# scverse advisory board meeting

# 2024-03-01

## Attendees:
* core-team: GS, GP, MK, DB, LH, IV, LM, PA, CEB,
* management: FF, AW, OS, FT
* advisory: DP

## Notes

FF: show planned events on scverse website

### Ecosystem
DP: balance between being inclusiv and high quality software. scverse: universe needs to be top tier, how to do that? is the pyopenscience a solution?
DP: not only software quality (technical) but also quality of the method: don’t include technically well-implemented but conceptually bad methods.
DP: people (her) choose scverse because only scientifically rigorous things are included
FT: this should only apply to core, early vetting didn’t work in HCA
OS: agrees with DP I think?
FF: we need both kinds of efforts
LH: integrate more with OpenProblems
OS: we should rank tools by prioritized features (“comes high in a benchmark”, …)
FT: authors need to provide that info if they want to be a “high ranked community package” / alternatively leverage community and have them do it (?)
FT: show them in bronze/silver/gold ranking

Fabian wants slide about “scaling scverse” to show next week.

### Scalability
Alex: scalability, how do you think about tiledb-SOMA.
Isaac: seems to be a way to do anndata on top.
Dana: how much can we just talk to CZI and ask them to incorporate their scalability into scverse.
Alex: tiledb is since the recent TileDB-SOMA really good, what if we just build on it.
Alex: people in high performance are converging on TileDB-SOMA
Dana: scverse serves academic instead of industrial community. The broad usership is PhD students.

### Grants
Danila: Focus on Numfocus
Dana: NIH you must have no overlap. You can submit 2 grants that aren't funded with the same name. What's important is, beyond ofc showing we are great, you need to have specific aims. This needs to be distinct from other things funded by grants. You can't have another formal grant with the same aim. Needs to be very specific, preferrably specific aims that address core things that a lot of US based users use. Aim should be building the software. This (U24) is for software that you can't fund for R01, but then it must also be an infrastructure, and also workshop, trainings etc on top.
* scaling could be an angle
* new modalities, e.g. spatial
*

### Social Media
FT and DP happy to forward all our announcements, but starting to use Xitter less.

# 2022-XX

## Introduction (Fabian)

-> this group is "engineering-focused"

## Presentation (Isaac)

BB: [Seq-language](https://seq-lang.org/) as Python accelarator

### Grants

DP: CZI review process is flawed
Aviv: We should talk to them

### Spatial

Talk to [Prisca Liberali](https://liberalilab.org/technologies).

## Epigenetics

DP: Flexibility is key at this stage (as the field has not settled yet
DP: Important to allow for peaks and bins, multiple resolutions of bins (close-to-raw data).

Talk to [Anshul](https://profiles.stanford.edu/anshul-kundaje)

## Perturbation data

Aviv: Perturbation data is growing. What are we doing to handle perturbation data?

2 things:
1. Direct perturbation data + forward pertubation data -> genetic screens -> Perturb-seq -> statistcal connection between perturbation and cell type / state / level of genes
2. Human genetics data -> Cis/trans associations in and between cell types -> variants associated to some trait in CTs

methods vary widely
* Dictionary for perturbations (idea by Fabian + agreed with by Aviv)
* Oli
* Previous work from human genetics community
* variant calling. [Hail](https://hail.is/docs/0.2/index.html).
* Long read + per cell info
* Aviv: For cancer, it's about mutations *in a cell*.
* Fabian: take home, outlook in paper. How to represent pertubation data?
* Dana: Information from perturbation can be quite noisy

## Scalability

(Isaac) ...

## Discussion

### Funding

* Aviv: NIH has several open calls (seconday /tertialry calls) [brain initiative](https://braininitiative.nih.gov/#:~:text=What%20is%20The%20BRAIN%20Initiative,understanding%20of%20the%20human%20brain.) – [BICAN](https://brainblog.nih.gov/brain-blog/brain-issues-suite-funding-opportunities-advance-brain-cell-atlases-through-centers)
* **Specifically**: We should talk to program officer at BICAM
* (Aviv) NIH sustainable funding, more than CZI
* (Dana) NHGRI [funding opportunities](https://www.genome.gov/):
* usage is main criterion
* ["U24"](https://grants.nih.gov/grants/funding/ac_search_results.htm?text_curr=u24) – "resource grants"
* also maybe [here](https://grants.nih.gov/funding/index.htm)

* (Aviv) [ITCR](https://itcr.cancer.gov/funding-opportunities)
* also extra money for tools to work with other tools

* Sarah: country-agnostic funding. Industry involvements
* Aviv: NIH is country agnostic
* Aviv: industry-funding tends to be less stable. You need to set up an industry consortium (e.g. UK biobank). "pre-competitive", otherwise actually forbidden.
* need to talk to champions in different companies and they need to come together.

* Dana: Philantropy grants ("Schmidt futures"), industry too complicated.

### Core

Fabian: are we missing any obvious core package
Dana: core already too wide... obviously a trade-off. It should possible to support the core packages at a very high level.

What fields to cover and which people to include:
* Do they match our standards in engineering and passion