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Visualizing Biodiversity with Voronoi Treemaps

Michael S. Horn, Matthew Tobiasz, Chia Shen
2009 2009 Sixth International Symposium on Voronoi Diagrams  
Introduced in 2005, the Voronoi treemap algorithm is an information visualization technique for displaying hierarchical data.  ...  In this paper, we present a multi-touch tabletop application called Involv that uses the Voronoi treemap algorithm to create an interactive visualization for the Encyclopedia of Life.  ...  ACKNOWLEDGMENTS We thank James Hanken from the Department of Organismic Evolutionary Biology at Harvard for his early discussions on the importance of visualizing phylogeny together with our initial taxonomy  ... 
doi:10.1109/isvd.2009.22 dblp:conf/isvd/HornTS09 fatcat:ugl4q2ntpjczdk6fe32o3cwibi

An Approach to Generate Spatial Voronoi Treemaps for Points, Lines, and Polygons

Song Tian, Ximin Cui, Yu Gong
2015 Journal of Electrical and Computer Engineering  
As a space-filling method, Voronoi Treemaps are used for showcasing hierarchies. Previously presented algorithms are limited to visualize nonspatial data.  ...  The approach of spatial Voronoi Treemaps is proposed in this paper to eliminate these problems by enabling the subdivisions for points, lines, and polygons with spatial coordinates and references.  ...  Subsequently, approaches to visualize the hierarchies with the nonrectangular regions were addressed, such as Voronoi Treemaps [11, 12] , Jigsaw Treemaps [13] , and Circular Treemaps [14] .  ... 
doi:10.1155/2015/787163 fatcat:t5w76vskqbgorn3qjkvc3li5sy

Indented Pixel Tree Browser for Exploring Huge Hierarchies [chapter]

Michael Burch, Hansjörg Schmauder, Daniel Weiskopf
2011 Lecture Notes in Computer Science  
By representing tree structures side-by-side, the viewer can easily compare them visually and detect similar patterns and also anomalies.  ...  We exploit the indented visual metaphor to map tree structures to one-dimensional zigzag curves to primarily achieve an overview representation for the entire hierarchy.  ...  [19] , cushion treemaps by van Wijk and van de Wetering [20] , or Voronoi treemaps by Balzer et al. [21] .  ... 
doi:10.1007/978-3-642-24028-7_28 fatcat:bl2hvetrdjgrjilhxeic6l6xpi

DevoWorm: data-theoretical synthesis of C. elegans development [article]

Bradly John Alicea, Richard Gordon, Thomas E. Portegys
2018 bioRxiv   pre-print
Compared with the great diversity and plasticity found across the tree of life, Caenorhabditis elegans development is a rather unique model system.  ...  C. elegans biology provides us with a highly-deterministic developmental cell lineage, and a clear linkage from zygote to cells of the adult phenotype.  ...  Voronoi treemaps and Voronoi diagrams more generally have been applied to the study of embryogenesis [18] and biodiversity [19] .  ... 
doi:10.1101/282004 fatcat:vzmkmtlhrjhlllbdyv7bha4nd4

Visualisation with treemaps and sunbursts in many-objective optimisation

David J. Walker
2018 Genetic Programming and Evolvable Machines  
trees with which to represent multi- and many-objective solutions.  ...  The presentation of the complex data arising in many-objective evolutionary algorithms remains a challenge, and this work examines the use of treemaps and sunbursts for visualising such data.  ...  organisms [2] and biodiversity [22] .  ... 
doi:10.1007/s10710-018-9329-0 pmid:30956541 pmcid:PMC6417388 fatcat:7ophklnyuzht7l4ts7mycklgoy

Soil and leaf litter metaproteomics—a brief guideline from sampling to understanding

Katharina M. Keiblinger, Stephan Fuchs, Sophie Zechmeister-Boltenstern, Katharina Riedel, Gerard Muyzer
2016 FEMS Microbiology Ecology  
Voronoi Treemaps. Voronoi treemaps can visualize highly complex hierarchically organized data in a space optimized manner.  ...  Voronoi treemaps have proven to be an excellent tool to visualize hierarchical data structures in a space optimized manner (Fig. 3) .  ... 
doi:10.1093/femsec/fiw180 pmid:27549116 pmcid:PMC5026301 fatcat:inxu4czxtzcbvjw7v43egtstze

In Silico Mining of Terpenes from Red-Sea Invertebrates for SARS-CoV-2 Main Protease (Mpro) Inhibitors

Mahmoud A. A. Ibrahim, Alaa H. M. Abdelrahman, Tarik A. Mohamed, Mohamed A. M. Atia, Montaser A. M. Al-Hammady, Khlood A. A. Abdeljawaad, Eman M. Elkady, Mahmoud F. Moustafa, Faris Alrumaihi, Khaled S. Allemailem, Hesham R. El-Seedi, Paul W. Paré (+2 others)
2021 Molecules  
Two hundred and twenty-seven terpene natural products isolated from the biodiverse Red-Sea ecosystem were screened for inhibitor activity against the SARS-CoV-2 main protease (Mpro) using molecular docking  ...  On the basis of in silico analyses, six terpenes demonstrated high potency as Mpro inhibitors with ΔGbinding ≤ −40.0 kcal/mol.  ...  A Voronoi treemap of erylosides B (226) top targeted pathway affected by the top 20 gene targets in response to erylosides B (226) in terms of SARS-CoV-2 infection was constructed Figure 9 . 9 The Voronoi  ... 
doi:10.3390/molecules26072082 pmid:33916461 pmcid:PMC8038614 fatcat:y337px6s3ndzni5pfweptyqzk4

Mangroves are an overlooked hotspot of insect diversity despite low plant diversity

Darren Yeo, Amrita Srivathsan, Jayanthi Puniamoorthy, Foo Maosheng, Patrick Grootaert, Lena Chan, Benoit Guénard, Claas Damken, Rodzay A. Wahab, Ang Yuchen, Rudolf Meier
2021 BMC Biology  
We here show how such knowledge gaps can be closed quickly with new cost-effective NGS barcoding techniques.  ...  Conclusions The discovery of such a sizeable and distinct insect fauna in a globally threatened habitat underlines how little is known about global insect biodiversity.  ...  Special thanks go to the team from the National Biodiversity Centre of NParks for their assistance in fieldwork (Permits: NP/RP12-022-4, NP/RP12-022-5, NP/RP12-022-6).  ... 
doi:10.1186/s12915-021-01088-z pmid:34521395 pmcid:PMC8442405 fatcat:zlxjc2qxdvehtaggauoxnsomzm

G-nome surfer

Orit Shaer, Guy Kol, Megan Strait, Chloe Fan, Catherine Grevet, Sarah Elfenbein
2010 Proceedings of the 28th international conference on Human factors in computing systems - CHI '10  
A first-use study with 16 participants found that G-nome Surfer enables users to gain biological insights that are based on multiple forms of evidence with minimal overhead.  ...  G-nome Surfer was developed in close collaboration with domain scientists and is aimed at lowering the threshold for using bioinformatics tools.  ...  Finally, Involv [9] is a tabletop application that uses the Voronoi treemap algorithm to create an interactive visualization for the Encyclopedia of Life.  ... 
doi:10.1145/1753326.1753539 dblp:conf/chi/ShaerKSFGE10 fatcat:sapkzxsrurecpejzg7pll4dg7y

Biofilm and Pathogenesis-Related Proteins in the Foodborne P. fluorescens ITEM 17298 With Distinctive Phenotypes During Cold Storage

Laura Quintieri, Francesca Fanelli, Daniela Zühlke, Leonardo Caputo, Antonio Francesco Logrieco, Dirk Albrecht, Katharina Riedel
2020 Frontiers in Microbiology  
In order to provide a new insight into phenotypic biodiversity of Pseudomonas spoilers isolated from cold stored cheese, in this work 19 Pseudomonas spp. were investigated for biofilm, pigments, exopolysaccharide  ...  In food chain, Pseudomonas spp. cause spoilage by reducing shelf life of fresh products, especially during cold storage, with a high economic burden for industries.  ...  FIGURE 1 | 1 Voronoi treemap visualization of P. fluorescens ITEM 17298 protein patterns after treatment with 0.75 mg/mL of HLF in M63 at 15 • C for 72 h.  ... 
doi:10.3389/fmicb.2020.00991 pmid:32670211 pmcid:PMC7326052 fatcat:icwwh2ex2bgkzlc5jgr4gq7724

Ecology of the Genus Burkholderia in the Soil

Nejc Stopnisek
2014
We are thankful to Stefanie Heller for help with microscopic observations.  ...  Acknowledgements We are grateful to Sandra Maass and Andreas Otto for helping with protein identification by mass spectrometry.  ...  Voronoi treemaps visualizing changes in the proteome composition of B. glathei LMG14190 during fungal co-cultivation.  ... 
doi:10.5167/uzh-101419 fatcat:x4o3aekjqbgwnij4ti7rda52wm

Comparative metabolic modeling and analysis of human pathogens

Alyaa M. Abdel-Haleem
2019
Here, constraint-based modeling (CBM) was deployed to integrate disparate data types with genome-scale metabolic models (GEMs) to advance our understanding of the pathogenesis of infectious agents with  ...  Further, comparative analysis of the essentiality of metabolic genes for V. cholerae, the causative agent of cholera, growth and survival in single and co-infections with other enteric pathogens led to  ...  A quantitative assessment of flux magnitude as well as co-set size across the different stages are visualized as Voronoi plots (Figure 2.4a) .  ... 
doi:10.25781/kaust-9g8os fatcat:hh5sm4uiq5c7nnyz7uhnkczhg4