ArticleBMC bioinformatics2009
A generic algorithm for layout of biological networks.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Layout of anatomical structures and blood vessels based on the foundational model of anatomy.Journal of integrative bioinformatics · 2024Article
- Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Briefings in bioinformatics · 2022Article
- Design considerations for representing systems biology information with the Systems Biology Graphical Notation.Journal of integrative bioinformatics · 2022Article
- Mental-Map Preserving Visualisation of Partitioned Networks in Vanted.Journal of integrative bioinformatics · 2019Article
- BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language.Database : the journal of biological databases and curation · 2018Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- Path2Models: large-scale generation of computational models from biochemical pathway maps.BMC systems biology · 2013Article
- Conversion of KEGG metabolic pathways to SBGN maps including automatic layout.BMC bioinformatics · 2013Article
- A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization.BioData mining · 2012Article
- Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.PloS one · 2012Article
- An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information.BMC bioinformatics · 2010Article
- Visualization of omics data for systems biology.Nature methods · 2010Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.
resultsWe present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.
conclusionThe presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.