The UCSC Genome Browser database: 2024 update.

The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation data on thousands of genome assemblies, ranging from human to SARS-CoV2. This year, we have introduced new data from the Human Pangenome Reference Consortium and on viral genomes including SARS-CoV2. We have added 1,200 new genomes to our GenArk genome system, increasing the overall diversity of our genomic representation. We have added support for nine new user-contributed track hubs to our public hub system. Additionally, we have released 29 new tracks on the human genome and 11 new tracks on the mouse genome. Collectively, these new features expand both the breadth and depth of the genomic knowledge that we share publicly with users worldwide.

Perceived Constraints to Pickleball Participation Among Black Older Adults.

Pickleball offers sociopsychological and physical activity benefits for older adults but lacks racial diversity. The purpose of this study was to identify constraints to pickleball participation with Black older adults (65+ years) as well as examine differences based on physical activity and sex. A Qualtrics panel included Black older adults (N = 292) who have heard of pickleball and are physically able to play but have not played. Results found Knowledge, Accessibility, Interpersonal, and Interest were the most salient constraints overall. Multivariate analysis of variance found that those who report low physical activity had significantly higher Interpersonal, Psychological, Costs, and Perceived Racism constraints. Additionally, females report significantly higher Knowledge, Psychological, and Cost constraints compared to males. The results further the theoretical application of constraints to physical activity research and provide insights into practitioner implications to grow the sport of pickleball for Black older adults.

GenArk: towards a million UCSC genome browsers.

Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI assemblies. Built on our established track hub system, this enables fast visualization of annotations. Assemblies come with gene models, repeat masks, BLAT, and in silico PCR. Users can add annotations via track hubs and custom tracks. We can bulk-import third-party resources, demonstrated with TOGA and Ensembl gene models for hundreds of assemblies.Three thousand two hundred sixty-nine GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be searched for on the Genome Browser gateway page.

GenArk: Towards a million UCSC Genome Browsers.

Interactive graphical genome browsers are essential tools for biologists working with DNA sequences. Although tens of thousands of new genome assemblies have become available over the last decade, accessibility is limited by the work involved in manually creating browsers and curating annotations. The results can push the limits of data storage infrastructure. To facilitate managing this increasing number of genome assemblies, we created the Genome Archive (GenArk) collection of UCSC Genome Browsers from assemblies hosted at NCBI(1). Built on our established assembly hub system, this collection enables fast, on-demand visualization of chromosome regions without requiring a database server. Available annotations include gene models, some mapped through whole-genome alignments, repeat masks, GC content, and others. We also modified our popular BLAT(2) aligner and in-silico PCR to support a large number of genomes using limited RAM. Users can upload additional annotations themselves via track hubs(3) and custom tracks. We can import more annotations in bulk from third-party resources, demonstrated here with TOGA(4) gene models. 2,430 GenArk assemblies are listed at https://hgdownload.soe.ucsc.edu/hubs/ and can be found by searching on the main UCSC gateway page. We will continue to add human high-quality assemblies and for other organisms, we are looking forward to receiving requests from the research community for ever more browsers and whole-genome alignments via http://genome.ucsc.edu/assemblyRequest.html.

The UCSC Genome Browser database: 2023 update.

The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen an emphasis in clinical data, with new tracks and an expanded Recommended Track Sets feature on hg38 as well as the addition of a single cell track group. SARS-CoV-2 continues to remain a focus, with regular annotation updates to the browser and continued curation of our phylogenetic sequence placing tool, hgPhyloPlace, whose tree has now reached over 12M sequences. Our GenArk resource has also grown, offering over 2500 hubs and a system for users to request any absent assemblies. We have expanded our bigBarChart display type and created new ways to visualize data via bigRmsk and dynseq display. Displaying custom annotations is now easier due to our chromAlias system which eliminates the requirement for renaming sequence names to the UCSC standard. Users involved in data generation may also be interested in our new tools and trackDb settings which facilitate the creation and display of their custom annotations.

Examination of Ecological Systems Contexts Within a Latino-Based Community Sport Youth Development Initiative.

Youth Development Programs (YDPs) can serve as effective mechanisms to alleviate social and psychological adversities while enhancing and developing resilience among youth. Recently, more YDPs have incorporated sport within Sport for Development (SFD) models to achieve these goals. Due to the growing Latino population in the US and the wide achievement gap between Latinos and other demographic populations, there is a need to explore programs that may support individual development as well as long-term change with regard to social inequality. There is also a need to better understand the ecological contexts within SFD programs and how these contexts may support underserved youth. Specifically, using an ecological systems perspective, this study seeks to explore the implementation of a sport program by a YDP in order to examine the ecological processes that may support or inhibit the efficacy of sport programs working with underserved youth. Juntos is a YDP that primarily serves Latinx youth and families by assisting youth with graduating high school and pursuing higher education opportunities. Juntos incorporates two annual soccer tournaments (i.e., Kicking it with Juntos and Copa Unidos). A qualitative case study approach was implemented in two counties in North Carolina. Interviews were conducted with tournament participants, county coordinators and planning committee members. Findings found three key themes related to three ecological levels 1. At the Microsystem level, sport was implemented to engage youth and connect to non-sport program outcomes, but divergent perceptions of goals among stakeholders potentially inhibited intentional implementation. At the Mesosystem level, sport provided a mechanism to engage in collaborative relationships and encouraged parental participation. At the Macrosystem level, sport celebrated Latino culture and attempted to address social barriers facing Latinx youth, but some aspects of culture may have created barriers to access for girls. Findings suggested that while the programs emphasized mesosystem engagement, more integration across exosystem and macrosystem levels may be needed for sustainable outcomes.

Variant interpretation: UCSC Genome Browser Recommended Track Sets.

The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The data, which are dispersed at many locations worldwide, are collected into one view on the Browser, where the graphical interface presents the data in one location. This supports the expertise of the researcher to interpret variants in the genome. Because the analysis of single nucleotide variants and copy number variants require interpretation of data at very different genomic scales, different data resources are required. We present here several Recommended Track Sets designed to facilitate the interpretation of variants in the clinic, offering quick access to datasets relevant to the appropriate scale.

The UCSC Genome Browser database: 2022 update.

The UCSC Genome Browser, https://genome.ucsc.edu, is a graphical viewer for exploring genome annotations. The website provides integrated tools for visualizing, comparing, analyzing, and sharing both publicly available and user-generated genomic datasets. Data highlights this year include a collection of easily accessible public hub assemblies on new organisms, now featuring BLAT alignment and PCR capabilities, and new and updated clinical tracks (gnomAD, DECIPHER, CADD, REVEL). We introduced a new Track Sets feature and enhanced variant displays to aid in the interpretation of clinical data. We also added a tool to rapidly place new SARS-CoV-2 genomes in a global phylogenetic tree enabling researchers to view the context of emerging mutations in our SARS-CoV-2 Genome Browser. Other new software focuses on usability features, including more informative mouseover displays and new fonts.

Objective Assessment of Physical Activity and Associated Contexts During High School Sport Practices.

Background: Organized sports provide children and adolescents with opportunities to achieve recommended amounts of moderate to vigorous physical activity (MVPA), and schools are a primary setting for sports programs. The main aims of this study were to examine participant physical activity (PA) levels during the most popular high school sports in the United States and to assess the influences of practice contextual factors on PA levels. Methods: Participant PA and its contexts were assessed during practices for the 10 most popular girls' and boys' high school sports in the United States. Data were obtained during 598 practice sessions in 12 schools in North Carolina using a validated direct observation instrument (System for Observing Fitness Instruction Time (SOFIT). A regression model was applied to understand the association between sport context and athletes' PA. Results: Overall, athletes were observed engaging in MVPA 60% of practice time. MVPA varied among sports and levels were highly influenced by practice contexts. Among girls' sports, cross country and soccer practices provided the highest proportion of MVPA and MVPA percent during boys' practice sessions was highest during cross country and track and field. Practice contexts were associated with MVPA accrual with time allocated for gameplay and fitness activities associated with the highest levels of PA. Conclusions: The results contribute to an understanding of which sports and how their practices are conducted facilitate increased PA. Findings indicate athletes accrue substantial amounts of PA during high school practices, but that it varies from sport to sport. As well, the context that characterizes sport practices is a significant determinant in how much PA occurs. Most sports that emphasized game simulation, fitness, and skill development drills had higher levels of MVPA. Given the length and frequency of practices and how the content is delivered, we can accurately predict how much PA athletes are likely to achieve during a given sport season. The findings from this study demonstrate that sport can make a useful, if not sufficient role in helping high school athletes reach recommended PA levels. PA engagement can be optimized by attending to the management of contexts surrounding the sports.

Pro-Environmental Sustainability and Political Affiliation: An Examination of USA College Sport Sustainability Efforts.

Political ideology is one of the most powerful predictors of perceptions about environmental sustainability and related behaviors. The purpose of this study was to investigate how sport fans' sustainability-specific values, perceptions, and norms related to awareness, engagement, and influence of USA collegiate sport sustainability efforts based on political affiliation, accounting for age and gender. Data were collected using an online survey distributed to season ticket holders after the 2019 college football season that featured three sponsored sustainability initiatives at each home game. Multivariate analysis of variance and chi-square difference tests found that self-identified Democrats reported significantly higher pro-environmental values and norms, but sustainability program engagement, sponsored initiatives awareness, and influence of initiatives on behavior were politically neutral. Path analysis found that ascription of responsibility was a significant predictor of sustainability-related engagement and behaviors for both Independents and Republicans. The results and discussion sections highlight how academics and practitioners can account for political affiliation when creating campaign messaging for environmental initiatives.

The UCSC Genome Browser database: 2021 update.

For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to the research community. As the field of genomics grows and more data become available, new modes of display are required to accommodate new technologies. New features released this past year include a Hi-C heatmap display, a phased family trio display for VCF files, and various track visualization improvements. Striving to keep data up-to-date, new updates to gene annotations include GENCODE Genes, NCBI RefSeq Genes, and Ensembl Genes. New data tracks added for human and mouse genomes include the ENCODE registry of candidate cis-regulatory elements, promoters from the Eukaryotic Promoter Database, and NCBI RefSeq Select and Matched Annotation from NCBI and EMBL-EBI (MANE). Within weeks of learning about the outbreak of coronavirus, UCSC released a genome browser, with detailed annotation tracks, for the SARS-CoV-2 RNA reference assembly.

UCSC Genome Browser enters 20th year.

The University of California Santa Cruz Genome Browser website (https://genome.ucsc.edu) enters its 20th year of providing high-quality genomics data visualization and genome annotations to the research community. In the past year, we have added a new option to our web BLAT tool that allows search against all genomes, a single-cell expression viewer (https://cells.ucsc.edu), a 'lollipop' plot display mode for high-density variation data, a RESTful API for data extraction and a custom-track backup feature. New datasets include Tabula Muris single-cell expression data, GeneHancer regulatory annotations, The Cancer Genome Atlas Pan-Cancer variants, Genome Reference Consortium Patch sequences, new ENCODE transcription factor binding site peaks and clusters, the Database of Genomic Variants Gold Standard Variants, Genomenon Mastermind variants and three new multi-species alignment tracks.

The UCSC Genome Browser database: 2019 update.

The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.

Psychological Connection to Pickleball: Assessing Motives and Participation in Older Adults.

The purpose of this study was to examine psychological connection to the sport of pickleball by investigating active older adults (55 years and older) in relation to behavioral involvement and motives for participation. Data were collected via an online survey of a representative sample of active pickleball players in North Carolina (N = 690). The psychological continuum model (PCM) categorized players into four distinct connection levels of Awareness, Attraction, Attachment, and Allegiance. Participants on each PCM level were analyzed based on playing length, play frequency, and motivations for participation (Competition, Diversion, Fitness, Skill Mastery, and Socialization). Results showed respondents at the highest PCM levels have played pickleball for at least 1 year and play at least 10 times per month. Although Fitness and Socialization were reported as the most important motives for the entire sample, Competition and Skill Mastery were viewed significantly higher for respondents at higher PCM levels.

The UCSC Genome Browser database: 2018 update.

The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences and an interactive navigator for gene interactions. Other upgrades from the past year include a command-line version of the Variant Annotation Integrator, support for Human Genome Variation Society variant nomenclature input and output, and a revised highlighting tool that now supports multiple simultaneous regions and colors.

The UCSC Genome Browser database: 2017 update.

Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities through a web-based, open source platform designed for the fast, scalable display of sequence alignments and annotations landscaped against a vast collection of quality reference genome assemblies. The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line utilities and more. This year's highlights include newly designed home and gateway pages; a new 'multi-region' track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species (brown kiwi, crab-eating macaque and Malayan flying lemur); eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.

UCSC Data Integrator and Variant Annotation Integrator.

UNLABELLED: Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores. AVAILABILITY AND IMPLEMENTATION: The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/ The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license. CONTACT: angie@soe.ucsc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The UCSC Genome Browser database: 2016 update.

For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the "Data Integrator", for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.

The UCSC Genome Browser database: 2015 update.

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

Navigating protected genomics data with UCSC Genome Browser in a Box.

UNLABELLED: Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. AVAILABILITY AND IMPLEMENTATION: Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/).