---
# System prepended metadata

title: 'Titus/Tessa Agenda, 05/04/2023'
tags: [' 2023', ' May 2023', ' agenda', ' titus', meetings]

---

---
tags: meetings, titus, agenda, 2023, May 2023
---

Titus/Tessa Agenda, 05/04/2023
===

## JOSS Paper

- most authors signed off, will go tally missing responses.


## SpillOver project
- seq classification via sourmash tax approach:
    - needed (done): [fix tax grep md5s PR](https://github.com/sourmash-bio/sourmash/pull/2602)
    - needs (in progress): [ICTV taxonomy PR](https://github.com/sourmash-bio/sourmash/pull/2608)
    - currently running subset to see how well k=21,scaled=1 works for classification. 
    - of 100:
      > cat output.spillover/gather/dna/*.k21.gather.txt | grep total | sort | uniq -c
     28 found 1 matches total;
      1 found 11 matches total;
     12 found 2 matches total;
     30 found 3 matches total;
     12 found 4 matches total;
      7 found 5 matches total;
      4 found 6 matches total;
      5 found 7 matches total;
      1 found 9 matches total;
      
not sure how useful these matches are yet

- Viral LINs for classification, clustering
    - need to reach out + talk with Boris, Reza et al, see what (if anything) they're already doing in the viral space
- CD-HIT clustering
    - (to do)

## FRO Updates

- Website plan update
    - Adam, Suzanne website is far ahead of my efforts. Hosting at USDA is hard because of paperwork for usda.gov site.
        - suggested us hosting
        - they said they could package and make public within ~a week
            - but it still needs cleanup, some work, so we should consider it a soft launch
        - Would add "A collaborative effort between UC Davis, JGI and USDA" at base of website
    - We could fork into sourmash-bio github, but not sure about maintenance/support responsibilities.
    - In the meantime, I will write sourmash docs on all the large-scale search sites (greyhound, mastiff), search parameters, guidelines, etc.

- [proposal](https://docs.google.com/document/d/1z4Nz3Tl1ycWHK2XNCmS3Lg9ccodRdbSeYV08AGKIg_A/edit): **revamped first two paragraphs** for pathogen workflows, urgency. Still need to revamp remaining text, want to better describe milestones + risks.


### Some highlights from meetings
- Adam + Suzanne / USDA chat
    - pathogen dashboard idea
    - neat metadata percentage info (e.g. 40% of datasets in mastiff have lat/long info)
    - list of high-priority pathogens
- Chris Gulvik (CDC) chat
    - "pathogen-agnostic" tool is lacking. CDC teams are working on an in-house tool, but still a long way off
    - wastewater surveillance folks may be interested
        - chatting with Shatavia Morrison 5/8/23
    - setting up a monitoring effort in/for Thailand. Resources are an issue, lightweight local tools would be ideal
        - suggested local mastiff db's for these sorts of situations
        - NOT web (e.g. MiSeq data transfer usually takes 10min in their lab, took 3 days there)
- Amanda 
    -  great context + suggestions re handling datasets shared across databases (e.g. present both in SRA, non-SRA)
    -  dataset discovery
- MetaSeek / Adrienne Hoarfrost chat
    - metadata search, start from MetaSeek approach
    - Metadata imputation:
        - MetaSeek used a series of manual rules. Learn from this + use an ML approach to do better
    - build workflow for ml/deep learning dataset identification
        - build test/train split (not random, make sure sequence similarity is appropriate). Also suggest a small, representative subset for testing

- **Rob Finn**: meeting 5/15
- **Rayan Chikhi**, **Rodney Brister** - no response

## Other

- contig-level workflow could be used for spillover, might be 