webweb: a tool for creating, displaying, and sharing interactive network visualizations on the web

Wapman, K. Hunter; Larremore, Daniel B.

doi:10.21105/joss.01458

Cited by 9 publications

(6 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Vertex colors represent specific barcode haplotypes for the corresponding strain. Figures were generated using webweb software [66].…”

Section: Methodsmentioning

confidence: 99%

Plasmodium falciparumpopulation genetic complexity influences transcriptional profile and immune recognition of highly related genotypic clusters

Larremore

Miura

et al. 2020

Preprint

View full text Add to dashboard Cite

As transmission intensity has declined in Senegal, so has the genetic complexity of circulating Plasmodium falciparum parasites, resulting in specific genotypes emerging and persisting over years. We address whether changes in parasite genetic signatures can alter the immune repertoire to variant surface antigens, and whether such responses can influence the expansion or contraction of specific parasite genotypes in the population. We characterize parasites within genotypic clusters, defined as identical by a 24-SNP molecular barcode and a haplotype identifier for other highly polymorphic loci; we measure expression of variant surface antigens (VSA) such as PfEMP-1 by transcript expression typing and expressed var DBL1α sequencing in ex vivo and short-term adapted RNA samples; and we measure IgG responses against VSAs from short-term adapted parasites. We find that parasites within genotypic clusters are genetically identical at other highly polymorphic loci. These parasites express similar Ups var classes and largely the same dominant var DBL1α sequences ex vivo. These parasites are recognized similarly by anti-VSA antibodies after short-term adaptation to culture; however, antibody responses do not correlate with genotype frequencies over time. Both genotype-specific and multiple genotype-reactive surface IgG responses are observed in this population. Parasites with identical genomes are extremely similar in their expression and host antibody recognition of VSAs. Monitoring changes in population-level parasite genomics and transmission dynamics is critical, as fluctuations will influence the breadth of resulting host immune responses to circulating parasite genotypes. These findings suggest shared immune recognition of genetically similar parasites, which has implications for both our understanding of immunity and vaccine development strategies in malaria elimination settings.

show abstract

“…Vertex colors represent specific barcode haplotypes for the corresponding strain. Figures were generated using webweb software [66].…”

Section: Methodsmentioning

confidence: 99%

Plasmodium falciparumpopulation genetic complexity influences transcriptional profile and immune recognition of highly related genotypic clusters

Larremore

Miura

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…In this step, COVATOR built a database from CDs instead of the input genome to generate the result in the targeted format needed for further analysis. BLAST results processed using view [12] to generate HTML file (figure 5), Clustal [16] COVATOR uses Plotly [18] and webweb [19] python libraries to visualize the distribution of results. This option can be used by the command line for network map construction (figure 9) and connection map between countries in which similar protein might be found ( figure 10) and both results open in an ordinary HTML browser.…”

Section: Discussionmentioning

confidence: 99%

“…COVATOR uses Plotly [18] and webweb [19] python libraries to visualize the distribution of results. This option can be used by the command line for network map construction (figure 9) and connection map between countries in which similar protein might be found (figure 10) and both results open in an ordinary HTML browser.…”

Section: Discussionmentioning

confidence: 99%

COVATOR: A Software for Chimeric Coronavirus Identification

Habib¹

2020

Preprint

View full text Add to dashboard Cite

The term chimeric virus was not popular in the last decades. Recently, according to current sequencing efforts in discovering COVID-19 Secrets, the generated information assumed the presence of 6 Coronavirus main strains, but coronavirus diverges into hundreds of sub-strains. the bottleneck is the mutation rate. With two mutation/month, humanity will meet a new sub-strain every month. Tracking new sequenced viruses is urgently needed because of the pathogenic effect of the new substrains. here we introduce COVATOR, A user-friendly and python-based software that identifies viral chimerism. COVATOR aligns input genome and protein that has no known source, against genomes and protein with known source, then gives the user a graphical summary.

show abstract

“…They are both Javabased and run desktop clients with a GUI where users save and load networks as separate files. Webweb (Wapman & Larremore, 2019) enables interactive visualization for Python and Matlab networks using the d3.js (Bostock, Ogievetsky, & Heer, 2011) force layout. Its main purpose, however, is exploration of network features and exporting one-time visualizations as SVG or HTML.…”

Section: Discussionmentioning

confidence: 99%