The UCSC Genome Browser is an online database providing access to genomic sequence and annotations for a wide range of organisms, with a focus on humans and mice. It offers web-based tools for visualizing, comparing, and analyzing genomic data. As of September 2013, the database included genomic sequences and annotation tracks for approximately 90 organisms. New annotations include a 60-species conservation track for the mouse, updated UCSC Genes tracks for humans and mice, and new variation and ENCODE data. New software tools include a Variant Annotation Integrator, an extension to UCSC Genes for haplotype alleles, and expanded data hubs. A European mirror site was added to improve access. The database contains genome sequences from GenBank for many organisms, with varying levels of annotation. Annotation data are displayed as 'tracks' aligned to genomic sequences. The human genome is heavily annotated, including conservation, evolutionary comparisons, gene models, regulation, expression, epigenetics, variation, and disease associations. Annotation data are often obtained through external collaboration, with links to complementary annotations in other browsers. The Genome Browser serves as a repository for human and mouse genome data contributed by the ENCODE Consortium. The ENCODE data portal and newly reprocessed data sets were added. New genome assemblies were added, including 35 vertebrate assemblies, with a focus on primates and other vertebrates. The human genome assembly GRCh38/hg38 was planned for release in late 2013 or early 2014. New annotations include updated gene annotations, variation data, and comparative alignments. The 60-species conservation track was released in 2012, and a 100-species conservation track was released in 2013. ENCODE data were improved for accessibility and usability, with reprocessed data sets and new data hubs. The Genome Browser also hosts ChIP-seq data on transcription factors and plans to release an extension to display motifs within peaks. New software updates include track and assembly data hubs, which allow users to import and display their own genome annotations. The Variant Annotation Integrator (VAI) helps annotate and prioritize variant calls. The Browser also includes gene haplotype alleles for protein-coding genes, providing information on allele frequencies and predicted protein sequences. The Genome Browser has improved its web interface, including navigation menus, chromosome ideograms, and display speed. User training and mirror support were expanded, with new documentation and training materials. The software makefile system was rearchitected to allow compilation of specific tools. UDR was adopted for faster data transfers to remote mirror sites. Future plans include adding new genome assemblies, expanding annotation data display types, and extending track hubs to support new file formats. The VAI will be expanded to include more input options and output formats. The Genome Browser continues to provide a comprehensive resource for genomic data, with ongoing updates and improvements.The UCSC Genome Browser is an online database providing access to genomic sequence and annotations for a wide range of organisms, with a focus on humans and mice. It offers web-based tools for visualizing, comparing, and analyzing genomic data. As of September 2013, the database included genomic sequences and annotation tracks for approximately 90 organisms. New annotations include a 60-species conservation track for the mouse, updated UCSC Genes tracks for humans and mice, and new variation and ENCODE data. New software tools include a Variant Annotation Integrator, an extension to UCSC Genes for haplotype alleles, and expanded data hubs. A European mirror site was added to improve access. The database contains genome sequences from GenBank for many organisms, with varying levels of annotation. Annotation data are displayed as 'tracks' aligned to genomic sequences. The human genome is heavily annotated, including conservation, evolutionary comparisons, gene models, regulation, expression, epigenetics, variation, and disease associations. Annotation data are often obtained through external collaboration, with links to complementary annotations in other browsers. The Genome Browser serves as a repository for human and mouse genome data contributed by the ENCODE Consortium. The ENCODE data portal and newly reprocessed data sets were added. New genome assemblies were added, including 35 vertebrate assemblies, with a focus on primates and other vertebrates. The human genome assembly GRCh38/hg38 was planned for release in late 2013 or early 2014. New annotations include updated gene annotations, variation data, and comparative alignments. The 60-species conservation track was released in 2012, and a 100-species conservation track was released in 2013. ENCODE data were improved for accessibility and usability, with reprocessed data sets and new data hubs. The Genome Browser also hosts ChIP-seq data on transcription factors and plans to release an extension to display motifs within peaks. New software updates include track and assembly data hubs, which allow users to import and display their own genome annotations. The Variant Annotation Integrator (VAI) helps annotate and prioritize variant calls. The Browser also includes gene haplotype alleles for protein-coding genes, providing information on allele frequencies and predicted protein sequences. The Genome Browser has improved its web interface, including navigation menus, chromosome ideograms, and display speed. User training and mirror support were expanded, with new documentation and training materials. The software makefile system was rearchitected to allow compilation of specific tools. UDR was adopted for faster data transfers to remote mirror sites. Future plans include adding new genome assemblies, expanding annotation data display types, and extending track hubs to support new file formats. The VAI will be expanded to include more input options and output formats. The Genome Browser continues to provide a comprehensive resource for genomic data, with ongoing updates and improvements.