Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

By Brian J. Raney, Timothy R. Dreszer, Galt P. Barber, Hiram Clawson, Pauline A. Fujita, Ting Wang, N. Nguyen, Benedict Paten, Ann S. Zweig, Donna Karolchik and 1 more. Bioinform., 2013

406 citations recorded by the source corpus.

Summary: Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror. Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu. Contact: donnak@soe.ucsc.edu

Subfields: Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/30ce555813a30e220c4d1a9381c2dcfe0645303a

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Citations in the corpus

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis (2018, methodology): “After finding relevant samples and filtering using quality control metrics, users can visualize sample batches on the WashU Epigenome Browser and on the UCSC Genome Browser.”
The UCSC Genome Browser database: 2017 update (2016, background): “Track hubs (44) are web-accessible directories of genomic data that can be viewed as a data portal through the UCSC Browser.”
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species (2017, background): “…make these thousands of tracks accessible in Ensembl Genomes, alignments derived from a single experiment (‘Study’ in the ENA data model) are organised in track hubs (23), a convenient format that can group sets of related positional data prior to their visualisation as tracks in a genome browser.”
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework (2017, methodology): “The predicted TFBSs are publicly available through a UCSC Genome Browser data hub (47) containing tracks for the human genome assemblies hg19 and hg38 (http://jaspar.”
The UCSC Genome Browser database: 2015 update (2014, background): “Collections of data sets can be organized with configuration and documentation as ‘track data hubs’, which can be viewed locally or shared (19).”
Ensembl Genomes 2016: more genomes, more complexity (2015, methodology): “It is likely that track hubs (39) (a data format proposed by the UCSC Genome Browser and now implemented in Ensembl) will be used as the vehicle to deliver (potentially complex) data sets into the browser on demand; programatic retrieval of specified data sets will also be of growing importance as t”
The UCSC Genome Browser database: 2018 update (2017, positive): “The Genome Browser team maintains a list of public track hubs (39) for the convenience of the community.”
The UCSC Genome Browser database: 2019 update (2018, background): “It is available under ‘My Data > Track Hubs’.”
Developmental regulation of human cortex transcription and its clinical relevance at base resolution (2014, positive): “Based on these results, we have created a custom UCSC “Track Hub” 33 called “LIBD Human DLPFC Development” which illustrates the coverage-level sequencing data within each age group, (Figure S8).”
The UCSC Genome Browser database: 2014 update (2013, background): “In 2011 we introduced track data hubs (26), a means for users to import collections of their own locally hosted genome annotations into the Genome Browser where they may be organized, conﬁgured and viewed alongside native tracks.”
LNCipedia 5: towards a reference set of human long non-coding RNAs (2018, methodology): “Finally, LNCipedia is also available as a UCSC genome browser track hub (30).”
The Genome 10K Project: A Way Forward (2015, positive): “TheG10KCOS also encourages that all new genomes should be loaded into a genome browser, such asGbrowse (132), JBrowse (133), track data hubs on theUCSCGenomeBrowser (134), NCBI, or Ensembl, for viewing and downloading.”
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework (2017, methodology): “The predicted TFBSs are publicly available through a UCSC Genome Browser data hub (47) containing tracks for the human genome assemblies hg19 and hg38 (http://jaspar.”
JASPAR 2020: update of the open-access database of transcription factor binding profiles (2019, methodology): “We updated the generation of genomic tracks that are publicly available through the UCSC Genome Browser data hub (39) for 7 organisms: human (hg19, hg38), mouse (mm10), zebrafish (danRer11), Drosophila melanogaster (dm6), Caenorhabditis elegans (ce10), Arabidopsis thaliana (araTha1) and baker’s yeas”