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  1. IGB
  2. IGBF-2413

Write first draft of Bioinformatics App Note for Genome Dashboard

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          Now that we have released Genome Dashboard, we should write a short article introducing it to the community.

          Bioinformatics Application Notes are short articles that introduce software tools to their readers. Let's write a Bioinformatics Application note for Genome Dashboard.

          From the Bioinformatics Web site: https://academic.oup.com/bioinformatics/pages/instructions_for_authors

          Application notes: approximately 1,300 words or 1,000 words plus one figure

          Let's do the 1000 words plus one figure option.

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              is blocked by

              Task - A task that needs to be done. IGBF-2419 Make a couple figure options that reduce white space

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-2552 Write second draft of article introducing Genome Dashboard

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2585 Reduce word count for genome dashboard paper

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment -

                Suggested outline:

                • Explain what IGB is - highlight it is a java desktop application you download from the Web site bioviz.org
                • IGB contains REST endpoints other programs can use to trigger loading of genomes and data sets.
                • IGB retrieves genome assembly information and gene model annotations files from pre-configured IGB Quickload sites.
                • The number of genomes is quite large. Normally IGB users would have to start IGB and then use a either menu (in the Current Genome tab) or one of several shortcuts on the IGB start screen to load a genome assembly.
                • To make this process of selecting a genome easier and also demonstrate the power of integrating desktop applications with Web apps, we created the Genome Dashboard for IGB.
                • Genome Dashboard is implemented as a node.js app.
                • Describe the App and how it works from the user's perspective.
                • Conclude by summarizing the benefits of the Dashboard - convenience for the user but also a quick way for them to find out if the genome version they need to use is available in the IGB system.

                Suggested Figure: Show genome dashboard following a search for "Ara" Insert a curved arrow pointing from a seleteced image to IGB opened and showing the selected genome.

                • References: 2009 and 2016 IGB papers only - to keep the article short.
                Show
                ann.loraine Ann Loraine added a comment - Suggested outline: Explain what IGB is - highlight it is a java desktop application you download from the Web site bioviz.org IGB contains REST endpoints other programs can use to trigger loading of genomes and data sets. IGB retrieves genome assembly information and gene model annotations files from pre-configured IGB Quickload sites. The number of genomes is quite large. Normally IGB users would have to start IGB and then use a either menu (in the Current Genome tab) or one of several shortcuts on the IGB start screen to load a genome assembly. To make this process of selecting a genome easier and also demonstrate the power of integrating desktop applications with Web apps, we created the Genome Dashboard for IGB. Genome Dashboard is implemented as a node.js app. Describe the App and how it works from the user's perspective. Conclude by summarizing the benefits of the Dashboard - convenience for the user but also a quick way for them to find out if the genome version they need to use is available in the IGB system. Suggested Figure: Show genome dashboard following a search for "Ara" Insert a curved arrow pointing from a seleteced image to IGB opened and showing the selected genome. References: 2009 and 2016 IGB papers only - to keep the article short.
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                pbadzuh Philip Badzuh (Inactive) added a comment -

                Please see a rough draft below:
                https://docs.google.com/document/d/1m7EQP_QBR9mwWrHoVW4Q07PKvAAY87lz-ZPuFRH5dIc/edit?usp=sharing

                The text in the image is somewhat difficult to see, due to its small size, so it may be better to screenshot specific components of the dashboard and IGB, for example those currently boxed in red. Please let me know.

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - Please see a rough draft below: https://docs.google.com/document/d/1m7EQP_QBR9mwWrHoVW4Q07PKvAAY87lz-ZPuFRH5dIc/edit?usp=sharing The text in the image is somewhat difficult to see, due to its small size, so it may be better to screenshot specific components of the dashboard and IGB, for example those currently boxed in red. Please let me know.
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                ann.loraine Ann Loraine added a comment -

                Let's make a couple more figure options (in a new ticket) that reduces white space. Images could be placed side-by-side or configured to consume 1 or 1.5 column widths.

                Draft is complete. Moving to Closed.

                Show
                ann.loraine Ann Loraine added a comment - Let's make a couple more figure options (in a new ticket) that reduces white space. Images could be placed side-by-side or configured to consume 1 or 1.5 column widths. Draft is complete. Moving to Closed.

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                      Updated:
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