WalkRollMap.org: Crowdsourcing barriers to mobility.

Walking is a simple way to improve health through physical activity. Yet many people experience barriers to walking from a variety of physical, social, and psychological factors that impact their mobility. A challenge for managing and studying pedestrian environments is that barriers often occur at local scales (e.g., sidewalk features), yet such fine scale data on pedestrian facilities and experiences are often lacking or out of date. In response, our team developed WalkRollMap.org an online mapping tool that empowers communities by providing them with tools for crowdsourcing their own open data source. In this manuscript we highlight key functions of the tool, discuss initial approaches to community outreach, and share trends in reporting from the first nine months of operation. As of July 27, 2022, there have been 897 reports, of which 53% served to identify hazards, 34% missing amenities, and 14% incidents. The most frequently reported issues were related to sidewalks (15%), driver behavior (19%), and marked crosswalks (7%). The most common suggested amenities were sidewalks, marked crosswalks, connections (i.e., pathways between streets), and curb cuts. The most common types of incidents all included conflicts with vehicles. Data compiled through WalkRollMap.org offer unique potential for local and timely information on microscale barriers to mobility and are available for use by anyone as data are open and downloadable.

Monitoring city wide patterns of cycling safety.

Many cities are making significant financial investments in cycling infrastructure with the aim of making cycling safer for riders of all ages and abilities. Methods for evaluating cycling safety tend to summarize average change for a city or emphasize change on a single road segment. Few spatially explicit approaches are available to evaluate how patterns of safety change throughout a city due to cycling infrastructure investments or other changes. Our goal is to demonstrate a method for monitoring changes in the spatial-temporal distribution of cycling incidents across a city. Using cycling incident data provided by the Insurance Corporation of British Columbia, we first compare planar versus network constrained kernel density estimation for visualizing incident intensity across the street network of Vancouver, Canada. Second, we apply a change detection algorithm explicitly designed for detecting statistically significant change in kernel density estimates. The utility of network kernel density change detection is demonstrated through the comparison of cycling incident densities following the construction of two cycle tracks in the downtown core of Vancouver. The methods developed and demonstrated for this study provide city planners, transportation engineers and researchers a means of monitoring city-wide change in the intensity of cycling incidents following enhancements to cycling infrastructure or other significant changes to the transportation network.

STBase: one million species trees for comparative biology.

Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user's query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed trees.

The PhyLoTA Browser: processing GenBank for molecular phylogenetics research.

As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics. The first release of the Browser is computed from 2.6 million sequences representing the taxonomically enriched subset of GenBank sequences for eukaryotes (excluding most genome survey sequences, ESTs, and other high-throughput data). In addition to summarizing sequence diversity and species diversity across nodes in the NCBI taxonomy, it reports 87,000 potentially phylogenetically informative clusters of homologous sequences, which can be viewed or downloaded, along with provisional alignments and coarse phylogenetic trees. At each node in the NCBI hierarchy, the user can display a "data availability matrix" of all available sequences for entries in a subtaxa-by-clusters matrix. This matrix provides a guidepost for subsequent assembly of multigene data sets or supertrees. The database allows for comparison of results from previous GenBank releases, highlighting recent additions of either sequences or taxa to GenBank and letting investigators track progress on data availability worldwide. Although the reported alignments and trees are extremely approximate, the database reports several statistics correlated with alignment quality to help users choose from alternative data sources.