ºÝºÝߣshows by User: nathandunneugene / http://www.slideshare.net/images/logo.gif ºÝºÝߣshows by User: nathandunneugene / Tue, 10 Mar 2020 16:46:00 GMT ºÝºÝߣShare feed for ºÝºÝߣshows by User: nathandunneugene (Digital resources) quick and easy genome annotation editing with apollo /slideshow/digital-resources-quick-and-easy-genome-annotation-editing-with-apollo/230013332 digitalresourcesquickandeasygenomeannotationeditingwithapollo-200310164600
PAG 2020 - Part of the Digital Resources session talk.]]>
PAG 2020 - Part of the Digital Resources session talk.]]> Tue, 10 Mar 2020 16:46:00 GMT /slideshow/digital-resources-quick-and-easy-genome-annotation-editing-with-apollo/230013332 nathandunneugene@slideshare.net(nathandunneugene) (Digital resources) quick and easy genome annotation editing with apollo nathandunneugene PAG 2020 - Part of the Digital Resources session talk. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/digitalresourcesquickandeasygenomeannotationeditingwithapollo-200310164600-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> PAG 2020 - Part of the Digital Resources session talk.
(Digital resources) quick and easy genome annotation editing with apollo from Nathan Dunn
]]> 100 0 https://cdn.slidesharecdn.com/ss_thumbnails/digitalresourcesquickandeasygenomeannotationeditingwithapollo-200310164600-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Apollo provides collaborative genome annotation editing with the power of jbrowse /nathandunneugene/apollo-provides-collaborative-genome-annotation-editing-with-the-power-of-jbrowse jbrowseapolloprovidescollaborativegenomeannotationeditingwiththepowerofjbrowse-200310164535
PAG 2020 - Part of the JBrowse session talk.]]>
PAG 2020 - Part of the JBrowse session talk.]]> Tue, 10 Mar 2020 16:45:35 GMT /nathandunneugene/apollo-provides-collaborative-genome-annotation-editing-with-the-power-of-jbrowse nathandunneugene@slideshare.net(nathandunneugene) Apollo provides collaborative genome annotation editing with the power of jbrowse nathandunneugene PAG 2020 - Part of the JBrowse session talk. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/jbrowseapolloprovidescollaborativegenomeannotationeditingwiththepowerofjbrowse-200310164535-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> PAG 2020 - Part of the JBrowse session talk.
Apollo provides collaborative genome annotation editing with the power of jbrowse from Nathan Dunn
]]> 44 0 https://cdn.slidesharecdn.com/ss_thumbnails/jbrowseapolloprovidescollaborativegenomeannotationeditingwiththepowerofjbrowse-200310164535-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Genome annotation with open source software: Apollo, Jbrowse and the GO in Galaxy /slideshow/genome-annotation-with-open-source-software-apollo-jbrowse-and-the-go-in-galaxy/226806961 genomesinactiongenomeannotationwithopensourcesoftwareapollojbrowseandgoingalaxy2-200203163050
Genome annotation with open source software: Apollo, Jbrowse and the GO in Galaxy]]>
Genome annotation with open source software: Apollo, Jbrowse and the GO in Galaxy]]> Mon, 03 Feb 2020 16:30:50 GMT /slideshow/genome-annotation-with-open-source-software-apollo-jbrowse-and-the-go-in-galaxy/226806961 nathandunneugene@slideshare.net(nathandunneugene) Genome annotation with open source software: Apollo, Jbrowse and the GO in Galaxy nathandunneugene Genome annotation with open source software: Apollo, Jbrowse and the GO in Galaxy <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/genomesinactiongenomeannotationwithopensourcesoftwareapollojbrowseandgoingalaxy2-200203163050-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Genome annotation with open source software: Apollo, Jbrowse and the GO in Galaxy
Genome annotation with open source software: Apollo, Jbrowse and the GO in Galaxy from Nathan Dunn
]]> 61 0 https://cdn.slidesharecdn.com/ss_thumbnails/genomesinactiongenomeannotationwithopensourcesoftwareapollojbrowseandgoingalaxy2-200203163050-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Apollo bosc-2018 /slideshow/apollo-bosc2018/103506095 apollo-bosc-2018-180628212736
https://github.com/GMOD/Apollo http://genomearchitect.org/]]>
https://github.com/GMOD/Apollo http://genomearchitect.org/]]> Thu, 28 Jun 2018 21:27:36 GMT /slideshow/apollo-bosc2018/103506095 nathandunneugene@slideshare.net(nathandunneugene) Apollo bosc-2018 nathandunneugene https://github.com/GMOD/Apollo http://genomearchitect.org/ <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/apollo-bosc-2018-180628212736-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> https://github.com/GMOD/Apollo http://genomearchitect.org/
Apollo bosc-2018 from Nathan Dunn
]]> 232 3 https://cdn.slidesharecdn.com/ss_thumbnails/apollo-bosc-2018-180628212736-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Ontology-based services for querying and mining plant genomic and phenomic data /slideshow/mon-am2-20601dunn51515/79898600 monam220601dunn51515-170918153336
Findingphenotypeassociationsacrossmultipleplantspecies, annotation strategies, and environments has become more di cult as the amount of annotated data has continued to increase. By associating annotations with ontologies as metadata, we can provide a structured, inferrable, and standardized context in which to improve our ability to mine data by more accurately defining our own data. To this end, the Planteome project (http://planteome.org) ingests over 20 database sources, 80 taxa, and 2 million bioentities (genes, germplasm, QTL). Over 17 million bioentities are annotated to defined ontology terms in a standardized manner. With this infrastructure in place, Planteome provides a browsable resource for multiple reference ontologies for plants such as Plant Ontology (PO) describing anatomy and growth and de- velopmental stages, Plant Trait Ontology (TO) describing phenotype traits, Gene Ontology (GO) describing molecular function, biological process and cellular components, Phenotype and Attribute Trait On- tology (PATO) and the Application ontologies that are species-specific Crop Ontology (CO). The database also allows for an ontology-based, faceted, cross-species search of plant phenomic and genomic data anno- tated with the reference ontologies. Data is denormalized using the GOlr infrastructure (http://wiki.geneontology.org/index.php/GOlr), built on top of the Solr search platform, providing quick and meaningful querying capabilities. Work is currently underway to allow adopt a standardized Biolink web- services API (https://github.com/biolink/biolink-api) that, with GOlr, has already been adopted by the Monarch Initiative (https://monarchinitiative.org), an ontology-based tool for search and aggregation service focused on hu- man disease through analysis of cross-species annotations.]]>
Findingphenotypeassociationsacrossmultipleplantspecies, annotation strategies, and environments has become more di cult as the amount of annotated data has continued to increase. By associating annotations with ontologies as metadata, we can provide a structured, inferrable, and standardized context in which to improve our ability to mine data by more accurately defining our own data. To this end, the Planteome project (http://planteome.org) ingests over 20 database sources, 80 taxa, and 2 million bioentities (genes, germplasm, QTL). Over 17 million bioentities are annotated to defined ontology terms in a standardized manner. With this infrastructure in place, Planteome provides a browsable resource for multiple reference ontologies for plants such as Plant Ontology (PO) describing anatomy and growth and de- velopmental stages, Plant Trait Ontology (TO) describing phenotype traits, Gene Ontology (GO) describing molecular function, biological process and cellular components, Phenotype and Attribute Trait On- tology (PATO) and the Application ontologies that are species-specific Crop Ontology (CO). The database also allows for an ontology-based, faceted, cross-species search of plant phenomic and genomic data anno- tated with the reference ontologies. Data is denormalized using the GOlr infrastructure (http://wiki.geneontology.org/index.php/GOlr), built on top of the Solr search platform, providing quick and meaningful querying capabilities. Work is currently underway to allow adopt a standardized Biolink web- services API (https://github.com/biolink/biolink-api) that, with GOlr, has already been adopted by the Monarch Initiative (https://monarchinitiative.org), an ontology-based tool for search and aggregation service focused on hu- man disease through analysis of cross-species annotations.]]> Mon, 18 Sep 2017 15:33:35 GMT /slideshow/mon-am2-20601dunn51515/79898600 nathandunneugene@slideshare.net(nathandunneugene) Ontology-based services for querying and mining plant genomic and phenomic data nathandunneugene Findingphenotypeassociationsacrossmultipleplantspecies, annotation strategies, and environments has become more di cult as the amount of annotated data has continued to increase. By associating annotations with ontologies as metadata, we can provide a structured, inferrable, and standardized context in which to improve our ability to mine data by more accurately defining our own data. To this end, the Planteome project (http://planteome.org) ingests over 20 database sources, 80 taxa, and 2 million bioentities (genes, germplasm, QTL). Over 17 million bioentities are annotated to defined ontology terms in a standardized manner. With this infrastructure in place, Planteome provides a browsable resource for multiple reference ontologies for plants such as Plant Ontology (PO) describing anatomy and growth and de- velopmental stages, Plant Trait Ontology (TO) describing phenotype traits, Gene Ontology (GO) describing molecular function, biological process and cellular components, Phenotype and Attribute Trait On- tology (PATO) and the Application ontologies that are species-specific Crop Ontology (CO). The database also allows for an ontology-based, faceted, cross-species search of plant phenomic and genomic data anno- tated with the reference ontologies. Data is denormalized using the GOlr infrastructure (http://wiki.geneontology.org/index.php/GOlr), built on top of the Solr search platform, providing quick and meaningful querying capabilities. Work is currently underway to allow adopt a standardized Biolink web- services API (https://github.com/biolink/biolink-api) that, with GOlr, has already been adopted by the Monarch Initiative (https://monarchinitiative.org), an ontology-based tool for search and aggregation service focused on hu- man disease through analysis of cross-species annotations. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/monam220601dunn51515-170918153336-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Findingphenotypeassociationsacrossmultipleplantspecies, annotation strategies, and environments has become more di cult as the amount of annotated data has continued to increase. By associating annotations with ontologies as metadata, we can provide a structured, inferrable, and standardized context in which to improve our ability to mine data by more accurately defining our own data. To this end, the Planteome project (http://planteome.org) ingests over 20 database sources, 80 taxa, and 2 million bioentities (genes, germplasm, QTL). Over 17 million bioentities are annotated to defined ontology terms in a standardized manner. With this infrastructure in place, Planteome provides a browsable resource for multiple reference ontologies for plants such as Plant Ontology (PO) describing anatomy and growth and de- velopmental stages, Plant Trait Ontology (TO) describing phenotype traits, Gene Ontology (GO) describing molecular function, biological process and cellular components, Phenotype and Attribute Trait On- tology (PATO) and the Application ontologies that are species-specific Crop Ontology (CO). The database also allows for an ontology-based, faceted, cross-species search of plant phenomic and genomic data anno- tated with the reference ontologies. Data is denormalized using the GOlr infrastructure (http://wiki.geneontology.org/index.php/GOlr), built on top of the Solr search platform, providing quick and meaningful querying capabilities. Work is currently underway to allow adopt a standardized Biolink web- services API (https://github.com/biolink/biolink-api) that, with GOlr, has already been adopted by the Monarch Initiative (https://monarchinitiative.org), an ontology-based tool for search and aggregation service focused on hu- man disease through analysis of cross-species annotations.
Ontology-based services for querying and mining plant genomic and phenomic data from Nathan Dunn
]]> 3030 7 https://cdn.slidesharecdn.com/ss_thumbnails/monam220601dunn51515-170918153336-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Apollo — Collaborative and Scalable Manual Genome Annotation /slideshow/apollo-collaborative-and-scalable-manual-genome-annotation/67736340 nathandunnapollo-cshl-data-2016small-161027153456
Manual curation is crucial to improving the quality of the annotations of a genome. It enables curators to refine automated gene predictions using experimental data and aligned predictions from closely related organisms to more accurately represent the underlying biology. Apollo is a web-based genome annotation editor that allows curators to manually revise and edit the structure and function of predicted genomic elements. Apollo, built on top of the JBrowse genome browser, offers an ‘Annotator Panel’ that allows users to efficiently navigate the genome and its annotations. Changes are reflected in real-time to all users (similar to Google Docs) and aggregated in a revertible, visual history of structural edits. Apollo allows the export of sequences and metadata associated with each annotated genomic element in FASTA, GFF3, or Chado. A single Apollo server can be scaled to support multiple genome projects and curators. Access to genomes is controlled with fine-grained permissions (e.g. administrator, curator, public). To support integration into larger workflows, we expose the suite of web services that drives user-interface functionality. These web- services have been leveraged to integrate with Docker and the Galaxy platform. Striving to increase Apollo’s repertoire of visual exploration and exploratory analytics tools, two major undertakings are currently under development. First, the ability to visualize variant data and to annotate their predicted effects, primarily on coding regions. New technology trends and scientific paradigms point to new needs in genomic analytic tools to leverage information about variants that impact human health. Driven by a growing need to identify disease causing variants across diverse groups, we are working towards providing full functionality in genomic variant analysis and curation. Second, is the transformation of separate genomic coordinates into a single, synthetic region. This will allow the visualization of two or more genomics regions, from the length of entire chromosomes to just a few exons, within an artificially constructed genomic region. Artificially joining scaffolds facilitates annotation of genomic features split across two or more regions of a fragmented assembly (e.g, scaffolds), likely informing potential improvements to the genome assembly in the process. Additionally, this will allow hiding (visual genome folding) intra- and intergenic regions to provide a more information-rich visualization of the genome. For example, bringing exons closer together will facilitate annotating gene models with long introns, as sequences at the edge of exons separated by thousands of base-pairs will be shown adjacently. Apollo is currently being used in over one hundred genome annotation projects around the world, ranging from annotation of a single species to lineage-specific efforts supporting the annotation of dozens of species at a time.]]>
Manual curation is crucial to improving the quality of the annotations of a genome. It enables curators to refine automated gene predictions using experimental data and aligned predictions from closely related organisms to more accurately represent the underlying biology. Apollo is a web-based genome annotation editor that allows curators to manually revise and edit the structure and function of predicted genomic elements. Apollo, built on top of the JBrowse genome browser, offers an ‘Annotator Panel’ that allows users to efficiently navigate the genome and its annotations. Changes are reflected in real-time to all users (similar to Google Docs) and aggregated in a revertible, visual history of structural edits. Apollo allows the export of sequences and metadata associated with each annotated genomic element in FASTA, GFF3, or Chado. A single Apollo server can be scaled to support multiple genome projects and curators. Access to genomes is controlled with fine-grained permissions (e.g. administrator, curator, public). To support integration into larger workflows, we expose the suite of web services that drives user-interface functionality. These web- services have been leveraged to integrate with Docker and the Galaxy platform. Striving to increase Apollo’s repertoire of visual exploration and exploratory analytics tools, two major undertakings are currently under development. First, the ability to visualize variant data and to annotate their predicted effects, primarily on coding regions. New technology trends and scientific paradigms point to new needs in genomic analytic tools to leverage information about variants that impact human health. Driven by a growing need to identify disease causing variants across diverse groups, we are working towards providing full functionality in genomic variant analysis and curation. Second, is the transformation of separate genomic coordinates into a single, synthetic region. This will allow the visualization of two or more genomics regions, from the length of entire chromosomes to just a few exons, within an artificially constructed genomic region. Artificially joining scaffolds facilitates annotation of genomic features split across two or more regions of a fragmented assembly (e.g, scaffolds), likely informing potential improvements to the genome assembly in the process. Additionally, this will allow hiding (visual genome folding) intra- and intergenic regions to provide a more information-rich visualization of the genome. For example, bringing exons closer together will facilitate annotating gene models with long introns, as sequences at the edge of exons separated by thousands of base-pairs will be shown adjacently. Apollo is currently being used in over one hundred genome annotation projects around the world, ranging from annotation of a single species to lineage-specific efforts supporting the annotation of dozens of species at a time.]]> Thu, 27 Oct 2016 15:34:56 GMT /slideshow/apollo-collaborative-and-scalable-manual-genome-annotation/67736340 nathandunneugene@slideshare.net(nathandunneugene) Apollo — Collaborative and Scalable Manual Genome Annotation nathandunneugene Manual curation is crucial to improving the quality of the annotations of a genome. It enables curators to refine automated gene predictions using experimental data and aligned predictions from closely related organisms to more accurately represent the underlying biology. Apollo is a web-based genome annotation editor that allows curators to manually revise and edit the structure and function of predicted genomic elements. Apollo, built on top of the JBrowse genome browser, offers an ‘Annotator Panel’ that allows users to efficiently navigate the genome and its annotations. Changes are reflected in real-time to all users (similar to Google Docs) and aggregated in a revertible, visual history of structural edits. Apollo allows the export of sequences and metadata associated with each annotated genomic element in FASTA, GFF3, or Chado. A single Apollo server can be scaled to support multiple genome projects and curators. Access to genomes is controlled with fine-grained permissions (e.g. administrator, curator, public). To support integration into larger workflows, we expose the suite of web services that drives user-interface functionality. These web- services have been leveraged to integrate with Docker and the Galaxy platform. Striving to increase Apollo’s repertoire of visual exploration and exploratory analytics tools, two major undertakings are currently under development. First, the ability to visualize variant data and to annotate their predicted effects, primarily on coding regions. New technology trends and scientific paradigms point to new needs in genomic analytic tools to leverage information about variants that impact human health. Driven by a growing need to identify disease causing variants across diverse groups, we are working towards providing full functionality in genomic variant analysis and curation. Second, is the transformation of separate genomic coordinates into a single, synthetic region. This will allow the visualization of two or more genomics regions, from the length of entire chromosomes to just a few exons, within an artificially constructed genomic region. Artificially joining scaffolds facilitates annotation of genomic features split across two or more regions of a fragmented assembly (e.g, scaffolds), likely informing potential improvements to the genome assembly in the process. Additionally, this will allow hiding (visual genome folding) intra- and intergenic regions to provide a more information-rich visualization of the genome. For example, bringing exons closer together will facilitate annotating gene models with long introns, as sequences at the edge of exons separated by thousands of base-pairs will be shown adjacently. Apollo is currently being used in over one hundred genome annotation projects around the world, ranging from annotation of a single species to lineage-specific efforts supporting the annotation of dozens of species at a time. <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/nathandunnapollo-cshl-data-2016small-161027153456-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Manual curation is crucial to improving the quality of the annotations of a genome. It enables curators to refine automated gene predictions using experimental data and aligned predictions from closely related organisms to more accurately represent the underlying biology. Apollo is a web-based genome annotation editor that allows curators to manually revise and edit the structure and function of predicted genomic elements. Apollo, built on top of the JBrowse genome browser, offers an ‘Annotator Panel’ that allows users to efficiently navigate the genome and its annotations. Changes are reflected in real-time to all users (similar to Google Docs) and aggregated in a revertible, visual history of structural edits. Apollo allows the export of sequences and metadata associated with each annotated genomic element in FASTA, GFF3, or Chado. A single Apollo server can be scaled to support multiple genome projects and curators. Access to genomes is controlled with fine-grained permissions (e.g. administrator, curator, public). To support integration into larger workflows, we expose the suite of web services that drives user-interface functionality. These web- services have been leveraged to integrate with Docker and the Galaxy platform. Striving to increase Apollo’s repertoire of visual exploration and exploratory analytics tools, two major undertakings are currently under development. First, the ability to visualize variant data and to annotate their predicted effects, primarily on coding regions. New technology trends and scientific paradigms point to new needs in genomic analytic tools to leverage information about variants that impact human health. Driven by a growing need to identify disease causing variants across diverse groups, we are working towards providing full functionality in genomic variant analysis and curation. Second, is the transformation of separate genomic coordinates into a single, synthetic region. This will allow the visualization of two or more genomics regions, from the length of entire chromosomes to just a few exons, within an artificially constructed genomic region. Artificially joining scaffolds facilitates annotation of genomic features split across two or more regions of a fragmented assembly (e.g, scaffolds), likely informing potential improvements to the genome assembly in the process. Additionally, this will allow hiding (visual genome folding) intra- and intergenic regions to provide a more information-rich visualization of the genome. For example, bringing exons closer together will facilitate annotating gene models with long introns, as sequences at the edge of exons separated by thousands of base-pairs will be shown adjacently. Apollo is currently being used in over one hundred genome annotation projects around the world, ranging from annotation of a single species to lineage-specific efforts supporting the annotation of dozens of species at a time.
Apollo — Collaborative and Scalable Manual Genome Annotation from Nathan Dunn
]]> 464 7 https://cdn.slidesharecdn.com/ss_thumbnails/nathandunnapollo-cshl-data-2016small-161027153456-thumbnail.jpg?width=120&height=120&fit=bounds presentation Black http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 Apollo: Improving Collaborative Genome Curation /slideshow/apollo-improving-collaborative-genome-curation/57038587 nathanpag2016talk-160114060457
Apollo enables collaborative, real-time curation (akin to Google Docs) of genomic elements using both structural and experimental information. Built on top of the JBrowse framework, Apollo is composed of a web-based client, an annotation-editing engine, and a server-side data service. Users can visualize gene models, protein alignments, and expression and variant data to conduct structural and/or functional annotations. In our most recent release, version 2.0.x, the improved architecture allows users to more easily query data and build extensions, supports multiple organisms per server, and allows additional types of sequence annotations based on the Sequence Ontology. The new, removable side-dock offers detailed view of annotations, sequences, and organisms, a new reporting structure, and WebSocket support to improve real-time communication. The new Grails framework (Spring / Hibernate / Groovy) in the server more robustly scales a single server over multiple organisms while better supporting additional curators. Apollo’s entire secure REST API is exposed, allowing genomic features to be injected into Apollo from an automated curation process or organization-specific metadata to be extracted directly from Apollo using a SQL query or REST. The new version offers improved features, including the ability to bring together 2 or more scaffolds in order to annotate genes split across them, and increases the ability to customize and integrate Apollo into modern curation pipelines. During this demonstration we will introduce the new architecture, highlight advantages for users, and detail our future plans. Project Website: http://genomearchitect.org/ Source Code: https://github.com/GMOD/Apollo License: Berkeley Software Distribution (BSD) License at https://github.com/GMOD/Apollo/blob/master/LICENSE.md]]>
Apollo enables collaborative, real-time curation (akin to Google Docs) of genomic elements using both structural and experimental information. Built on top of the JBrowse framework, Apollo is composed of a web-based client, an annotation-editing engine, and a server-side data service. Users can visualize gene models, protein alignments, and expression and variant data to conduct structural and/or functional annotations. In our most recent release, version 2.0.x, the improved architecture allows users to more easily query data and build extensions, supports multiple organisms per server, and allows additional types of sequence annotations based on the Sequence Ontology. The new, removable side-dock offers detailed view of annotations, sequences, and organisms, a new reporting structure, and WebSocket support to improve real-time communication. The new Grails framework (Spring / Hibernate / Groovy) in the server more robustly scales a single server over multiple organisms while better supporting additional curators. Apollo’s entire secure REST API is exposed, allowing genomic features to be injected into Apollo from an automated curation process or organization-specific metadata to be extracted directly from Apollo using a SQL query or REST. The new version offers improved features, including the ability to bring together 2 or more scaffolds in order to annotate genes split across them, and increases the ability to customize and integrate Apollo into modern curation pipelines. During this demonstration we will introduce the new architecture, highlight advantages for users, and detail our future plans. Project Website: http://genomearchitect.org/ Source Code: https://github.com/GMOD/Apollo License: Berkeley Software Distribution (BSD) License at https://github.com/GMOD/Apollo/blob/master/LICENSE.md]]> Thu, 14 Jan 2016 06:04:56 GMT /slideshow/apollo-improving-collaborative-genome-curation/57038587 nathandunneugene@slideshare.net(nathandunneugene) Apollo: Improving Collaborative Genome Curation nathandunneugene Apollo enables collaborative, real-time curation (akin to Google Docs) of genomic elements using both structural and experimental information. Built on top of the JBrowse framework, Apollo is composed of a web-based client, an annotation-editing engine, and a server-side data service. Users can visualize gene models, protein alignments, and expression and variant data to conduct structural and/or functional annotations. In our most recent release, version 2.0.x, the improved architecture allows users to more easily query data and build extensions, supports multiple organisms per server, and allows additional types of sequence annotations based on the Sequence Ontology. The new, removable side-dock offers detailed view of annotations, sequences, and organisms, a new reporting structure, and WebSocket support to improve real-time communication. The new Grails framework (Spring / Hibernate / Groovy) in the server more robustly scales a single server over multiple organisms while better supporting additional curators. Apollo’s entire secure REST API is exposed, allowing genomic features to be injected into Apollo from an automated curation process or organization-specific metadata to be extracted directly from Apollo using a SQL query or REST. The new version offers improved features, including the ability to bring together 2 or more scaffolds in order to annotate genes split across them, and increases the ability to customize and integrate Apollo into modern curation pipelines. During this demonstration we will introduce the new architecture, highlight advantages for users, and detail our future plans. Project Website: http://genomearchitect.org/ Source Code: https://github.com/GMOD/Apollo License: Berkeley Software Distribution (BSD) License at https://github.com/GMOD/Apollo/blob/master/LICENSE.md <img style="border:1px solid #C3E6D8;float:right;" alt="" src="https://cdn.slidesharecdn.com/ss_thumbnails/nathanpag2016talk-160114060457-thumbnail.jpg?width=120&amp;height=120&amp;fit=bounds" /><br> Apollo enables collaborative, real-time curation (akin to Google Docs) of genomic elements using both structural and experimental information. Built on top of the JBrowse framework, Apollo is composed of a web-based client, an annotation-editing engine, and a server-side data service. Users can visualize gene models, protein alignments, and expression and variant data to conduct structural and/or functional annotations. In our most recent release, version 2.0.x, the improved architecture allows users to more easily query data and build extensions, supports multiple organisms per server, and allows additional types of sequence annotations based on the Sequence Ontology. The new, removable side-dock offers detailed view of annotations, sequences, and organisms, a new reporting structure, and WebSocket support to improve real-time communication. The new Grails framework (Spring / Hibernate / Groovy) in the server more robustly scales a single server over multiple organisms while better supporting additional curators. Apollo’s entire secure REST API is exposed, allowing genomic features to be injected into Apollo from an automated curation process or organization-specific metadata to be extracted directly from Apollo using a SQL query or REST. The new version offers improved features, including the ability to bring together 2 or more scaffolds in order to annotate genes split across them, and increases the ability to customize and integrate Apollo into modern curation pipelines. During this demonstration we will introduce the new architecture, highlight advantages for users, and detail our future plans. Project Website: http://genomearchitect.org/ Source Code: https://github.com/GMOD/Apollo License: Berkeley Software Distribution (BSD) License at https://github.com/GMOD/Apollo/blob/master/LICENSE.md
Apollo: Improving Collaborative Genome Curation from Nathan Dunn
]]> 413 10 https://cdn.slidesharecdn.com/ss_thumbnails/nathanpag2016talk-160114060457-thumbnail.jpg?width=120&height=120&fit=bounds presentation 000000 http://activitystrea.ms/schema/1.0/post http://activitystrea.ms/schema/1.0/posted 0 https://cdn.slidesharecdn.com/profile-photo-nathandunneugene-48x48.jpg?cb=1612832854 I enjoy delivering solutions to complex problems rapidly. I've worked primarily on science applications via web applications (Grails, Spring/Hibernate, GWT, JavaScript, RoR, etc.), iOS/MacOS programming, C++, and high-performance programming. I'm a highly versatile programmer having worked in a variety of domains including biology, psychology, automated speech recognition, automated content layout and am proficient with ontologies. berkeleybop.github.io/ https://cdn.slidesharecdn.com/ss_thumbnails/digitalresourcesquickandeasygenomeannotationeditingwithapollo-200310164600-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/digital-resources-quick-and-easy-genome-annotation-editing-with-apollo/230013332 (Digital resources) qu... https://cdn.slidesharecdn.com/ss_thumbnails/jbrowseapolloprovidescollaborativegenomeannotationeditingwiththepowerofjbrowse-200310164535-thumbnail.jpg?width=320&height=320&fit=bounds nathandunneugene/apollo-provides-collaborative-genome-annotation-editing-with-the-power-of-jbrowse Apollo provides collab... https://cdn.slidesharecdn.com/ss_thumbnails/genomesinactiongenomeannotationwithopensourcesoftwareapollojbrowseandgoingalaxy2-200203163050-thumbnail.jpg?width=320&height=320&fit=bounds slideshow/genome-annotation-with-open-source-software-apollo-jbrowse-and-the-go-in-galaxy/226806961 Genome annotation with...