BioFabric
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{{Infobox Software
| name = BioFabric
| logo =
| screenshot =
| caption = BioFabric home page
| developer = Institute for Systems Biology
| latest_release_version = 1.0.0
| latest_release_date = 27 July 2012
| operating_system = Any (Java-based)
| license = LGPL
| genre =
| website = {{URL|http://biofabric.org}}
}}
BioFabric is an open-source software application for graph drawing.{{citation | last = Longabaugh | first = William | doi = 10.1186/1471-2105-13-275 | journal = BMC Bioinformatics | pages = 275 | title = Combing the hairball with BioFabric: a new approach for visualization of large networks | url= | pmid = 23102059 | volume = 13 | year = 2012 | pmc=3574047 | doi-access = free }}.{{cite web | last = Andrews | first = Christopher | title = Middlebury College CS465 Spring 2014, Lecture 18: Hierarchies, Graphs, and Networks (oh my) part two | date = 2014-04-15 | url = http://www.cs.middlebury.edu/~candrews/archive/infovis_s14/lectures/cs465_lecture18.pdf | accessdate = 2016-01-07 }}{{cite web | last = Kirk | first = Andy | title = Best of the visualisation web... January 2013 - Visualising Data | date = 2013-02-19 | url = http://www.visualisingdata.com/index.php/2013/02/best-of-the-visualisation-web-january-2013/ | accessdate = 2015-02-10 | archive-url = https://web.archive.org/web/20150211085159/http://www.visualisingdata.com/index.php/2013/02/best-of-the-visualisation-web-january-2013/ | archive-date = 2015-02-11 | url-status = dead }} 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.{{cite web | last = Iliinsky | first = Noah | title = Deeper Visualization Examples | date = 2013 | url = https://www.analyticszone.com/files/form/anonymous/api/library/b1ddb392-7474-4b15-80c3-33ceb5c090e0/document/2bf5c6f2-cb25-4983-a9f1-5fa7c359d6ef/media/Creating%20Effective%20Visualiza%E2%80%8Btion%20Series%20-%20Noah%20Iliinsky%20(Talk%202%20of%205).pdf | accessdate = 2015-02-10 | url-status = dead | archiveurl = https://web.archive.org/web/20150211074559/https://www.analyticszone.com/files/form/anonymous/api/library/b1ddb392-7474-4b15-80c3-33ceb5c090e0/document/2bf5c6f2-cb25-4983-a9f1-5fa7c359d6ef/media/Creating%20Effective%20Visualiza%E2%80%8Btion%20Series%20-%20Noah%20Iliinsky%20%28Talk%202%20of%205%29.pdf | archivedate = 2015-02-11 }}{{cite web | last = Jeffries | first = Tanya | title = BioFabric: Combing the Lines Out of Hairballs! | date = 2013-02-06 | url = http://torus2torus.blogspot.com/2013/02/biofabric-combing-hairballs-through.html | accessdate = 2015-02-10 }}
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'.{{cite journal|last1=Krzywinski|first1=M.|last2=Birol|first2=I.|last3=Jones|first3=S. J.|last4=Marra|first4=M. A.|title=Hive plots--rational approach to visualizing networks|journal=Briefings in Bioinformatics|volume=13|issue=5|year=2011|pages=627–644|issn=1467-5463|doi=10.1093/bib/bbr069|pmid=22155641|doi-access=free}}{{cite web | last = Kosara | first = Robert | title = Graphs Beyond the Hairball | date = 2012-02-01 | url = https://eagereyes.org/techniques/graphs-hairball | accessdate = 2015-02-10 }} BioFabric is one of a number of alternative approaches designed explicitly to tackle this scalability issue, 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.{{Citation needed|date=May 2024}}
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,{{cite web |url=https://github.com/wjrl/RBioFabric |title=GitHub: wjrl/RBioFabric |last=Longabaugh |first=William |website=GitHub |date= 2013-07-01 |accessdate=2015-03-07 }} for use with the igraph package,{{cite web |url=http://igraph.org/r/ |title=igraph R package |author=The igraph core team |accessdate=2015-03-07 |quote=Install and start using the igraph R package }} and subsequently described on the project weblog.{{cite web |url=http://biofabric.blogspot.co.uk/2013_07_01_archive.html |title=Combing the hairball: July 2013 |last=Longabaugh |first=William |date=2013-07-01 |accessdate=2015-03-07 |quote=Commentary about BioFabric (www.BioFabric.org), a new way to visualize networks. }}
Features
Input
- Networks can be imported using SIF files as input.
Related work
Blakley et al.{{cite arXiv | title=How to Draw Graphs: Seeing and Redrafting Large Networks in Security and Biology"| date= 3 Mar 2014 | eprint=1405.5523 | last1 = Blakley | first1 = Bob | last2 = Blakley | first2 = G R | last3 = Blakley | first3 = Sean M |class=cs.HC}} 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{{citation | last1 = Rossi | first1 = Luca | last2 = Magnani | first2 = Matteo | doi = 10.1016/j.chaos.2014.12.022 | journal = Chaos, Solitons & Fractals | title =Towards effective visual analytics on multiplex and multilayer networks | volume = 72 | pages = 68–76 | year = 2015| arxiv = 1501.01666 | bibcode = 2015CSF....72...68R | s2cid = 7102328 }}.{{cite arXiv | title=Towards effective visual analytics on multiplex and multilayer networks | date= 7 Jan 2015 | eprint=1501.01666| last1 = Rossi | first1 = Luca | last2 = Magnani | first2 = Matteo | class=cs.SI}} 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.
See also
References
{{Reflist}}
External links
- [http://www.BioFabric.org/ BioFabric site]
Category:Graph drawing software