Introduction to Web Apollo for the i5K Pilot species project. WebApollo is genome annotation editor; it provides a web-based environment that allows multiple distributed users to review, edit, and share manual annotations. Let's get started!
This presentation is a thorough guide to the use of Web Apollo, with details on User Navigation, Functionality, and the thought process behind manual annotation.
During this workshop, participants:
- Learn to identify homologs of known genes of interest in your newly sequenced genome.
- Become familiar with the environment and functionality of the Web Apollo genome annotation editing tool.
- Learn how to corroborate or modify automatically annotated gene models using all available evidence in Web Apollo.
- Understand the process of curation in the context of genome annotation.
An introduction to Web Apollo for i5K Pilot Species Projects - HemipteraMonica Munoz-Torres
Introduction to Web Apollo for the i5K Pilot species project. WebApollo is genome annotation editor; it provides a web-based environment that allows multiple distributed users to review, edit, and share manual annotations. This presentation includes information specific to the projects of the Global Initiative to sequence the genomes of 5,000 species of arthropods, i5K. Let's get started!
Web Apollo: Lessons learned from community-based biocuration efforts.Monica Munoz-Torres
This presentation tries to highlight the importance and relevance of community-based curation of biological data. It describes the results of harvesting expertise from dispersed researchers assigning functions to predicted and curated peptides, as well as collaborative efforts for standardization of genes and gene product attributes across species and databases.
An introduction to Web Apollo for the Biomphalaria glabatra research community.Monica Munoz-Torres
Web Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Web Apollo. It is addressed to the members of the Biomphalaria glabatra research community.
Three's a crowd-source: Observations on Collaborative Genome AnnotationMonica Munoz-Torres
It is impossible for a single individual to fully curate a genome with precise biological fidelity. Beyond the problem of scale, curators need second opinions and insights from colleagues with domain and gene family expertise, but the communications constraints imposed in earlier applications made this inherently collaborative task difficult. Apollo, a client-side, JavaScript application allowing extensive changes to be rapidly made without server round-trips, placed us in a position to assess the difference this real-time interactivity would make to researchers’ productivity and the quality of downstream scientific analysis. To evaluate this, we trained and supported geographically dispersed scientific communities (hundreds of scientists and agreed-upon gatekeepers, in ~100 institutions around the world) to perform biologically supported manual annotations, and monitored their findings. We observed that: 1) Previously disconnected researchers were more productive when obtaining immediate feedback in dialogs with collaborators. 2) Unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore curators now face additional work correcting for more frequent assembly errors and annotating genes that are split across multiple contigs. 3) Automated annotations were improved as exemplified by discoveries made based on revised annotations, for example ~2800 manually annotated genes from three species of ants granted further insight into the evolution of sociality in this group, and ~3600 manual annotations contributed to a better understanding of immune function, reproduction, lactation and metabolism in cattle. 4) There is a notable trend shifting from whole-genome annotation to annotation of specific gene families or other gene groups linked by ecological and evolutionary significance. 5) The distributed nature of these efforts still demand strong, goal-oriented (i.e. publication of findings) leadership and coordination, as these are crucial to the success of each project. Here we detail these and other observations on collaborative genome annotation efforts.
Apollo and i5K: Collaborative Curation and Interactive Analysis of GenomesMonica Munoz-Torres
Precise elucidation of the many different biological features encoded in a genome requires a careful curation process that involves reviewing all available evidence to allow researchers to resolve discrepancies and validate automated gene models, protein alignments, and other biological elements. Genome annotation is an inherently collaborative task; researchers only rarely work in isolation, turning to colleagues for second opinions and insights from those with expertise in particular domains and gene families.
The i5k initiative seeks to sequence the genomes of 5,000 insect and related arthropod species. The selected species are known to be important to worldwide agriculture, food safety, medicine, and energy production as well as many used as models in biology, those most abundant in world ecosystems, and representatives in every branch of the insect phylogeny in an effort to better understand arthropod evolution and phylogeny. Because computational genome analysis remains an imperfect art, each of these new genomes sequenced will require visualization and curation.
Apollo is an instantaneous, collaborative, genome annotation editor, and the new JavaScript based version allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. The i5K is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process and Apollo is serving as the platform to empower this community. Here we offer details about this collaboration.
This presentation is a thorough guide to the use of Web Apollo, with details on User Navigation, Functionality, and the thought process behind manual annotation.
During this workshop, participants:
- Learn to identify homologs of known genes of interest in your newly sequenced genome.
- Become familiar with the environment and functionality of the Web Apollo genome annotation editing tool.
- Learn how to corroborate or modify automatically annotated gene models using all available evidence in Web Apollo.
- Understand the process of curation in the context of genome annotation.
An introduction to Web Apollo for i5K Pilot Species Projects - HemipteraMonica Munoz-Torres
Introduction to Web Apollo for the i5K Pilot species project. WebApollo is genome annotation editor; it provides a web-based environment that allows multiple distributed users to review, edit, and share manual annotations. This presentation includes information specific to the projects of the Global Initiative to sequence the genomes of 5,000 species of arthropods, i5K. Let's get started!
Web Apollo: Lessons learned from community-based biocuration efforts.Monica Munoz-Torres
This presentation tries to highlight the importance and relevance of community-based curation of biological data. It describes the results of harvesting expertise from dispersed researchers assigning functions to predicted and curated peptides, as well as collaborative efforts for standardization of genes and gene product attributes across species and databases.
An introduction to Web Apollo for the Biomphalaria glabatra research community.Monica Munoz-Torres
Web Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Web Apollo. It is addressed to the members of the Biomphalaria glabatra research community.
Three's a crowd-source: Observations on Collaborative Genome AnnotationMonica Munoz-Torres
It is impossible for a single individual to fully curate a genome with precise biological fidelity. Beyond the problem of scale, curators need second opinions and insights from colleagues with domain and gene family expertise, but the communications constraints imposed in earlier applications made this inherently collaborative task difficult. Apollo, a client-side, JavaScript application allowing extensive changes to be rapidly made without server round-trips, placed us in a position to assess the difference this real-time interactivity would make to researchers’ productivity and the quality of downstream scientific analysis. To evaluate this, we trained and supported geographically dispersed scientific communities (hundreds of scientists and agreed-upon gatekeepers, in ~100 institutions around the world) to perform biologically supported manual annotations, and monitored their findings. We observed that: 1) Previously disconnected researchers were more productive when obtaining immediate feedback in dialogs with collaborators. 2) Unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore curators now face additional work correcting for more frequent assembly errors and annotating genes that are split across multiple contigs. 3) Automated annotations were improved as exemplified by discoveries made based on revised annotations, for example ~2800 manually annotated genes from three species of ants granted further insight into the evolution of sociality in this group, and ~3600 manual annotations contributed to a better understanding of immune function, reproduction, lactation and metabolism in cattle. 4) There is a notable trend shifting from whole-genome annotation to annotation of specific gene families or other gene groups linked by ecological and evolutionary significance. 5) The distributed nature of these efforts still demand strong, goal-oriented (i.e. publication of findings) leadership and coordination, as these are crucial to the success of each project. Here we detail these and other observations on collaborative genome annotation efforts.
Apollo and i5K: Collaborative Curation and Interactive Analysis of GenomesMonica Munoz-Torres
Precise elucidation of the many different biological features encoded in a genome requires a careful curation process that involves reviewing all available evidence to allow researchers to resolve discrepancies and validate automated gene models, protein alignments, and other biological elements. Genome annotation is an inherently collaborative task; researchers only rarely work in isolation, turning to colleagues for second opinions and insights from those with expertise in particular domains and gene families.
The i5k initiative seeks to sequence the genomes of 5,000 insect and related arthropod species. The selected species are known to be important to worldwide agriculture, food safety, medicine, and energy production as well as many used as models in biology, those most abundant in world ecosystems, and representatives in every branch of the insect phylogeny in an effort to better understand arthropod evolution and phylogeny. Because computational genome analysis remains an imperfect art, each of these new genomes sequenced will require visualization and curation.
Apollo is an instantaneous, collaborative, genome annotation editor, and the new JavaScript based version allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. The i5K is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process and Apollo is serving as the platform to empower this community. Here we offer details about this collaboration.
Precise elucidation of the many different biological features encoded in any genome requires careful examination and review by researchers, who gather and evaluate the available evidence to corroborate and modify gene predictions and other biological elements. This curation process allows them to resolve discrepancies and validate automated gene model hypotheses and alignments. This approach is the well-established practice for well-known genomes such as human, mouse, zebrafish, Drosophila, et cetera. Desktop Apollo was originally developed to meet these needs.
The cost of sequencing a genome has been dramatically reduced by several orders of magnitude in the last decade, and the natural consequence is that more and more researchers are sequencing more and more new genomes, both within populations and across species. Because individual researchers can now readily sequence many genomes of interest, the need for a universally accessible genomic curation tool logically follows. Each new exome or genome sequenced requires visualization and curation to obtain biologically accurate genomic features sets, even for limited set of genes, because computational genome analysis remains an imperfect art. Additionally, unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore researchers now face additional work correcting for more frequent assembly errors and annotating genes split across multiple contigs.
Genome annotation is an inherently collaborative task; researchers only very rarely work in isolation, turning to colleagues for second opinions and insights from those with with expertise in particular domains and gene families. The new JavaScript based Apollo, allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. We are also focused on training the next generation of researchers by reaching out to educators to make these tools available as part of curricula via workshops and webinars, and through widely applied systems such as iPlant and DNA Subway. Here we offer details of our progress.
Presentation at Genome Informatics, Session (3) on Databases, Data Mining, Visualization, Ontologies and Curation.
Authors: Monica C Munoz-Torres, Suzanna E. Lewis, Ian Holmes, Colin Diesh, Deepak Unni, Christine Elsik.
This presentation is a thorough guide to the use of Web Apollo, with details on User Navigation, Functionality, and the thought process behind manual annotation.
During this workshop, participants:
- Learn to identify homologs of known genes of interest in a newly sequenced genome.
- Become familiar with the environment and functionality of the Web Apollo genome annotation editing tool.
- Learn how to corroborate or modify automatically annotated gene models using available evidence in Web Apollo.
- Understand the process of curation in the context of genome annotation.
Microbiome studies using 16S ribosomal DNA PCR: some cautionary tales.jennomics
Presentation at a workshop conducted by the UC Davis Bioinformatics Core Facility: Using the Linux Command Line for Analysis of High Throughput Sequence Data, September 15-19, 2014
Introduction to 16S rRNA gene multivariate analysisJosh Neufeld
Short introductory talk on multivariate statistics for 16S rRNA gene analysis given at the 2nd Soil Metagenomics conference in Braunschweig Germany, December 2013. A previous talk had discussed quality filtering, chimera detection, and clustering algorithms.
Unique Capabilities
Sponsors – Biometrics projects at CUBS
Technology Transfer Record
Current Leveraged Projects
People – Faculty, Staff, Students
Biometrics Community Leadership
Web Apollo Tutorial for the i5K copepod research community.Monica Munoz-Torres
Introduction to Web Apollo for the i5K i5K copepod research community. WebApollo is genome annotation editor; it provides a web-based environment that allows multiple distributed users to review, edit, and share manual annotations. This presentation includes information specific to the projects of the Global Initiative to sequence the genomes of 5,000 species of arthropods, i5K. Let's get started!
Introduction to Apollo - i5k Research Community – Calanoida (copepod)Monica Munoz-Torres
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5k, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project working on species of the order Calanoida (copepod).
Precise elucidation of the many different biological features encoded in any genome requires careful examination and review by researchers, who gather and evaluate the available evidence to corroborate and modify gene predictions and other biological elements. This curation process allows them to resolve discrepancies and validate automated gene model hypotheses and alignments. This approach is the well-established practice for well-known genomes such as human, mouse, zebrafish, Drosophila, et cetera. Desktop Apollo was originally developed to meet these needs.
The cost of sequencing a genome has been dramatically reduced by several orders of magnitude in the last decade, and the natural consequence is that more and more researchers are sequencing more and more new genomes, both within populations and across species. Because individual researchers can now readily sequence many genomes of interest, the need for a universally accessible genomic curation tool logically follows. Each new exome or genome sequenced requires visualization and curation to obtain biologically accurate genomic features sets, even for limited set of genes, because computational genome analysis remains an imperfect art. Additionally, unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore researchers now face additional work correcting for more frequent assembly errors and annotating genes split across multiple contigs.
Genome annotation is an inherently collaborative task; researchers only very rarely work in isolation, turning to colleagues for second opinions and insights from those with with expertise in particular domains and gene families. The new JavaScript based Apollo, allows researchers real-time interactivity, breaking down large amounts of data into manageable portions to mobilize groups of researchers with shared interests. We are also focused on training the next generation of researchers by reaching out to educators to make these tools available as part of curricula via workshops and webinars, and through widely applied systems such as iPlant and DNA Subway. Here we offer details of our progress.
Presentation at Genome Informatics, Session (3) on Databases, Data Mining, Visualization, Ontologies and Curation.
Authors: Monica C Munoz-Torres, Suzanna E. Lewis, Ian Holmes, Colin Diesh, Deepak Unni, Christine Elsik.
This presentation is a thorough guide to the use of Web Apollo, with details on User Navigation, Functionality, and the thought process behind manual annotation.
During this workshop, participants:
- Learn to identify homologs of known genes of interest in a newly sequenced genome.
- Become familiar with the environment and functionality of the Web Apollo genome annotation editing tool.
- Learn how to corroborate or modify automatically annotated gene models using available evidence in Web Apollo.
- Understand the process of curation in the context of genome annotation.
Microbiome studies using 16S ribosomal DNA PCR: some cautionary tales.jennomics
Presentation at a workshop conducted by the UC Davis Bioinformatics Core Facility: Using the Linux Command Line for Analysis of High Throughput Sequence Data, September 15-19, 2014
Introduction to 16S rRNA gene multivariate analysisJosh Neufeld
Short introductory talk on multivariate statistics for 16S rRNA gene analysis given at the 2nd Soil Metagenomics conference in Braunschweig Germany, December 2013. A previous talk had discussed quality filtering, chimera detection, and clustering algorithms.
Unique Capabilities
Sponsors – Biometrics projects at CUBS
Technology Transfer Record
Current Leveraged Projects
People – Faculty, Staff, Students
Biometrics Community Leadership
Web Apollo Tutorial for the i5K copepod research community.Monica Munoz-Torres
Introduction to Web Apollo for the i5K i5K copepod research community. WebApollo is genome annotation editor; it provides a web-based environment that allows multiple distributed users to review, edit, and share manual annotations. This presentation includes information specific to the projects of the Global Initiative to sequence the genomes of 5,000 species of arthropods, i5K. Let's get started!
Introduction to Apollo - i5k Research Community – Calanoida (copepod)Monica Munoz-Torres
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5k, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project working on species of the order Calanoida (copepod).
This presentation explains the meaning of curation and includes an introduction to the Apollo genome annotation editing tool and its curation environment.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
An introduction on gene annotation & curation for the IAGC and BIPAA research communities.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project working on species of the order Hemiptera.
Connecting life sciences data at the European Bioinformatics InstituteConnected Data World
Tony Burdett's slides from his talk at Connected Data London. Tony is a Senior Software Engineer at The European Bioinformatics Institute. He presented the complexity of data at the EMBL-EBI and what is their solution to make sense of all this data.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
A Workshop at the Stowers Institute for Medical Research.
There are many characteristics of biological data. All these characteristics make the management of biological information a particularly challenging problem. Here mainly we will focus on characteristics of biological information and multidisciplinary field called bioinformatics. Bioinformatics, now a days has emerged with graduate degree programs in several universities.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Similar to Introduction to Web Apollo for the i5K pilot species. (20)
This presentation contains details about the Apollo genome annotation editor functionality. It also includes a step-by-step example about curating a gene of interest.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
An introduction to use and functionality for the IAGC and BIPAA research communities.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
Apollo annotation guidelines for i5k projects Diaphorina citriMonica Munoz-Torres
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
This is a brief update about the genome browser JBrowse and the genome annotation editor Apollo, addressed to the members of the Alliance of Genome Resources (AGR).
Learn more about JBrowse at jbrowse.org
Learn more about Apollo at GenomeArchitect.org
Apollo Genome Annotation Editor: Latest Updates, Including New Galaxy Integra...Monica Munoz-Torres
Manual curation is crucial to improving the quality of the annotations for a genome sequencing project. During this portion of the genome sequencing workflow, curators use a variety of experimental evidence to improve on automated predictions to more accurately represent the underlying biology.
Apollo is a web-based genome annotation editor that allows curators to manually revise and edit genomic elements. It provides a reporting structure for annotated genomic elements and an ‘Annotator Panel’ that allows users to quickly browse the genome and all available annotations. Users can manually edit the structure of a genomic element as well as add metadata, including references to other databases, adding functional assignments to genes and gene products with specific lookup support for Gene Ontology (GO) terms, as well as including references to published literature in support of these annotations.
Apollo is currently used in more than one hundred genome annotation projects around the world, ranging from the annotation of a single species to lineage-specific efforts supporting annotation for dozens of organisms at a time. Apollo enables collaborative, real-time curation (akin to Google Docs); researchers may restrict access to certain annotations depending on the role of users and groups within the community, as well as share tracks of evidence data with the public. Users are able to export their manual annotations via FASTA and GFF3 files, the Chado database schema, and web services. The news hot of the presses is that Apollo is now available for integration with Galaxy via Docker! This allows users to run analyses on their genome of interest, including a step of manual curation, all from the comfort of their installation of the versatile Galaxy platform.
Scientific research is inherently a collaborative task; in our case it is a dialog among different researchers to reach a shared understanding of the underlying biology. To facilitate this dialog we have developed two web-based annotation tools: Apollo (http://genomearchitect.org/), a genomic feature editor, designed to support structural annotation of gene models, and Noctua (http://noctua.berkeleybop.org/), a biological-process model builder designed for describing the functional roles of gene products. Here we wish to outline an inventory of essential requirements that, in our experience, enable an annotation tool to meet the needs of both professional biocurators as well as other members of the research community. Here are the general requirements, beyond specific functional requirements, that any annotation tool must satisfy.
Comparative genome analysis requires high quality annotations of all genomic elements. Today’s sequencing projects face numerous challenges including lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Precise elucidation of the many different biological features encoded in any genome requires careful examination and review. We need genome annotation editing tools to modify and refine the location and structure of the genome elements that predictive algorithms cannot yet resolve automatically. During the manual annotation process, curators identify elements that best represent the underlying biology and eliminate elements that reflect systemic errors of automated analyses.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Researchers from nearly one hundred institutions worldwide are currently using Apollo for distributed curation efforts in over sixty genome projects across the tree of life: from plants to arthropods, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog.
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project on Eurytemora affinis
Introduction to Apollo: A webinar for the i5K Research CommunityMonica Munoz-Torres
Apollo is a web-based application that supports and enables collaborative genome curation in real time, allowing teams of curators to improve on existing automated gene models through an intuitive interface. Apollo allows researchers to break down large amounts of data into manageable portions to mobilize groups of researchers with shared interests.
The i5K, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community.
This presentation is an introduction to Apollo for the members of the i5K Pilot Project Species.
This is an introduction to conducting manual annotation efforts using Apollo. This webinar was offered to members of the i5K Research community on 2015-10-07.
CONSORCIO ONTOLOGÍA DE GENES: herramientas para anotación funcionalMonica Munoz-Torres
Esta presentación contiene información impartida durante el curso de Ontología de Genes en BIOS. Los temas de la charla incluyen una descripción de la estructura de la ontología, cómo se construyen los términos y porqué es necesario usar ontologías. También discutimos los análisis estadísticos de enriquecimiento y representación de términos. Los ejercicios son parte del entrenamiento del grupo de GOA en EMBL-EBI.
La presentación fue dada en Español.
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Apollo. It is addressed to the members of the American Chestnut & Chinese Chestnut Genomics research community.
Apollo: A workshop for the Manakin Research Coordination NetworkMonica Munoz-Torres
Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Apollo. It is addressed to the members of the Manakin Genomics research community.
Apollo - A webinar for the Phascolarctos cinereus research communityMonica Munoz-Torres
Web Apollo is a web-based, collaborative genomic annotation editing platform. We need annotation editing tools to modify and refine precise location and structure of the genome elements that predictive algorithms cannot yet resolve automatically.
This presentation is an introduction to how the manual annotation process takes place using Web Apollo. It is addressed to the members of the Phascolarctos cinereus research community.
Continuing with the theme of DNA repair via homologous recombination, I will discuss the following family during the PAINT call:
PTHR13451 CLASS II CROSSOVER JUNCTION ENDONUCLEASE MUS81
Talk at the 8th International Biocuration Conference. Beijing, China. April 23-26, 2015.
Obtaining meaningful results from genome analyses requires high quality annotations of all genomic elements. Today’s sequencing projects face challenges such as lower coverage, more frequent assembly errors, and the lack of closely related species with well-annotated genomes. Apollo is a web-based application that supports and enables collaborative genome curation in real time, analogous to Google Docs, allowing curators to improve on existing automated gene models through an intuitive interface. Apollo’s extensible architecture is built on top of JBrowse; its components are a web-based client, an annotation-editing engine, and a server-side data service. It allows users to visualize automated gene models, protein alignments, expression and variant data, and conduct structural and/or functional annotations.
Apollo is actively used within a variety of projects, including the initiative to sequence the genomes of 5,000 Arthropod species (i5K), and will become essential to the thousands of genomes now being sequenced and analyzed. Researchers from nearly 100 institutions worldwide are currently using Apollo on distributed curation efforts for over sixty genome projects across the tree of life; from plants to echinoderms, to fungi, to species of fish and other vertebrates including human, cattle (bovine), and dog. We are training the next generation of researchers by reaching out to educators to make these tools available as part of curricula, offering workshops and webinars to the scientific community, and through widely applied systems such as iPlant and DNA Subway. We are currently integrating Apollo into an annotation environment combining gene structural and functional annotation, transcriptomic, proteomic, and phenotypic annotation. In this presentation we will describe in detail its utility to users, introduce the architecture to developers interested in expanding on this open-source project, and offer details of our future plans.
Authors:
Monica Munoz-Torres(1), Nathan Dunn(1), Colin Diesh(2), Deepak Unni(2), Seth Carbon(1), Heiko Dietze(1), Christopher Mungall(1), Nicole Washington(1), Ian Holmes(3), Christine Elsik(2), and Suzanna E. Lewis(1)
1Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA
2Divisions of Animal and Plant Sciences, University of Missouri, Columbia, MO
3University of California Berkeley, Bioengineering, Berkeley, CA
Data Visualization And Annotation Workshop at Biocuration 2015Monica Munoz-Torres
8th International Biocuration Conference. Beijing, China. April 23-26, 2015.
Workshop 2: Data Visualization and Annotation.
Chairs: Rama Balakrishnan, Stanford University, USA and Monica Munoz-Torres, Lawrence Berkeley National Laboratory, USA
Explaining the most intricate biological processes often requires a degree of detail beyond the scope of equations and algorithms; in fact, most biological knowledge is represented visually as illustrations, graphs, and diagrams. Genomics data in particular require specialized forms of visualization to improve our understanding and increase our chances of extracting meaningful conclusions from our analyses. Furthermore, the heterogeneity and abundance of genomic data include widely varied sources, techniques for their obtention, and intrinsic experimental error. And even data obtained under similar conditions from two or more individuals are loaded with biological variation. So what is the best way to interpret the stories the data are telling us? Given the questions we wish to answer and the data we are generating, which tools would be most useful and effective? In this workshop we will explore the tools available for human interpretation of genomic data, specifically in the context of annotation.
Presentations and perspectives, panelists/presenters:
- Lorna Richardson, IGMM, University of Edinburgh, United Kingdom
- Justyna Szostak, PMI Research & Development, Switzerland
The workshop included a brief introduction to a landscape of tools available - as updated as the constantly changing field allows-, brief presentations chosen from abstract submissions and invited speakers, as well as ample discussion to capture the contributions and questions from attendants. In the end, we hope participants walked away with a toolset in hand that may benefit the progress of their own research.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
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• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
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Introduction to Web Apollo for the i5K pilot species.
1. UNIVERSITY OF
CALIFORNIA
An introduction to Web Apollo.
A webinar for the i5K Pilot Species Projects
Monica Munoz-Torres, PhD
Biocurator & Bioinformatics Analyst | @monimunozto
Genomics Division, Lawrence Berkeley National Laboratory
04 February, 2014
2. Outline
An introduction to
Web Apollo.
A webinar for the i5K
Pilot Species Projects.
1. What is Web Apollo?:
• Definition & working concept.
2. Community based curation from our
experience.
3. Lessons Learned.
4. Becoming acquainted with Web
Apollo.
Outline
2
3. What is Web Apollo?
• Web Apollo is a web-based genomic annotation editing
platform.
We need annotation editing tools to modify and refine the
precise location and structure of the genome elements that
predictive algorithms cannot yet resolve automatically.
Find more about Web Apollo at
http://GenomeArchitect.org
and
Genome Biol 14:R93. (2013).
1. What is Web Apollo?
3
4. Brief history of Apollo*:
Biologists could finally visualize computational analyses and
experimental evidence from genomic features and build
manually-curated consensus gene structures. Apollo became a
very popular, open source tool (insects, fish, mammals, birds, etc.).
a. Desktop:
one person at a time editing a
specific region, annotations
saved in local files; slowed down
collaboration.
*
b. Java Web Start:
users saved annotations directly
to a centralized database;
potential issues with stale
annotation data remained.
1. What is Web Apollo?
4
5. Web Apollo
• Browser-based; plugin for JBrowse.
• Allows for intuitive annotation creation and
editing, with gestures and pull-down menus to
create transcripts, add/delete/resize
exons, merge/split exons or transcripts, insert
comments
(CV, freeform text), etc.
• Customizable rules and
appearance.
• Edits in one client are
instantly pushed to all other
clients.
1. What is Web Apollo?
5
6. Our Working
Concept
In the context of gene manual annotation,
curation tries to find the best examples
and/or eliminate (most) errors.
To conduct manual annotation efforts:
Automated gene models
Evidence:
cDNAs, HMM domain
searches, alignments with
assemblies or genes from other
species.
Manual annotation & curation
2. In our experience.
Gather and evaluate all available evidence
using quality-control metrics to
corroborate or modify automated
annotation predictions.
Perform sequence similarity searches
(phylogenetic framework) and use
literature and public databases to:
• Predict functional assignments from
experimental data.
• Distinguish orthologs from paralogs,
and classify gene membership in
families and networks.
6
7. Dispersed, community-based gene
manual annotation efforts.
Using Web Apollo, we* have trained
geographically dispersed scientific
communities to perform biologically
supported manual annotations, and
monitored their findings: ~80
institutions, 14 countries, hundreds of
scientists, and gate keepers.
– Training
workshops and geneborees.
– Tutorials with detailed instructions.
*Collaboration with Elsik Lab,
Hymenoptera Genome
– Personalized user support.
Database.
2. In our experience.
7
8. What have we learned?
Harvesting expertise from dispersed researchers who
assigned functions to predicted and curated peptides,
we have developed more interactive and responsive
tools, as well as better visualization, editing, and
analysis capabilities.
Assessment:
1. Was it helpful / productive to work together?
2. Were manual annotations improved?
3. Did the shared and distributed annotation effort help improve the quality
of scientific findings?
3. Lessons Learned
8
9. It is helpful to work together.
Scientific community efforts bring together domainspecific and natural history expertise that would have
otherwise remain disconnected.
3. Lessons Learned
9
10. Improved Automated Annotations*
In many cases, automated annotations have been
improved.
Also, learned of the challenges of newer sequencing
technologies, e.g.:
– Frameshifts and indel errors
– Split genes across scaffolds
– Highly repetitive sequences
To face these challenges, we train annotators in
recovering coding sequences in agreement with all
available biological evidence.
3. Lessons Learned
10
11. Understanding the evolution of sociality.
… groups of
communities
have taught us a
lot!
Comparison of the genomes of 7 species of
ants contributed to a better understanding
of the evolution and organization of insect
societies at the molecular level.
Insights drawn mainly from six core aspects of
ant biology:
1. Alternative morphological castes
2. Division of labor
3. Chemical Communication
4. Alternative social organization
5. Social immunity
6. Mutualism
Libbrecht et al. 2012. Genome Biology 2013, 14:212
3. Lessons Learned
11
12. A little training goes a long way!
With the right tools, wet lab scientists make exceptional
curators who can easily learn to maximize the
generation of accurate, biologically supported gene
models.
3. Lessons Learned
12
13. Web Apollo
‘File’:
Upload your own
evidence: GFF3,
BAM, BigWig,
VCF*. Add
combination and
sequence search
tracks.
‘View’: change
color by
CDS, toggle
strands, set
highlight.
‘Tools’:
Use BLAT to query the
genome with a protein
or DNA sequence.
Grey bar of coordinates
indicates location. You can
also select here in order to
zoom to a sub-region.
Navigation tools:
pan and zoom
Search box: go
to a scaffold or a
gene model.
‘User-created Annotations’ Track
Evidence Tracks Area
Login
Available Tracks
Graphical User Interface (GUI) for editing annotations
14. Web Apollo
The editing logic is on the server:
selects longest ORF as CDS
flags non-canonical splice sites
‘User-created Annotations’ Track
Evidence Tracks Area
Flags non-canonical
splice sites.
Selection of features and
sub-features
Edge-matching
15. Web Apollo
Two new kinds of tracks:
DNA Track
‘User-created Annotations’ Track
annotation editing
sequence alteration editing
19. [Some of the] Functionality:
Protein-coding gene annotation (that you know and love)
Sequence alterations (less coverage = more fragmentation)
Visualization of stage and cell-type specific transcription
data as coverage plots, heat maps, and alignments
21. •
Thanks!
Berkeley Bioinformatics Open-source Projects
(BBOP), Berkeley Lab: Web Apollo and Gene
Ontology teams. Suzanna Lewis (PI).
•
Ian Holmes Lab (PI). *U. of California Berkeley.
BBOP
•
The team at Hymenoptera Genome Database.
§U. of Missouri. Christine G. Elsik (PI).
•
Arthropod genomics community (fringy
Richards, Monica Poelchau, Alexie
Papanicolaou, Gene Robinson, Juergen
Gadau, Chris R Smith, Owen McMillan, Owain
Edwards, Kevin Hackett, and a few hundred
more).
•
i5K Steering Committee, NAL (USDA), HGSCBCM, BGI, 1KITE.
•
Web Apollo is supported by NIH grants 5R01GM080203
from NIGMS, and 5R01HG004483 from NHGRI, and by
the Director, Office of Science, Office of Basic Energy
Sciences, of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.
•
Images used with permission: AlexanderWild.com
Web Apollo
Gene Ontology
Gregg Helt
Chris Mungall
Ed Lee
Seth Carbon
Rob Buels *
Heiko Dietze
Mitch Skinner *
Justin Reese §
Chris Childers §
Web Apollo: http://GenomeArchitect.org
GO: http://GeneOntology.org
i5K: http://arthropodgenomes.org/wiki/i5K
• For your attention, thank you!
Thank you.
21
Editor's Notes
File: GFF3, BAM, BigWig, VCF (soon).Tools: The plug-in architecture of the annotation editing engine allows for sequence alignment searches using BLAT
The editing logic is on the server:It selects the longest ORF as CDSAnd flags non-canonical splice sitesThe server is a Java servlet- it uses the GMOD biological object layer (gbol) data model: object model & API, based on the Chado schema
A BerkeleyDB stores annotations, annotation edits, and their History