Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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Labels:None
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Story Points:5
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Sprint:Spring 7, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5
Description
Bob Goldstein, faculty from UNC Chapel Hill, is coming to Charlotte to give a seminar on Friday April 5 at 2:30.
His research Web site: https://goldsteinlab.weebly.com/
His tardigrades site: http://tardigrades.bio.unc.edu/
Ann Loraine signed up for a meeting with him at 1:30 in the third floor conference room. (We might use my office instead, depending on whether they finished repairing the walls yet - long story!)
Our goal is to talk with him about the tardigrade genome project and how we can represent tardigrade (water bears) in IGB.
Water bears are an emerging model system for studying how animals survive in extreme environments.
According to the UCSC Genome Browser, they now have three tardigrade genome assemblies available.
Bob Goldstein's tardigrades web site (http://tardigrades.bio.unc.edu/) mentions that they are "developing the water bear Hypsibius exemplaris as a new model for studying evo-devo and resistance to extremes."
Their tardigrade site has a "links" page that includes a blast search link hosted at NCBI. That page allows users to search genome assembly
"Hypsibius dujardini GenBank assembly GCA_002082055.1"
UCSC appears to also feature this same genome assembly on their site. They call it "nHd_3.1 Apr. 2017 H.dujardini (Z151 2017 tardigrades) (GCA_002082055.1)"
See:
For this task:
- Get reference 2bit genome sequence file for the above genome assembly
- Investigate and get reference gene model annotations for the above assembly
- Add reference genome assembly to IGB Quickload main
- Add reference gene model annotations to IGB Quickload main
- Review Goldstein lab publications to identify foundational RNA-Seq data for this organism
Let's aim to get the tardigrade data added to IGB QL before Friday so that we can:
- show Dr. Goldstein an IGB demo with the tardigrade genome data
- ask Dr. Goldstein which RNA-Seq data sets are most relevant to his research
- tentatively schedule an on-line demo of IGB with Dr. Goldstein lab members
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2809 [ 19325 ] |
| Rank | Ranked higher |
| Summary | Investigate: Adding tardigrade to IGB Quickload Main | Investigate: Add tardigrade to IGB Quickload Main |
| Epic Link | IGBF-2809 [ 19325 ] | IGBF-1478 [ 17563 ] |
| Link | This issue relates to IGBF-3681 [ IGBF-3681 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Comment |
[ Paper: https://www.nature.com/articles/ncomms12808
Website: http://kumamushi.org/database.html NCBI: https://www.ncbi.nlm.nih.gov/nuccore/BDGG00000000.1 Note: UCSC does have the [R. varieornatus|https://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_2790993_GCA_001949185.1&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=BDGG01000001.1%3A3111028%2D3121028&hgsid=2077278096_b5zQo29khGhNnPNEOOamtx0cKoXg] genome in the browser, but I am not seeing it in the [Table Browser|https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=2062754252_TCzwwWpelErfii1tZNtOWAOU96T6&clade=insect&org=0&db=0&hgta_group=genes&hgta_track=augustusGene&hgta_table=augustusGene&hgta_regionType=genome&position=&hgta_outputType=primaryTable&hgta_outFileName=knownGene.bed], [UCSC API|https://api.genome.ucsc.edu/list/ucscGenomes], or [UCSC Genome Downloads|https://hgdownload.soe.ucsc.edu/downloads.html]. ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Summary | Investigate: Add tardigrade to IGB Quickload Main | Add tardigrade to IGB Quickload Main |
| Story Points | 0.5 | 2 |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Story Points | 2 | 4 |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 7 [ 191 ] | Spring 7, Spring 8 [ 191, 192 ] |
| Rank | Ranked higher |
| Summary | Add tardigrade to IGB Quickload Main | Add tardigrade genome assemblies to IGB Quickload Main |
| Sprint | Spring 7, Spring 8 [ 191, 192 ] | Spring 7, Spring 9 [ 191, 193 ] |
| Sprint | Spring 7, Spring 9 [ 191, 193 ] | Spring 7, Spring 9, Spring 10 [ 191, 193, 194 ] |
| Rank | Ranked higher |
| Sprint | Spring 7, Spring 9, Spring 10 [ 191, 193, 194 ] | Spring 7, Spring 9, Summer 1 [ 191, 193, 195 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Sprint | Spring 7, Spring 9, Summer 1 [ 191, 193, 195 ] | Spring 7, Spring 9, Summer 1, Summer 2 [ 191, 193, 195, 196 ] |
| Rank | Ranked higher |
| Summary | Add tardigrade genome assemblies to IGB Quickload Main | Add both tardigrade genome assemblies to IGB Quickload Main |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 7, Spring 9, Summer 1, Summer 2 [ 191, 193, 195, 196 ] | Spring 7, Spring 9, Summer 1, Summer 2, Summer 3 [ 191, 193, 195, 196, 197 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | RvY_00053.png [ 18425 ] |
| Attachment | RvY_01679-GDV.png [ 18426 ] |
| Attachment | RvY_00053.png [ 18425 ] |
| Attachment | RvY_01679-IGB.png [ 18427 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Attachment | Screenshot 2024-06-28 at 2.32.58 PM.png [ 18436 ] |
| Sprint | Spring 7, Spring 9, Summer 1, Summer 2, Summer 3 [ 191, 193, 195, 196, 197 ] | Spring 7, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4 [ 191, 193, 195, 196, 197, 198 ] |
| Rank | Ranked higher |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Story Points | 4 | 5 |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Paige Kulzer [ pkulzer ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Ann Loraine [ aloraine ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 7, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4 [ 191, 193, 195, 196, 197, 198 ] | Spring 7, Spring 9, Summer 1, Summer 2, Summer 3, Summer 4, Summer 5 [ 191, 193, 195, 196, 197, 198, 199 ] |
| Rank | Ranked higher |
| Assignee | Dylan Marrotte [ dmarrott ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Assignee | Dylan Marrotte [ dmarrott ] | Ann Loraine [ aloraine ] |
| Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Comment |
[ To do:
* -Fix typo in [annots.xml|https://igbquickload-main.bioviz.org/quickload/H_exemplaris_Z151_Apr_2017/annots.xml] - change March 3, 2022 -> March 4, 2022- * Add [R. varieornatus|https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001949185.1/] tardigrade genome and annotation to IGB Quickload. * Update gff3ToBedDetail.py in [GenomeSource|https://bitbucket.org/lorainelab/genomesource/src/master/] repo so that it handles non protein coding genes. ] |
| Assignee | Ann Loraine [ aloraine ] |
| Fix Version/s | 10.0.1 [ 10901 ] |
| Fix Version/s | 10.0.0 Major Release [ 10900 ] | |
| Fix Version/s | 10.0.1 [ 10901 ] |