BioFabric

BioFabric is an open source software application for graph drawing.[1][2][3] It presents graphs as a node-link diagram, but unlike other graph drawing tools that depict the nodes using discrete symbols, it represents nodes using horizontal lines.[4][5]

BioFabric
Developer(s)Institute for Systems Biology
Stable release
1.0.0 / 27 July 2012
Operating systemAny (Java-based)
LicenseLGPL
WebsiteBioFabric home

Rationale

Traditional node-link methods for visualizing networks deteriorate in terms of legibility when dealing with large networks, due to the proliferation of edge crossings amassing as what are disparagingly termed 'hairballs'.[6] [7] BioFabric is one of a number of alternative approaches designed explicitly to tackle this scalability issue,[6] choosing to do so by depicting nodes as lines on the horizontal axis, one per row; edges as lines on the vertical axis, one per column, terminating at the two rows associated with the endpoint nodes. As such, nodes and edges are each provided their own dimension (as opposed to solely the edges with nodes being non-dimensional points). BioFabric exploits the additional degree of freedom thus produced to place ends of incident edges in groups. This placement can potentially carry semantic information, whereas in node-link graphics the placement is often arbitrarily generated within constraints for aesthetics, such as during force-directed graph drawing, and may result in apparently informative artifacts.

Edges are drawn (vertically) in a darker shade than (horizontal) nodes, creating visual distinction. Additional edges increase the width of the graph.

Both ends of a link are represented as a square to reinforce the above effect even at small scales. Directed graphs also incorporate arrowheads.

Development

The first version, 1.0.0, was released in July 2012. Development work on BioFabric is ongoing. An open source R implementation was released in 2013, RBioFabric,[8] for use with the igraph package,[9] and subsequently described on the project weblog.[10]


Features

Input

  • Networks can be imported using SIF files as input.

Blakley et al.[11] have described how the technique used by BioFabric, which they refer to as a cartographic representation, can be used to compare the networks A and B by juxtaposing the edges in (A ∖ B), (A ∩ B), and (B ∖ A), a technique that is evocative of a Venn Diagram. Rossi and Magnani[12][13] have developed ranked sociograms, which is a BioFabric-like presentation where the node ordering is based upon a ranking metric. This approach attaches semantic meaning to the length of the edge lines, and can be used to visualize the assortativity or dissortativity of a network.

gollark: I think so...
gollark: Promises!
gollark: ~~all my code works, it's functional then, right?~~
gollark: Probably.
gollark: Waiting for 10 million increment requests to go through...

References
  1. Longabaugh, William (2012), "Combing the hairball with BioFabric: a new approach for visualization of large networks" (PDF), BMC Bioinformatics, 13: 275, doi:10.1186/1471-2105-13-275, PMC 3574047, PMID 23102059.
  2. Andrews, Christopher (2014-04-15). "Middlebury College CS465 Spring 2014, Lecture 18: Hierarchies, Graphs, and Networks (oh my) part two" (PDF). Retrieved 2016-01-07.
  3. Kirk, Andy (2013-02-19). "Best of the visualisation web... January 2013 - Visualising Data". Archived from the original on 2015-02-11. Retrieved 2015-02-10.
  4. Iliinsky, Noah (2013). "Deeper Visualization Examples" (PDF). Archived from the original (PDF) on 2015-02-11. Retrieved 2015-02-10.
  5. Jeffries, Tanya (2013-02-06). "BioFabric: Combing the Lines Out of Hairballs!". Retrieved 2015-02-10.
  6. Krzywinski, M.; Birol, I.; Jones, S. J.; Marra, M. A. (2011). "Hive plots--rational approach to visualizing networks". Briefings in Bioinformatics. 13 (5): 627–644. doi:10.1093/bib/bbr069. ISSN 1467-5463. PMID 22155641.
  7. Kosara, Robert (2012-02-01). "Graphs Beyond the Hairball". Retrieved 2015-02-10.
  8. Longabaugh, William (2013-07-01). "GitHub: wjrl/RBioFabric". Retrieved 2015-03-07.
  9. The igraph core team. "igraph R package". Retrieved 2015-03-07. Install and start using the igraph R package
  10. Longabaugh, William (2013-07-01). "Combing the hairball: July 2013". Retrieved 2015-03-07. Commentary about BioFabric (www.BioFabric.org), a new way to visualize networks.
  11. Blakley, Bob; Blakley, G R; Blakley, Sean M (3 Mar 2014). "How to Draw Graphs: Seeing and Redrafting Large Networks in Security and Biology"". arXiv:1405.5523 [cs.HC].
  12. Rossi, Luca; Magnani, Matteo (2015), "Towards effective visual analytics on multiplex and multilayer networks", Chaos, Solitons & Fractals, 72: 68–76, arXiv:1501.01666, Bibcode:2015CSF....72...68R, doi:10.1016/j.chaos.2014.12.022.
  13. Rossi, Luca; Magnani, Matteo (7 Jan 2015). "Towards effective visual analytics on multiplex and multilayer networks". arXiv:1501.01666 [cs.SI].

See also
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