An algorithm for automated layout of process description maps drawn in SBGN

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dc.citation.epage7en_US
dc.citation.issueNumber1en_US
dc.citation.spage1en_US
dc.citation.volumeNumber32en_US
dc.contributor.authorGenc, B.en_US
dc.contributor.authorDogrusoz, U.en_US
dc.date.accessioned2019-01-28T07:32:58Z
dc.date.available2019-01-28T07:32:58Z
dc.date.issued2015-09-10en_US
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractMotivation: Evolving technology has increased the focus on genomics. The combination of today’s advanced techniques with decades of molecular biology research have yielded huge amounts of pathway data. A standard, named the Systems Biology Graphical Notation (SBGN), was recently introduced to allow scientists to represent biological pathways in an unambiguous, easy-tounderstand, and efficient manner. Although there are a number of automated layout algorithms for various types of biological networks, currently none specialize on process description maps as defined by SBGN. Results: We propose a new automated layout algorithm for process description maps drawn in SBGN. Our algorithm is based on a force-directed automated layout algorithm called Compound Spring Embedder (CoSE). On top of the existing force scheme, additional heuristics employing new types of forces and movement rules are defined to address SBGN-specific rules. Our algorithm is the only automatic layout algorithm that properly addresses all SBGN rules for drawing process description maps, including placement of substrates and products of process nodes on opposite sides, compact tiling of members of molecular complexes, and extensively making use of nested structures (compound nodes) to properly draw cellular locations and molecular complex structures. As demonstrated experimentally, the algorithm results in significant improvements over use of a generic layout algorithm such as CoSE in addressing SBGN rules on top of commonly accepted graph drawing criteria. Availability: An implementation of our algorithm in Java is available within ChiLay library (https://github.com/iVis-at-Bilkent/chilay).en_US
dc.identifier.doi10.1093/bioinformatics/btv516en_US
dc.identifier.issn1367-4803
dc.identifier.urihttp://hdl.handle.net/11693/48405
dc.language.isoEnglishen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttps://doi.org/10.1093/bioinformatics/btv516en_US
dc.source.titleBioinformaticsen_US
dc.titleAn algorithm for automated layout of process description maps drawn in SBGNen_US
dc.typeArticleen_US
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