PopBio is part of our ongoing efforts to integrate genomic, phenotypic and population data for traits such as insecticide resistance genotypes (>5.000 assays) and phenotypes (>11.000 assays), genetic variation with microsatellites, chromosomal inversions and SNPs, population abundance (>22.6 million mosquitoes), pathogen infection status (>44.000 assays) and blood meal identification (>49.000 assays). How to query, browse and visualize the data? There are three options:

1. With a map that includes data tables and plots. The tutorial below has insecticide resistance (IR) as use case. In addition to IR other four map 'views' are available, sample queries for all are available bellow. More views are under development. The map displays circular markers, each one is a data point with rich metadata including publication citation, dates and etc.
2. With the site Search, tutorial below. Follow this link for a basic/introductory Search tutorial and follow this link for a tutorial of Advanced Search with PopBio as a use case
3. With the Sample Explorer. Follow this link for a tutorial.

PopBio raw data is available for download and export. Raw and processed data, including images, plots or screen shots, can be used in presentations or publications with proper citations.

Map sample queries

Samples

• PCR-based species identification
• animal baited net trap catch, genus Anopheles
• genotyping by high throughput sequencing, pyrethrum spray catch

Insecticide Resistance

Insecticide resistance assay results can be filtered by species, sample type, collection protocol, project, assay protocol and insecticide.

• Anopheles gambiae, West Africa, malathion
• pyrethroid, genus Aedes, 0 to 0.2
• WHO larvicide dose response test, temephos, collection of larvae
• WHO paper kit DT

Genotypes

Shows the distribution and proportion of insecticide resistance alleles. It can be filtered by a single locus or allele, species, sample type, collection protocol, project or assay protocol.

• Madagascar, Kdr L1014, Anopheles arabiensis
• Anopheles gambiae, Anopheles gambiae sensu lato, Anopheles gambiae x Anopheles coluzzii
• AChE1 G119, Rdl A296
• India (displaying the markers as 'Allele')

Abundance

Temporal abundance that can be filtered by species, sample type, collection protocol, project and assay protocol. We have large multiyear datasets from regular US mosquito control district surveillance. Records for >22.6 million mosquitoes collected from ~3500 locations during >100K collection events (100K occurrence records). We also have records from other countries.

• State of Iowa, genus Culex, CDC gravid trap, Lyric Bartholomay
• VBP0000213, morphological examination, RT-PCR assay
• pool, house resting-daytime catch
• Aedes albopictus

Pathogen

The pathogen status view provides vector pathogen-status testing, which can be filtered by pathogen, infection status, vector species, sample type, collection protocol, project and protocol assay.

• West Nile virus, Culex pipiens group
• Query with no keywords
• Plasmodium

Search sample queries

Start typing the query terms in the Search box, and in the Filter Results box filter by Population Biology Domain. Specific filter for each case are provided below.

• Anopheles AND kenya. Filter with sample (sub-domain) > Anopheles merus (species) > false (has abundance data). Export download.
• Culex. Filter with sample genotype (sub-domain) > Culex quinquefasciatus (species) >microsatellite (genotype class) > MCQ33 (genotype name). Export download.
• Type the wild card '*'. Filter with Population Biology > sample phenotype (sub-domain) > infection status (phenotype class). Export download.
• Type the wild card '*'. Filter with sample (sub-domain) > Aedes albopictus (species) > true (has abundance data). Export download.
• Aedes AND resistance. Filter with sample phenotype (sub-domain) > Aedes aegypti (species) > deltamethrin, permethrin, lambda-cyalothrin, cyfluthrin, cypermethrin (insecticide). Export download.
• Anopheles. Filter with sample phenotype (sub-domain) > Anopheles hinesorum, Anopheles arabiensis (species) > VBP0000155, VBP0000158 (project/experiment) > blood meal identification (phenotype class). Export download.

If you want to discuss any issues raised in this tutorial then please contact the help desk.