hierarchical
  4. Getting Familiar with the Interface
    1. Default node name and label
    2. Naming the Network Project
      1. Changing name in top left area
      2. Info > Description
    3. Manipulating the interface
      1. Panning; Zooming; Re-setting the view
      2. Clicking on nodes (Info > Single node)
      3. Marquee Selection
    4. Fixed Positions
    5. Storing Positions
  5. Network Statistics
    1. Summary Statistics (Summary > Info Tab)
      1. # Nodes
      2. # Edges
      3. Density
      4. Isolated Nodes
      5. Self Loops
      6. Max Degree
      7. Average Degree
    2. Summary Visualizations
      1. Degree Distribution
      2. Frequency Table
      3. Density Function
        1. PDF function
        2. CDF function
  6. Node/Edge Statistics
    1. Node
      1. Navigating to the node by finding in the list
      2. Node ID, label and renaming
      3. Node Degree (# of edges)
      4. Node P(i) Preferentially
      5. Description
    2. Legend
  7. Visualization of the Network
    1. Node
      1. Sizing
        1. By Value
        2. Size Range
      2. Coloring
        1. By Value
        2. Interpolating
      3. Label
        1. By Attribute
      4. Visibility
      5. Style
        1. Drop-shadow
    2. Edge
      1. Sizing/Thickness
      2. Color
        1. Opacity
      3. Visiblity
      4. Labels
      5. Smooth/Solid
    3. Layout
      1. Physics/Arbitrary Positions
      2. Setting a background color/image
      3. Storing positions
  8. Interactively Adjusting Network
    1. Add nodes
    2. Add links
    3. Delete nodes
    4. Delete links
    5. Attaching nodes using multiple selections
    6. Attaching nodes via algorithm
      1. ERRG
      2. BAPA
  9. Managing Networks
    1. Favorites
    2. Created by Me
    3. Shared by Others
    4. Sorting by Metadata
      1. Last Edited
      2. # Nodes
      3. # Links
  10. Collaborating
    1. Permissions, shared and private networks
    2. Manage Network > Invite others to collaborate on the project
    3. Manage Network > Publish/private, get public URL
    4. Saving an image of the network
    5. Public profile for network scientist
    6. Exporting .a2e to other software for more rigorous analysis
  11. Advanced Statistics
    1. Clustering coefficient
    2. Closeness centrality
    3. P(i) Preferentially
    4. Adding custom attributes
    5. Group/Modularity
      1. Naming group
      2. Summary group statistics
      3. Coloring by group
  12. Advanced Custom Visualizations
    1. Selection-based coloring
      1. Nodes
      2. Edges
      3. Labels
    2. Adding images
    3. Spotlight view on selection, opacity of connected nodes
    4. Advanced background physics
  13. Conclusion
    1. Afterword
    2. Future Goals/Roadmap
    3. Glossary

Atoms to Eve is an interactive network science research platform created to discover, explore, and visualize the networks of complex systems. The mission of Atoms to Eve is to empower the next generation of network scientists across physical, biological and social analysis disciplines, as well as provide the public tools to understand the networks in their everyday lives.

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