Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud
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{"title"=>"Genomics Virtual Laboratory: A practical bioinformatics workbench for the cloud", "type"=>"journal", "authors"=>[{"first_name"=>"Enis", "last_name"=>"Afgan", "scopus_author_id"=>"8858676200"}, {"first_name"=>"Clare", "last_name"=>"Sloggett", "scopus_author_id"=>"9639509700"}, {"first_name"=>"Nuwan", "last_name"=>"Goonasekera", "scopus_author_id"=>"35242297600"}, {"first_name"=>"Igor", "last_name"=>"Makunin", "scopus_author_id"=>"6701767532"}, {"first_name"=>"Derek", "last_name"=>"Benson", "scopus_author_id"=>"56996758100"}, {"first_name"=>"Mark", "last_name"=>"Crowe", "scopus_author_id"=>"8945804800"}, {"first_name"=>"Simon", "last_name"=>"Gladman", "scopus_author_id"=>"55221967000"}, {"first_name"=>"Yousef", "last_name"=>"Kowsar", "scopus_author_id"=>"55912668500"}, {"first_name"=>"Michael", "last_name"=>"Pheasant", "scopus_author_id"=>"8605964800"}, {"first_name"=>"Ron", "last_name"=>"Horst", "scopus_author_id"=>"56996876300"}, {"first_name"=>"Andrew", "last_name"=>"Lonie", "scopus_author_id"=>"15061630600"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84949503780", "sgr"=>"84949503780", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0140829", "pmid"=>"26501966", "isbn"=>"19326203 (Electronic)", "pui"=>"607159183"}, "id"=>"50fecf9a-db13-3ae5-9459-4edfda3d3779", "abstract"=>"BACKGROUND: Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.\\n\\nRESULTS: We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.\\n\\nCONCLUSIONS: This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the value added to the research community through the suite of services and resources provided by our implementation.", "link"=>"http://www.mendeley.com/research/genomics-virtual-laboratory-practical-bioinformatics-workbench-cloud", "reader_count"=>104, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>22, "Librarian"=>1, "Student > Doctoral Student"=>6, "Researcher"=>24, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>4, "Student > Bachelor"=>12, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>22, "Librarian"=>1, "Student > Doctoral Student"=>6, "Researcher"=>24, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>4, "Student > Bachelor"=>12, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>14, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>35, "Medicine and Dentistry"=>1, "Design"=>1, "Business, Management and Accounting"=>1, "Sports and Recreations"=>1, "Social Sciences"=>1, "Computer Science"=>35, "Immunology and Microbiology"=>1, "Mathematics"=>1, "Engineering"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>3}, "Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>6}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>35}, "Computer Science"=>{"Computer Science"=>35}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}}, "reader_count_by_country"=>{"United States"=>1, "Philippines"=>1, "United Kingdom"=>1, "Paraguay"=>1, "Libya"=>1, "Spain"=>1, "Austria"=>1, "Netherlands"=>1, "Sweden"=>1, "China"=>2, "Luxembourg"=>1, "Denmark"=>1, "Italy"=>2}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2376832"], "description"=>"<p>A summary of the criteria that would define a general genomics workbench environment, and suggested implications on technical requirements.</p>", "links"=>[], "tags"=>["implementation", "platform", "throughput genomics data", "Cloud BackgroundAnalyzing", "data transformation", "Genomics Virtual Laboratory", "visualisation options", "reference data sets", "Software tools", "upfront investment", "Practical Bioinformatics Workbench", "workflow", "interface", "analyses", "machine images", "research community", "cloud management tools", "researcher", "service", "Amazon Web Services cloud", "Research Cloud", "configured bioinformatics tools", "demand", "data resources", "design considerations", "reference datasets", "practice genomics analysis", "visualisation tools", "ipython notebook", "middleware layer", "gvl", "user"], "article_id"=>1585403, "categories"=>["Biological Sciences"], "users"=>["Enis Afgan", "Clare Sloggett", "Nuwan Goonasekera", "Igor Makunin", "Derek Benson", "Mark Crowe", "Simon Gladman", "Yousef Kowsar", "Michael Pheasant", "Ron Horst", "Andrew Lonie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140829.t001", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_summary_of_the_criteria_that_would_define_a_general_genomics_workbench_environment_and_suggested_implications_on_technical_requirements_/1585403", "title"=>"A summary of the criteria that would define a general genomics workbench environment, and suggested implications on technical requirements.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-26 02:56:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2376830"], "description"=>"<p>Each GVL instance is, at runtime, composed of a number of components that the GVL provides: a virtual machine image, a volume snapshot or an archive of the tools file system, and a snapshot or a hosted instance of the indices file system. Combined at runtime by CloudMan into a virtual cluster, the components enable a flexible and feature-full bioinformatics workbench.</p>", "links"=>[], "tags"=>["implementation", "platform", "throughput genomics data", "Cloud BackgroundAnalyzing", "data transformation", "Genomics Virtual Laboratory", "visualisation options", "reference data sets", "Software tools", "upfront investment", "Practical Bioinformatics Workbench", "workflow", "interface", "analyses", "machine images", "research community", "cloud management tools", "researcher", "service", "Amazon Web Services cloud", "Research Cloud", "configured bioinformatics tools", "demand", "data resources", "design considerations", "reference datasets", "practice genomics analysis", "visualisation tools", "ipython notebook", "middleware layer", "gvl", "user"], "article_id"=>1585402, "categories"=>["Biological Sciences"], "users"=>["Enis Afgan", "Clare Sloggett", "Nuwan Goonasekera", "Igor Makunin", "Derek Benson", "Mark Crowe", "Simon Gladman", "Yousef Kowsar", "Michael Pheasant", "Ron Horst", "Andrew Lonie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140829.g005", "stats"=>{"downloads"=>1, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Architectural_components_of_the_GVL_8217_s_management_layer_/1585402", "title"=>"Architectural components of the GVL’s management layer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-26 02:56:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2376820"], "description"=>"<p><b>(a)</b> A user initiates the launch process via the launch service (<i>launch</i>.<i>genome</i>.<i>edu</i>.<i>au</i>) by providing their cloud credentials to the launcher application and <b>(b)</b> within a few minutes is able to access the management interface (CloudMan) on the deployed instance of the workbench. <b>(c)</b> After workbench services have started, the researcher can use the applications as desired (e.g., Galaxy).</p>", "links"=>[], "tags"=>["implementation", "platform", "throughput genomics data", "Cloud BackgroundAnalyzing", "data transformation", "Genomics Virtual Laboratory", "visualisation options", "reference data sets", "Software tools", "upfront investment", "Practical Bioinformatics Workbench", "workflow", "interface", "analyses", "machine images", "research community", "cloud management tools", "researcher", "service", "Amazon Web Services cloud", "Research Cloud", "configured bioinformatics tools", "demand", "data resources", "design considerations", "reference datasets", "practice genomics analysis", "visualisation tools", "ipython notebook", "middleware layer", "gvl", "user"], "article_id"=>1585393, "categories"=>["Biological Sciences"], "users"=>["Enis Afgan", "Clare Sloggett", "Nuwan Goonasekera", "Igor Makunin", "Derek Benson", "Mark Crowe", "Simon Gladman", "Yousef Kowsar", "Michael Pheasant", "Ron Horst", "Andrew Lonie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140829.g001", "stats"=>{"downloads"=>3, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_GVL_launch_process_for_starting_self_launched_instances_of_the_GVL_workbench_/1585393", "title"=>"The GVL launch process for starting self-launched instances of the GVL workbench.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-26 02:56:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2376833"], "description"=>"<p>Summary of specific technical solutions used to meet the design requirements of the GVL.</p>", "links"=>[], "tags"=>["implementation", "platform", "throughput genomics data", "Cloud BackgroundAnalyzing", "data transformation", "Genomics Virtual Laboratory", "visualisation options", "reference data sets", "Software tools", "upfront investment", "Practical Bioinformatics Workbench", "workflow", "interface", "analyses", "machine images", "research community", "cloud management tools", "researcher", "service", "Amazon Web Services cloud", "Research Cloud", "configured bioinformatics tools", "demand", "data resources", "design considerations", "reference datasets", "practice genomics analysis", "visualisation tools", "ipython notebook", "middleware layer", "gvl", "user"], "article_id"=>1585404, "categories"=>["Biological Sciences"], "users"=>["Enis Afgan", "Clare Sloggett", "Nuwan Goonasekera", "Igor Makunin", "Derek Benson", "Mark Crowe", "Simon Gladman", "Yousef Kowsar", "Michael Pheasant", "Ron Horst", "Andrew Lonie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140829.t002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_specific_technical_solutions_used_to_meet_the_design_requirements_of_the_GVL_/1585404", "title"=>"Summary of specific technical solutions used to meet the design requirements of the GVL.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-26 02:56:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2376829"], "description"=>"<p>The GVL leverages cloud resource and is compatible with multiple cloud technologies. Through a set of cloud resource management tools, the details of cloud resources are hidden enabling non-cloud aware applications to readily execute in this environment.</p>", "links"=>[], "tags"=>["implementation", "platform", "throughput genomics data", "Cloud BackgroundAnalyzing", "data transformation", "Genomics Virtual Laboratory", "visualisation options", "reference data sets", "Software tools", "upfront investment", "Practical Bioinformatics Workbench", "workflow", "interface", "analyses", "machine images", "research community", "cloud management tools", "researcher", "service", "Amazon Web Services cloud", "Research Cloud", "configured bioinformatics tools", "demand", "data resources", "design considerations", "reference datasets", "practice genomics analysis", "visualisation tools", "ipython notebook", "middleware layer", "gvl", "user"], "article_id"=>1585401, "categories"=>["Biological Sciences"], "users"=>["Enis Afgan", "Clare Sloggett", "Nuwan Goonasekera", "Igor Makunin", "Derek Benson", "Mark Crowe", "Simon Gladman", "Yousef Kowsar", "Michael Pheasant", "Ron Horst", "Andrew Lonie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140829.g004", "stats"=>{"downloads"=>3, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_basic_architectural_layers_composing_the_GVL_workbench_/1585401", "title"=>"Three basic architectural layers composing the GVL workbench.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-26 02:56:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2376828"], "description"=>"<p>Initially, standalone and purpose-specific tools were most prevalent. As the complexity of analyses grew, new platforms formed that aggregate many standalone tools and support different types of computational infrastructures to offer more versatile functionality. The GVL represents another step in this evolution where it aggregates a large number of the best-of-breed software and technologies available today.</p>", "links"=>[], "tags"=>["implementation", "platform", "throughput genomics data", "Cloud BackgroundAnalyzing", "data transformation", "Genomics Virtual Laboratory", "visualisation options", "reference data sets", "Software tools", "upfront investment", "Practical Bioinformatics Workbench", "workflow", "interface", "analyses", "machine images", "research community", "cloud management tools", "researcher", "service", "Amazon Web Services cloud", "Research Cloud", "configured bioinformatics tools", "demand", "data resources", "design considerations", "reference datasets", "practice genomics analysis", "visualisation tools", "ipython notebook", "middleware layer", "gvl", "user"], "article_id"=>1585400, "categories"=>["Biological Sciences"], "users"=>["Enis Afgan", "Clare Sloggett", "Nuwan Goonasekera", "Igor Makunin", "Derek Benson", "Mark Crowe", "Simon Gladman", "Yousef Kowsar", "Michael Pheasant", "Ron Horst", "Andrew Lonie"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140829.g003", "stats"=>{"downloads"=>6, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_evolution_of_the_data_analysis_solutions_for_genomics_/1585400", "title"=>"An evolution of the data analysis solutions for genomics.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-26 02:56:56"}
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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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