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  1. IGB
  2. IGBF-2885

Create bibliography of crispr design tool articles

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          5
        • Epic Link:
        • Sprint:
          Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23

          Description

          Create bibliography of crispr design tool articles.

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              Activity

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              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
              Field Original Value New Value
              Epic Link IGBF-2883 [ 21320 ]
              ann.loraine Ann Loraine made changes -
              Sprint Summer 1 2021 Jun 14 - Jun 25 [ 123 ]
              nfreese Nowlan Freese made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
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              nfreese Nowlan Freese added a comment -

              I am currently working on an excel spreadsheet (tools.xlsx) located in Dropbox > IGB > Qi Collaboration > Literature > tools.xlsx

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              nfreese Nowlan Freese added a comment - I am currently working on an excel spreadsheet (tools.xlsx) located in Dropbox > IGB > Qi Collaboration > Literature > tools.xlsx
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              nfreese Nowlan Freese added a comment -

              This website effectively does exactly what we were looking for:
              https://bioinfogp.cnb.csic.es/tools/wereview/crisprtools/

              Next step is to determine which of the top cited tools supports activation/repression and plants.

              Show
              nfreese Nowlan Freese added a comment - This website effectively does exactly what we were looking for: https://bioinfogp.cnb.csic.es/tools/wereview/crisprtools/ Next step is to determine which of the top cited tools supports activation/repression and plants.
              ann.loraine Ann Loraine made changes -
              Sprint Summer 1 2021 Jun 14 - Jun 25 [ 123 ] Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9 [ 123, 124 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
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              nfreese Nowlan Freese added a comment -

              Slide deck summarizing the data is located in Dropbox > IGB > Qi Collaboration > Literature > crisprDesignSummary

              Show
              nfreese Nowlan Freese added a comment - Slide deck summarizing the data is located in Dropbox > IGB > Qi Collaboration > Literature > crisprDesignSummary
              nfreese Nowlan Freese made changes -
              Story Points 2 5
              nfreese Nowlan Freese made changes -
              Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
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              ann.loraine Ann Loraine added a comment -

              Editing & memorizing slide deck (for future use)

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              ann.loraine Ann Loraine added a comment - Editing & memorizing slide deck (for future use)
              ann.loraine Ann Loraine made changes -
              Sprint Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9 [ 123, 124 ] Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23 [ 123, 124, 125 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              nfreese Nowlan Freese made changes -
              Assignee Ann Loraine [ aloraine ] Nowlan Freese [ nfreese ]
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              nfreese Nowlan Freese added a comment -

              I have added two columns to help summarize the visualizations that are included as part of each CRISPR design tool.

              Visualization asks whether a genome browser style visualization of the results is included. Some browsers include what appears to be a fully interactive genome browser. Others include static images. Most include non-interactive text based results.

              Annotation asks whether the genome browsers with interactive genome browsers or static images also include the gene annotation.

              I have also included comments if the CRISPR design links out to other genome browsers such as UCSC, ENSEMBL, IGV, etc.

              Show
              nfreese Nowlan Freese added a comment - I have added two columns to help summarize the visualizations that are included as part of each CRISPR design tool. Visualization asks whether a genome browser style visualization of the results is included. Some browsers include what appears to be a fully interactive genome browser. Others include static images. Most include non-interactive text based results. Annotation asks whether the genome browsers with interactive genome browsers or static images also include the gene annotation. I have also included comments if the CRISPR design links out to other genome browsers such as UCSC, ENSEMBL, IGV, etc.
              nfreese Nowlan Freese made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              nfreese Nowlan Freese made changes -
              Assignee Nowlan Freese [ nfreese ]
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              ann.loraine Ann Loraine added a comment -

              I reviewed the spreadsheet and the slidedeck, adding some notes & refinements to the slide deck. We showed the work to Yipeng Qi last week in advance of the more formal meeting coming up this week.
              Moving to Done.
              Note: Materials and notes are stored in the IGB Dropbox in a folder named for Dr. Qi.

              Show
              ann.loraine Ann Loraine added a comment - I reviewed the spreadsheet and the slidedeck, adding some notes & refinements to the slide deck. We showed the work to Yipeng Qi last week in advance of the more formal meeting coming up this week. Moving to Done. Note: Materials and notes are stored in the IGB Dropbox in a folder named for Dr. Qi.
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              ann.loraine Ann Loraine made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              ann.loraine Ann Loraine made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              ann.loraine Ann Loraine made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
              ann.loraine Ann Loraine made changes -
              Assignee Nowlan Freese [ nfreese ]

                People

                • Assignee:
                  nfreese Nowlan Freese
                  Reporter:
                  ann.loraine Ann Loraine
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                  Dates

                  • Created:
                    Updated:
                    Resolved: