Agenda for Training Meeting

1. Overview of the reannotation project: where are we?
2. What is the scope of the manual review phase?
3. Apollo: making user accounts
4. Apollo: tour
5. Slack channel
6. Demo: general functions
7. Activity: try moving around, searching by coordinates, by AGI identifier
8. Demo: common review workflow
9. Activity: Breakout groups: each group with one gene to review
10. Demo: more complicated stuff
11. Activity: Breakout groups: each group with one gene to review
12. Gene set assignment
    1. split
    2. merged
    3. deleted
    4. novel
    5. locus type changed
    6. cds changed
    7. BUSCO gene disappeared
    8. desired gene family
13. Tracking work and review: Google Sheet and Excel spreadsheet (no Google Drive access)
14. Reconvene in one month - update and assess status
15. ICAR 2023? meetup?

Need:

off screen facilitator to handle questions and technical issues, create breakout rooms

check concurrent users

prerequisites

learning objectives

Reading

...

Specific Use Cases

Recorded Sessions

1. Apollo basics (May 26 session):  https://us06web.zoom.us/rec/share/AbAWtFP-LUcs1OL1LszoH_WNnJsjKzbKYNW-XN414srWwR9ZUuKIl_IAQqiP9NPI.TSd77fNvC0-FfnWx
2. Apollo editing (June 29 session): https://us06web.zoom.us/rec/share/AXQB56B1l3xo8Z6wEYQLvu-60hR5OlvsR1yOwpKg1suhv4Yd_rPO7hHbzZeChARR.ol3bv8rmf7CHcf34
   

Slides

Apollo Basics Training Slides (May 23 and 26, 2023)

Apollo Editing Training Slides (May 31 and June 1, 2023)

Tab links

• Apollo
  • https://apollo-sandbox.arabidopsis.org/apollo/annotator/index

• Apollo Help Docs (longer, keep link handy):

  • https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html

• NCBI Protein BLAST (use Reference proteins refseq_proteins as dataset)
  • https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=
• JBrowse
  • https://jbrowse.arabidopsis.org/index.html?data=Araport11&loc=Chr4%3A9054219..9058227&tracks=TAIR10_genome%2CA11-GL-Jan23%2CA11-PC-Jan23%2Cpollen_tophat%2Clight_tophat%2Cram_tophat%2Cleaf_tophat%2Cdark_tophat%2Csam_tophat%2Caerial_tophat%2Creceptacle_tophat%2Croot_tophat%2Cflower12_tophat%2Ccarpel_tophat&highlight=

Reading

• Grapedia materials (how to - general principles apply)
  • https://integrape.eu/resources/data-management/how-to-manually-curate-genes/
• Maize materials (how to - general principles apply)

• Apollo: Democratizing genome annotation (software summary and background)
  • https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006790

• Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens (see: 'Lessons Learnt for Future Collaborative Annotation Projects' section)
  • https://www.frontiersin.org/articles/10.3389/fmicb.2019.02477/full

• Application of a bioinformatics training delivery method for reaching dispersed and distant trainees (training background)

  • https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008715

• Double triage to identify poorly annotated genes in maize: The missing link in community curation (community annotation)

  • https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224086
• Grapedia materials
  • https://integrape.eu/resources/data-management/how-to-manually-curate-genes/
Maize materials

Related Videos from Other Training Sessions in Other Organisms

General

...

...

...

Apollo Help Docs (longer, keep link handy):

• https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html

Videos

Very detailed, lots of examples.

Changing intron/exon boundaries.