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  1. IGB
  2. IGBF-3672

Draft a workshop outline for ASPB 2024

        Details

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

          Description

          We've been accepted to present a workshop at ASPB 2024.

          Task: Draft an outline for the workshop to be presented virtually at ASPB (June 11 @ 1PM). See IGBF-3443 for a brief workshop description to start building off of. Aim for a 45 minute presentation.

          This outline can be broken up into sections like the following:

          1. Using scaled coverage graphs to find the most differentially expressed genes "by eye"
          2. Using sequence alignments to assess alternative transcript structures across sample types
          3. Develop hypotheses about gene function by searching for conserved protein motifs
          4. Looking up information quickly about all the genes in a region using Google and the NCBI Entrez Gene Database

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              Task - A task that needs to be done. IGBF-3673 Draft key concepts/topics to be covered in the ASPB 2024 workshop

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Task - A task that needs to be done. IGBF-3711 Set up SRA-downloaded Muday datasets in the RNA-Seq Quickload

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3737 Create introductory slides for the ASPB2024 workshop

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3740 Reorganize the Muday Lab folder in the RNA-Seq Quickload

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3744 Finalize a workshop outline for ASPB 2024

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3443 Write and submit workshop for ASPB 2024

              • Major - Major loss of function.
              • Closed

                Activity

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                pkulzer Paige Kulzer created issue -
                pkulzer Paige Kulzer made changes -
                Field Original Value New Value
                Epic Link IGBF-3532 [ 22751 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3443 [ IGBF-3443 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3673 [ IGBF-3673 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 6 [ 190 ] Spring 8 [ 192 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 8 [ 192 ]
                pkulzer Paige Kulzer made changes -
                Sprint Spring 9 [ 193 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3711 [ IGBF-3711 ]
                pkulzer Paige Kulzer made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                pkulzer Paige Kulzer added a comment -

                Link to the workshop outline: https://docs.google.com/document/d/1GqhiyTq8DQG-VKgKMvskqp_1O0UEkQGfEvbxrIDf2Q0/edit?usp=sharing

                Using the key concepts outlined in IGBF-3673, I've created a workshop outline for ASPB 2024 and linked it above. I will plan to make a new ticket for creating slides to accompany this workshop so that this ticket relates solely to the outline.

                For review, Ann Loraine and Nowlan Freese and I should plan to sit down and discuss the outline. I will take notes during that meeting and report them on this ticket.

                Show
                pkulzer Paige Kulzer added a comment - Link to the workshop outline: https://docs.google.com/document/d/1GqhiyTq8DQG-VKgKMvskqp_1O0UEkQGfEvbxrIDf2Q0/edit?usp=sharing Using the key concepts outlined in IGBF-3673 , I've created a workshop outline for ASPB 2024 and linked it above. I will plan to make a new ticket for creating slides to accompany this workshop so that this ticket relates solely to the outline. For review, Ann Loraine and Nowlan Freese and I should plan to sit down and discuss the outline. I will take notes during that meeting and report them on this ticket.
                pkulzer Paige Kulzer made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 9 [ 193 ] Spring 9, Spring 10 [ 193, 194 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3737 [ IGBF-3737 ]
                ann.loraine Ann Loraine made changes -
                Assignee Paige Kulzer [ pkulzer ]
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                ann.loraine Ann Loraine added a comment -

                Passing this back to Paige Kulzer to add new comments on notes from the meeting, as mentioned in the previous comment.

                Show
                ann.loraine Ann Loraine added a comment - Passing this back to Paige Kulzer to add new comments on notes from the meeting, as mentioned in the previous comment.
                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 ] To-Do [ 10305 ]
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3740 [ IGBF-3740 ]
                Hide
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                pkulzer Paige Kulzer added a comment -

                Notes from our meeting on 17 May 2024:

                1. The Muday Lab folder is currently organized in a way that makes sense, but I think that we could optimize this folder for the upcoming ASPB workshop by organizing it a bit differently. See IGBF-3740 for a ticket addressing the reorganization of this folder.
                2. We need to add keywords such as "F3H" and "FLAVANONE 3 HYDROXYLASE" to the gene annotations labeled "PRAM_26184.1" in SL5 and "solyc02g083860" in SL4 so that I can quickly search for and locate the gene where the point mutation occurs in the are genotype. See IGBF-3712 for a ticket addressing this needed addition.
                3. I'd like a slide that depicts an overview of the experiment so that I can show the audience where the data we'll be working with came from. Gloria Muday might have a slide just like that already, so we'll need to reach out soon and ask her about it.
                4. Idea for handout materials: Create an activity for users to zoom to the F3H gene and find the SNP occurring at that locus in the are genotypes, then figure out what amino acid is encoded by that mutant protein. Predict how the protein function might be different based on that SNP, and then have them look up its function.
                5. Idea to end on: There are more advanced features we're working on that I don't have time to talk about today, but if you'd like to know more, here's how you can get in touch...
                Show
                pkulzer Paige Kulzer added a comment - Notes from our meeting on 17 May 2024: The Muday Lab folder is currently organized in a way that makes sense, but I think that we could optimize this folder for the upcoming ASPB workshop by organizing it a bit differently. See IGBF-3740 for a ticket addressing the reorganization of this folder. We need to add keywords such as "F3H" and "FLAVANONE 3 HYDROXYLASE" to the gene annotations labeled "PRAM_26184.1" in SL5 and "solyc02g083860" in SL4 so that I can quickly search for and locate the gene where the point mutation occurs in the are genotype. See IGBF-3712 for a ticket addressing this needed addition. I'd like a slide that depicts an overview of the experiment so that I can show the audience where the data we'll be working with came from. Gloria Muday might have a slide just like that already, so we'll need to reach out soon and ask her about it. Idea for handout materials: Create an activity for users to zoom to the F3H gene and find the SNP occurring at that locus in the are genotypes, then figure out what amino acid is encoded by that mutant protein. Predict how the protein function might be different based on that SNP, and then have them look up its function. Idea to end on: There are more advanced features we're working on that I don't have time to talk about today, but if you'd like to know more, here's how you can get in touch...
                pkulzer Paige Kulzer made changes -
                Link This issue relates to IGBF-3744 [ IGBF-3744 ]
                Hide
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                pkulzer Paige Kulzer added a comment -

                Now that a workshop outline has been drafted and reviewed, I am closing this ticket and creating a new ticket for finalizing the outline (see IGBF-3744).

                Show
                pkulzer Paige Kulzer added a comment - Now that a workshop outline has been drafted and reviewed, I am closing this ticket and creating a new ticket for finalizing the outline (see IGBF-3744 ).
                pkulzer Paige Kulzer made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pkulzer Paige Kulzer made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                pkulzer Paige Kulzer made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                pkulzer Paige Kulzer made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                pkulzer Paige Kulzer made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                pkulzer Paige Kulzer made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                pkulzer Paige Kulzer made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    pkulzer Paige Kulzer
                    Reporter:
                    pkulzer Paige Kulzer
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                      Updated:
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