--- tags: scverse, governance, meeting --- # Link: https://numfocus-org.zoom.us/j/82205837318?pwd=537Z2ZmLBAm1o4SKGFlXKPT6bkTRBM.1 # scverse governance meeting notes * anndataR grant # 2024-04-23 ### Attendees Mikaela, Isaac, Emma, Roshan, Phil, Martin, Anna, iPhone, Giovanni, Danila, Can ## Agenda * Coordination team * Stein Aerts (Danila) * [Danila] Migrate analysis and plotting funcs to scanpy and muon. * Governance doc (Mika) * Governance doc:[Emma] Expand the document and the roles so everyone can contibute and know how and who to contact. * Developers team * * Community Engagement Team * 10x events (Anna) --> will respond and arrange the meeting * [Anna] Overall Paris --> interesting * [Anna] Patric said there is a donation that can give to scverse * [Anna] Sponsorship for scverse conf. --> Jekaterina will come back to us * [Anna] Discussion for hiring scverse buiseness related to teaching * [Isaac] Sponsorship structure via NumFocus --> pay scverse for talk/workshop * [Anna] We can propose the details during the meeting * [Isaac] Workshops only or more events? --> They want us to do more of these things --> If we come to an agreement would be beneficial. * [Mika] What about more people if they want to host a workshop? --> We should negotiate. * [Emma] Ask from companies to donate, when they ask for talks/workshops from scverse * [Can] It can be tricky to get 'paid' by someone else than your employer, atleast US people. * [Can] Ask NumFocus * Owkin hackathon (Emma) --> will respond * similar situation to latch but how do we handle it? * [Danila] Location and collaboration is great --> we have people there. * [Emma] Do we have to organize the scientific program? * [Giovanni] Spatial Data group in Paris (Pasteur) * [Mika] Date? 2024? 2025? * Conference updates (briefly) * [Anna] Website, speakers: Fabian, Ale, Angela * Registration: 1st of May * We are missing two speakers * [Roshan] will contact the next 3 speakers * [Anna] Julio? * YouTube comment (Mika) * [Can] Block comments on YouTube * Short update on NIH U24 grant (Roshan) * https://docs.google.com/document/d/15IRy4hK3W2xE0I7kfXZW-_AoyiCJS44g6zxnkLODq1Q/edit?usp=sharing * One page specific aims --> core should contribute * MSK won't be able to contribute on this grant * Hard to do the budget/salary by ourselves * We need to find a way around it or just drop it. * Not only Europeans --> we need US PI * Roshan will talk to Dana for hosting the grant, etc. --> Then we get the support. * Also ask NumFocus ## Notes # 2024-04-09 ### Attendees Mikaela, Danila, Gregor, Likas, Giovanni, Martin, Can, Phil, Isaac ## Agenda * Governance structure (Mikaela) * Ilan for core (isaac) * Also Tim for core * Joe meeting (isaac) * Next meeting * boston hackathon follow up (isaac) * Upd on discussions Stein Aerts (Danila) ## Notes * Governance: * Q: how do the different teams relate * A: core team = union of coorindation, developers and community. The subteams can overlap, but there's no further restriction * next steps: make PR, everyone to comment until next governance meeting. Formally vote on this next time. * Ilan for core * join as core dev, potentially also coordination team. * Tim for core * Tim to take over squidpy, once significant contributions promote to core team member * Wouter for core * Giovanni: He does a lot of contributions, but he's alreay in napari core so not sure if interested * retire Ila * Put to Alumni section, if he has time later on, we can promte him to core team member again * write an email to him first * offboarding checklist? onboarding checklist in reverse? * Joe meeting * What do we want to get out of this? * Can: make list of functions where "flavors" could be easily implemented to make things consistent * Gregor: Limits of reproducibility. We can't even reproduce a neighborhood graph between different CPUs, CPU vs. GPU so why would be bother with languages * Gregor: Most of the analysis steps Lior comments about are not best practice anymore * Giovanni: Better document implementation details. Making things reproducible is waste of time. * Update on Stein Aerts Lab * discuss next time # 2024-03-26 ### Attendees Isaac, Lukas, Mikaela, Gregor, Giovanni, Phil, Emma, Can, Martin ## Agenda * Core package for flow cytometry data? (Gregor) * Trademark update (Lukas) * Governance structure (Mikaela) * Intro @ Boston Hackathon (any other talks?) (Mikaela) * eoss grants? (Isaac) ## Notes * There are several different links to the governance meeting. The numfocus one is the one we want. Mikaela to fix the link in the calendar * flow cytometry: * all agree that this only works if an external person takes lead on this. * Gregor to write potentially interested people and preliminary scope of the package. Then let's see. * Governance slides: https://docs.google.com/document/d/18rWZSY0CawlDwhlgv6Ia1LHngI9Qo_GWlZsB7sFwryA/edit?usp=sharing * Phil: Who can speak on behalf of scverse? * Isaac: What is the authority of a working group? * Phil: accountability? * Gregor: who resolves conflicts as ultimate instance? * Emma: handbook for working groups for easier onboarding (calendar, notes, current activities) * Isaac: Minimum documentation for a working group – calendar event, events, chair? * # 2024-03-12 ### Attendees *Mikaela, Isaac, Emma, Roshan, Gregor, Anna, Lukas, Martin, Can* ## Agenda * Meeting agenda - ask people to put points on the agenda * Governance restructure * Advisory board meeting * 10x Paris - anyone going? * If time permits: update on NIH U24 grant ## Notes * Meeting agenda * possible to setup automated zulip reminder 1h before meeting? * sometimes there's just nothing to discuss * Governance restructure * No updates * Advisory board meeting * Summary for people not present * Benchmarks seem to be the new black - 10x proposed to offer datasets for benchmarking of methods, etc * 10x Paris - anyone going? * Anna will go if Fabian allows * NIH U24 grant * alternative: R13 grant * more for training * U24 not suitable for training, but software engineering, community building, hackathons * more like a "collaborative effort", NIH heavily involved * regular "milestone" checks * no limit on money, for 5 years, indefinitely renewable * reporter.nih.gov overview of previous grants and their applications * NIH matchmaker: chatbot that tells you which grant to apply for * reach out to program officer (PO) asap * Pauline and the Hackathon * clearly our expenctations don't align * She will go on do her thing, but without scverse branding # 2024-02-27 ### Attendees *Mikaela, Isaac, Emma, Danila, Anna, Roshan, Luca, Lukas, Giovani* ## Agenda * Governance restructure * Advisory board meeting * Paulina ## Notes * Advisory board meeting * Questions from last year: * Topics we should be addressing * Funding options * Questions * Ask for sharing previous grants * Funding models * TODO: Things to add to slides * Mikaela Community packages * Pyopensci * Add project specifics * scanpy/ anndata – isaac * Future plans * spatial – giovanni/ luca * Future work: * Kinds of packages/ adoption * Community meetings * Add topics to slide – danila * Isaac suggestion: structure as community, technical, funding * * U24 grant ([slides](https://docs.google.com/presentation/d/1aPLRPvIxidtC1sOAiIFzhik3n6cnjnsJvosoO0-dG20/edit#slide=id.g2bc80cf0b02_0_0)) * LOI due 60 days prior to application * Due dates: Jan 25, May 25, Sept 25 * Eligibility also fine probably * Organization registration takes 6 weeks * We should figure out which organizations would get funding soon * Giovanni: we should try and get an example of this grant from someone else * For pres, ask for sharing previous grants – have a small overview of this * # 2024-02-13 ### Attendees *Mikaela, Isaac, Emma, Danila, Anna, Can, Giovanni, Lukas, Martin* ## Agenda * Governance restructure * numfocus meetings * conference: * speaker ranking * legal signatures * Paulina (Standford hackathon) ## Notes * Meeting for gov restructure on Thursday * TODO: Make sure everyone in scverse org is on a group/ calendar * Numfocus meetings * Lukas will attend next project/ staff meeting * Town Hall slide deck and transcripts: https://github.com/numfocus/TownHallCommunityFeedback/issues/3 * Conference * Documents for signing – probably ask numfocus * Speaker ranking * Isaac: Suggests having talks * Paulina * More enthusiastic that we were expecting * Martin may be able to go if on a sunday # 2024-02-02 Management committee meeting ## Feedback * Tracking metrics on website * BMBF funding calls recently out that we should look at? * NIH funding * Like to keep the money in the US * One european PI works fine * SAIL could * NHGRI possible funding opportunity * Dana Suggests https://grants.nih.gov/grants/guide/pa-files/PAR-23-124.html * * Expanding * Fabian: good to expand internationally, not just within europe * AACR workshop Roshan Last comments form Fabian: > or using one of upcoming CZI meetings, too > good point w scverse conf, too or using one of upcoming CZI meetings, too > plz send around dates for these to PIs too to have them advertise on slides - I usually put an scverse ad, anyway > (oh and i *love* the booth idea at scg) ## Follow up meeting # 2024-01-30 Attendees: Mikaela, Iphone 12 mini (giovanni), Lukas, Danila, Emma, Anna, Martin, Can, Isaac ## Agenda * Core members: Emma * Tim * Emails * Management meeting friday * scverse conference - should we move the currently blocked dates? * pyOpensci ## Notes * TODO: Start onboarding process for Emma * Start looking at governance project * Management meeting * Grants * NCI * Roshan & Dana * BMBF (Can) * Hackathons * Industry contacts * Conference * Meeting frequency * Consulting/ Sponsoring * Vision # 2024-01-16 Attendees: Lukas, Isaac, Gregor, Giovanni, Martin, Luca, Phil, Roshan, Can ## Agenda * Happy new year! * Goals for 2024? * NIH grants * scverse business * scverse email accounts * board meetings * media/ outreach strategy ## Notes * 2024 goals * Get fancy pants big NIH grant * scverse conference with blackjack and talks * 2 Hackathons of which at least 1 is in the US * -> define goals for individual projects * NIH grants * Fabian wants to ask Dana in February * Roshan has applied for a R25 recently (not recieved) but has some foundation for applying * scverse business * Fabian doesn't want Theislab consulting but scverse consulting * Is happy to try to organize (VC) money to get started * Wants to involve Alex Wolf because of industry contacts * Wants to meet with Isaac, Anna, Alex, me * Lukas does NOT want to do anything without scverse approval * (D) happy to get involved more actively! maybe we need a pilot run with *some* structure and a company? * (Gio) Start with some pilot structure * (Gre) Start with free-lancing * media/outreach * more people/structure? * more blogposts? * Presentation for Advisory board meeting * https://docs.google.com/presentation/d/1Np4CpY42ToZ8ieOolm1E_cBi9PBT8ENfVvoAgSrmrHQ/edit?usp=drive_link * TODO: * Prepare project goals * Set up working group on governance and adding more people * Lukas: setting up dates * Isaac: getting email set up * Roshan: Talk to Ushma about NIH/ NCA grant # 2023-12-05 Attendees: *Isaac, Gregor Mikaela, Anna, Danila, Martin, Lukas, Ilan* ## Agenda * Hackathon recap * Follow up * Project summary doc * conference * [Quick decisions](https://docs.google.com/document/d/1bweO7ufiA4b8unouwnuoXpc2Pb3oJlk_2UrxKeGBnRA/edit#heading=h.tupi6zal09dd) * Grants * ECCB ## Notes * Where's Roshan? * Try to follow up with Anna/ Phillip * Ilan says hi * Hackathon recap * [Summary doc](https://docs.google.com/document/d/1tEYVZEu9E0xrB6I9YwAckZC6YZX9LxaUKtLW1BXGU2s/edit?usp=sharing) * Looks good! * TODO: set up a follow up call with local organizers (Mikaela) * Hybrid: * talk to nf-core how it went with distributed event * Organize earlier (at least fix dates and write invitation letters) * Conference * Prices: room specific prices * EUR 266-586 * Food may be weirdly expensive * Fabian: * Probably keynote, opening okay * Costs * How much can we cover for invited speakers? * Hackathon / core stuff after? # 2023-11-07 Attendees: *Mikaela, Gregor, Giovanni, Anna, Isaac, Danila, Martin, Luca* ## Agenda * towards `ImmuneData` - Do we need new data structure for AIRR data? * Cambridge hackathon * Conference planning ## Attendees ## Notes * Cambridge * Stickers? * contact Jim on numfocus slack * CZI meeting * numfocus * "Immunarch" data loader * Maybe someone will be working a new datastructure for this? * Vadim Nazarov may be working on specs and implementation here * Awkward array AnnData PR * views of awkward arrays need to be initalized on view creation * issue with garbage loading? Isaac to double-check and/or merge * scverse conference * Trouble with room finding – some cost at TUM * Looking for speakers * Focus and overlap * Probably do invites after finalizing location * Ilan joining * Maybe joining in cambridge? ## Follow up - [x] Get giovanni on numfocus slack - Invite sent - [ ] # 2023-10-24 ## Agenda * hackathon * conference? * pyopensci updates * google workspace * Testing downstream * grants? ## Notes * Hackathon * Talks? * ~2hr flash talk session * Are invites out yet? * Yes, people should hear back from friday * Conference * Anna is in touch with TUM regarding rooms * Other conferences * June 10-12th https://coursesandconferences.wellcomeconnectingscience.org/event/single-cell-biology-20240610/ * Sept 16-20th https://eccb2024.fi * TODO: * [Anna] Start doc on potential speakers? * [Mikaela] Set up monthly meeting for planning * pyopensci updates * Need editors * Lukas + Gregor * editor checks if package is elegible for the community (data structures etc. ) * Can start with review for Davide * Need to recruit * Have some way to review packages * pitch it at hackathon * Mikaela: there was interest when this was pitched at 10x * Google workspace * TODO: Isaac and Danila will talk this week * Can Ergen-Behr * Postdoc with Nir * Doing large scale genetic info * Previously doing some spatial stuff * Interests * Data loader from scvi tools * SpatialVI tools * Testing downstream packages * Please ping * tooling in the future! * Grants EOSS * scvi tools + scanpy and anndata * Grants NCI * Big! Soon! * HTAN hackathon coming soon! * # 2023-09-26 ## Agenda * pyopensci collab * Conference * Monthly meeting * Room in Munich * Dates? * CPH update * numfocus updates * Hackathon * Send out invites * eurobioconductor update ## Notes * pyopensci * integration, would we be up for this? * Can we find enough reviewers? * 1 core person for review * Lukas: can we do a trial period * Generally would * Isaac: lessons from bioconductor * Originally only core team * Source of CoC complaints * Mikaela: main point is making sure it's maintainable in the future * Pilot: * Can we start with some current packages? * schist? * Mikaela will follow up * Conference * September 2nd week – 9, 16, 23rd * due to oktober fest maybe 9th * Length * more or less 3 days * Maybe 1.5 days workshop + 1.5 days of talks * Alternatively, half day workshop + half day talks every day * Room * ez in copenhagen * TUM may charge 10% for setting up stuff * bioc * Expenses: * flying in speakers * Sponsors for bioc * just posters * We could do talks for something like 10x? * Numfocus updates * Anna: pilot programs * social aspects for projects * forming a company, training * scverse llm * open teams * funding * direct support * tiers * in kind contributions * Meetup in munich * EOSSS * Mikaela * Hackathon * Spot distribution * 30-35 max * 10 core, 15 from sanger, 10 open invite * Potentialy ask for motiation through a GDoc for open spot people * Consider 10-20€ to cover for no shows or ask for hotel confirmation * Likely not needed because we know more or less everyone? * Also complicated to set up? * Just post the zulip link on linkedin, twitter, ... * Grants * EOSS * LOI is Oct 17th * Zarr * Training & Diversity * Wouter – Napari? * Bioc – Travel and hackathon + interoperability * Data insights * * Something bigger? * NCI: * Cancer * francesca, da'na, nils * * Advisory board meeting * * Follow up: * Talk to nolan about training/ business * Talk to nolan about sponsorship * # 2023-08-29 * Governance model: https://github.com/scverse/governance/issues/56 # 2023-08-22 ## Agenda * Review issue board * Hackathon Cambridge * Package review and pyopensci * Numfocus agreement ## Notes * Conference * Organizing a scverse conference * Finding dates, waiting to hear back on SCG and SCOG * NumFocus events: Want to organize 6 months before * Figure out if we want to make money from conference * Isaac: Survey? * Sponsorship? * Danila: not hybrid? * Not hybrid * Cambridge hackathon * Set up a meeting for this * Package review * Lukas: can be a bit more serious * Editors can be hard on getting things done * Like 30 min * Bioconductor * Follow up: probably worth it # 2023-08-03 ## Agenda * Finance - who decides show to spend money and what we reimburse? Simple process? (LH) * Board meetings polls (LH) * Governance structure * Board members that don't do shit * ## Notes * Finance * Approval structure for spending * Async * $100 limit on when you should have a wider vote * Must request 3 working days before * Board meeting polls * Finally sent out polls for schedeule meeting polls * Question from Mikaela: what are these meetings for * Governance structure * Topics * steering council role * governance team * Ideas for responsibilities * Funding, how things are run * Maybe liquid democracy: people can donate their votes to others they trust to allocate them * Core + community team * Chair structure for core teams * E.g. representative who show up to governance * Multiple * Rotation of chairs * Summary * Pro subteams * gov has representatives selected/sent from subteams * We like some level of rotation for executive positions * Recognitions * Having titles, reported/ validated by governance team * Publications? * Something more than every ten years nature subjournal, maybe reports from events? * Expanding * Onramps for * Especially towards less represented * Follow up * Finance stuff (@Lukas) * Document how this works * Make sure names of people on the open collective are available * Remind PIs about board meetings * Ping people about governance * Anna will talk to CZI about DEI initiatives # 2023-07-18 ## Agenda * Review action items * NumFocus meeting in sept * Funding follow up * Core team hackathon * Giovanni HCA * Anna Meeting about teaching ## Notes * Introduce Luca * Hackathon orga * Giovanni * TODO: Document of what we're working on * Update your repos with numfocus info! * Did we send contact info to numfocus * numfocus meeting in sept * Anna + Isaac * Funding * Sanger hackathon * Dates? Still a little unclear. * Multisample condition * Scalability? * Maybe differential expression * Giovanni: HCA * scverse not well represented * data: scalability * especially around imaging * foudation models * People are excited * Discussion of transformer foundation models * Teaching: Anna * Core teaching role * Funding for teaching * Possible paid things through numfocus * Who would like to be involve in teaching? * Mikaela * Lukas * Isaac * [Mikaela question] Who makes disseminates/ creates teaching materials * Core team * Are there people who we'd like to reach out to? * [Giovanni] Shalek group/ capacity building in CZI * Mark Sanborn * ISMB: * Luca Marconato + Mikaela ## Action items * Ping sanger people about getting hackathon set up * @ivirshup start one page on funding * Check in on who's interested in teaching * @anna create proposal for teaching role # 2023-07-04 ## Agenda * review action items from last time * proposal: track tasks for core team using issues and kanban board (private or public?) * reason: it's hard to keep track of TODOs in zulip conversations and it's often unclear who is in charge of resolving them. * action items in these meeting notes can link to issues * Governance models follow-up * https://docs.google.com/document/d/1oYLRoCRHkWVd-qBmeQPng35pqWjCcE2HxRz1yYIwXXs/edit?usp=drive_web&ouid=108290132614903375205 * wait for Arliss to come back to us * Community team * events * August core team hackathon? ## Action items - See https://github.com/orgs/scverse/projects/24/views/1 ## Notes * Community team * Conference * Target audience? * Workshop/ tutorial for users * Hackathon for dev? * 1 year time? * Munich? * Copenhagen? * 2 years of * fix date now-ish # 2023-06-06 ## Agenda * review action items from last time * advisory board meeting and management team meeting * onboarding Mikaela, Anna, (Martin -> anything missing?) * announce on twitter * offboarding Adam (numfocus?) * numfocus (https://hackmd.io/wH8CVp5GQ2aA2GQO7vjzAQ) * PyData conferences * swag * zoom * updates on governance structure? * numfocus offers help on governace structures * Grants deadlines ## Notes * Ilia will remain core developer but not involved in governance * Isaac: CZI workshop about data loaders ## Action items - [ ] DB: (postponed) reach out to SnapATAC devs to find alignments - [ ] Logo with font: Danila and Mikaela follow up on this - [x] Isaac: add new core team members to core-team@scverse.org - [X] Lukas follows up on board meetings - [ ] Remove access for Adam as appropriate - [x] github core team - [x] add to website - [x] add to core-team@scverse.org - [x] add to zulip - [x] add to password manager - [x] add to google drive - [x] Announce core team changes on twitter - [x] Add new core team members to core+PI channel - [x] Mikaela replaces Adam in numfocus committee - Organize meetings with NumFOCUS representatives: NumFOCUS Developer advocate - Governance structures - Gregor + Lukas + Danila NumFOCUS Business (first?) - Lukas + Anna + Isaac X? - [ ] Contact Business Director NumFOCUS Events - Anna, Isaac (Gregor if available) - [ ] Loop in Emma into a meeting with the events team for the hackathon - [ ] Plan a hackathon at the west coast for 2024 - [ ] Plan a conference in Europe in 2024 NumFOCUS Marketing/Social Media/Corporate design - Mikaela, Anna, Gregor (Lukas, Danila if available) - logo/slide deck - swag - tutorial thumbnails - advice on social media campaigns NumFOCUS Operations - Isaac - [ ] zoom - [ ] domain # 2023-05-09 *Attendees: Lukas, Giovanni, Martin, Adam, Gregor, Danila* ## Agenda * Additional core team members * advisory and mgmt board meeting? * logo? ## Notes * Additional core team members * see notes from 2023-04-26 * should we consider Daniel Dimitrov instead of Pau? * DP: Add Luca as core dev because of SpatialData * Discuss proposal to separate governance function from core team member function. * advisory and mgmt board meeting? * Sabine is on holiday and will follow up after the holiday * logo * we use black-and-white logo for now * we should make a logo + «scverse» text * community meeting next week about genomic ranges * Grants: * discuss at management board meeting * might be worth following up on the Bioconductor grant sooner ## Action items - [x] IV, GS: reach out to Mikaela - [x] LH: reach out to Anna Schaar - [ ] DB: reach out to SnapATAC devs to find alignments - [ ] DB: talk to Ilia if he is still interested in being a core team member - [x] GS: ping Phil because of scverse PyPI organisation - [x] GS: tweet about community meeting # 2023-04-26 *This meeting takes place offline at the hackathon in Heidelberg* *Attendees: Isaac, Lukas, Giovanni, Luca, Martin, Gregor, Danila* ## Agenda * Martin onboarding * Additional core team members * https://scverse.zulipchat.com/#narrow/stream/315186-core-team/topic/scverse.20sustainability * https://scverse.zulipchat.com/#narrow/stream/315186-core-team/topic/Potential.20new.20core-team.20members * advisory board meeting * management board meeting * numfocus --> anything pending? * reducing the bus factor (who can release critical patches, PyPI org, ...) * improving outreach and social management * solidifying roadmaps * how to reduce the number of stale issues * how to improve branding & recognition * post a blog post now? ## Notes ### Martin * mailing list * Martin is now officially a core dev * github org * -> make list for future members ### Clean up core team members * Alex removed * probably remove Ilia, but talk to him first ### New core team members * Mikaela (outreach) * Gregor + Isaac talk about meeting organization * Anna Schaar (teaching) * Teaching (Lukas) * Pau * Core developer (still rethinking core packages, see below) * talk at hackathon * SnapATAC2 * -> Isaac and Danila reach out * Core packages rethink * "core maintained" & "community maintained" labels (LH + GS) * Splitting data structures and frameworks -> allows us to be more loose for framework requirements * Potentially we'll ask other packages to move over to the scverse organization that might explicitly NOT be core maintained ### Meetings * LS and GS organize adivsory board and management board meetings ### Bus factor * PyPI org - unanimous yes * We need to schedule releases # 2023-04-11 *Attendees: Martin Kim, Adam Gayoso, Giovanni Palla, Danila Bredikin, Isaac Virshup, Lukas Heumos* ## Agenda * IO packages * scverse meeting on genomic ranges * hackathon prep * Paper is out! Merge citation PRs. Make noise * AnnData 0.9.0 release? Advertisements? * Follow up from last week ## Notes * Introduction for Martin * Hackathon org: * Spatial * OME-Zarr reader in R * Napari things with Kevin * Lukas: Knowledge graph side of things * IO packages stuff (a little) * Knowledge graph * Small issues * Danila: * R interop * Factor models stuff * Adam: Could scvi-tools pyro infra be used here. e.g. [LDA](https://docs.scvi-tools.org/en/stable/tutorials/notebooks/amortized_lda.html) or Cell2location * Isaac * Interoperability * Annotations * Gregor * IO packages * General clean ups * Doing something on the last day * IO Packages * Maybe one package for everything except spatial? * Metadata: maintaining schemas * Genomic Range meting * Still on for next week * We can hae another in May * Danila * Scaling * downsampling * Seurat v5 * https://imbalanced-learn.org/stable/ * # 2023-03-14 *Attendees: Giovanni Palla, Gregor Sturm, Adam Gayoso, Isaac Virshup* ## Agenda * Numfocus * Sustainability (https://scverse.zulipchat.com/#narrow/stream/315186-core-team/topic/scverse.20sustainability) * Fabian: > we need to think though what our *ask* is, ie what would be need and do with say more software engineers, community manager etc ## Notes * Numfocus * Lukas sends reminder * Sustainability * Adding more people * Social Media activity * Blog post Danila: should be [pretty close to go](https://docs.google.com/document/d/1CFgZUNDrFSnKGFxh-rTTtbHlABm6EBzgrj3byzfNIOs/edit) * Mailing list * Talks at meeting (Gregor could maybe use help) * reach out to people who submitted ecosytem packages * Geography * everything is EU-based currently * we should increase our presence in the US * rest of the world? * Other involvement * regulatory genomics * scvi-tools * New people * Maren (scvi-tools) * Ask PIs to invest * every management committee member should fund a core-team member * otherwise they should move to advisory board * it seems weird if therer are management committee members who don't have a core developer * Follow up * with GHGA * Add scvi-tools core member * Ask PIs for involvement at next meeting * We should do announcements of ecosystem packages * We should announce ecosystem packages as a concept * Let's use the next package added as proof-of-concept * Presentations at meeting * Ask people to contact gregor if they would like to present * potential future core team members * snapATAC2 * Anna Schaar * Karin Hrovatin * Emma Dann [-> hackathon] * Mikaela * Saez-Lab [-> hackathon] * Luca Pinello's lab * Talk to saez lab at hackathon * Find date for managment committee meeting [Lukas/Isaac] * Find date for advisory board meeting [Lukas/Isaac] * Projects * Data loaders * Pytorch loader * Graph/ pytorch loader * Scanpy 2.0 # 2023-01-17 *Attendees: IV, AG, DB, GS* ## Agenda * Paper * Numfocus recap * Tutorials website * Hackathon(s) * Open meetings * Blog announcement * AnnData awkward arrays ## Notes * Numfocus - submitted * Paper * Finish up sentence, then lock on paper for 2 tomorrow * Write response to editor * Hiring * For reaching out further, a position would be good * Health AI institute in Heidelberg: https://www.aih-cluster.ai/ * Tutorials website * What needs to be done * Basic tutorial (Isaac) * Adata mudata for beginners (Danila) * Axes (Danila) * How do we frame the tutorial website on the `/learn` page * Currently blocking by just the content * Required for announce: https://github.com/orgs/scverse/projects/6/views/1?pane=issue&itemId=15881770 * Other hackathon follow up * Ask for feedback (Lukas) * New hackathon (Heidelberg) * Saez Rodriguez quite positive about us * Danila follow up: timeframe, preference on topic * Open meetings week after next (Isaac announce thursday) * Blog * https://docs.google.com/document/d/1CFgZUNDrFSnKGFxh-rTTtbHlABm6EBzgrj3byzfNIOs/edit * "What have we done" * Roadmap * Advisory board meeting * Hackathon # 2023-01-10 *Attendees: Danila, Lukas* ## Agenda Numfocus application # 2022-12-13 *Attendees: AG, IV, GS* ## Agenda * US Hackthon? * Follow up from hackathon * Dev onboarding * Numfocus ## Notes * Dev onboarding for core * @Adam take lead on pushing the process * US hackathon * Updating packages, cookiecutter-izing * Remote hackathons also good * nf-core – hybrid * April/ May? * Topics * https://github.com/scverse/governance/issues/32 * Should be paired with other event for europeans to participate * Hackathon follow-up * next time ask people to add PR links to hackmd (for better reporting) * Blog post? Would need to collect results – Aim for in a month * What's needed for tutorials to go live: * Overview page (GS) * Review of PRs * We should have a project tracking what needs to be done (IV) * Rendering? * currently on GH actions. AWS runner eventually? * numfocus * Did another pass, try to send out end of the week? # 2022-11-29 *Attendees: Isaac, Giovanni, Gregor, Lukas, Danila* ## Agenda * numfocus * Hackathon * Decide on platform for executable tutorials * Meetings * Ecosystem listing * What goes into the authorship field, are we checking with authors before adding them * New packages ## Notes * numfocus * Jan 15th numfocus * https://numfocus.org/projects-overview * Roadmap biggest missing part? * Send an enquiry – @ivirshup * Draft email to organizing comittee – @ivirshup * Meetings with management committee? * Idea: regular meetings with management * Come up with agenda? * Time to lobby for what we need * Frequency * Hackathon * Decide on platform for executable tutorials * For running: colab vs binder * Environments: * binder: yaml * colab: in notebook * What's the priority? * Danila says both were easy * Lukas creates sheet where participants can assign themselves to tasks * How are we rendering/ executing notebooks? * myst-db? * jupyter-cache * scverse-tutorials repository (@grst + @ivirshup) * Meetings * Next year, open meetings this time slot? * Private meetings once a month * Alternating * Announce discourse, zulip, twitter(?) * Epigenomics agenda? @danila * Is it a governance meetings * Ecosystem listing * What goes into the authorship field, are we checking with authors before adding them * Emails? Emails would be good * Also number of authors? * Danila – how does bioconductor do authors/ maintainers? * Approval of authors – from now on * New packages # 2022-11-15 *Attendees:* GS, AG, IV, LH, GP ## Agenda * Hackathon * Paper * Last call * Package listing * Add `decoupler` * Open meeting ## Notes * Hackathon * Francesca – Getting dinner + catering * We should send out email * Gregor will send * Should have link to program * Decoupler – finish * Discuss more, some on zulip * Packages * add a few more Theislab packages * scvelo, scCODA * Email to ask for permission, but it's a small # so good to go ahead * get rid of support level statement - [ ] Lukas: add more packages - [ ] Gregor: merge as many PRs as possible # 2022-11-01 *Attendees:* ## Agenda * Paper (!!!) ([v2](https://docs.google.com/document/d/1nQr6fhDHmRbAkyiSE-TAGetuffXi6VfbDw0fE1yXG5s/edit#heading=h.1yclwrv1xnl4), [response to reviewers](https://docs.google.com/document/d/1b453zyuwQnmatjfzRJcSOk5fWs3HFqkR9qplJjoCuOY/edit#heading=h.5d0xlwmhz2au)) * Review of status * What's left to do * Are we cutting anything from the response (package listing?) * Hackathon * How are we on partipants, how are we going to contact them * Open meetings * Isaac would like to scheduele an open meeting for this time next week ## Notes * Things from review to resolve: - [x] How are we responding to interchange? https://docs.google.com/document/d/1b453zyuwQnmatjfzRJcSOk5fWs3HFqkR9qplJjoCuOY/edit?disco=AAAAhMXxEMs - [ ] merge anndata doc change and link to it - [ ] How are we including a listing of all dependent packages? Supplemental with zenodo?https://docs.google.com/document/d/1b453zyuwQnmatjfzRJcSOk5fWs3HFqkR9qplJjoCuOY/edit?disco=AAAAhMXxEfg - [ ] A table? - [x] Mikaela authorship? - yes, unsure of blob vs named - [x] Whats up with the package listing? https://docs.google.com/document/d/1b453zyuwQnmatjfzRJcSOk5fWs3HFqkR9qplJjoCuOY/edit?disco=AAAAhMXxEfc - We'll go for it - [ ] Danila will make a pull request for viz - [ ] Add packages (need to figure out testing) – follow up on zulip - [ ] Comparison/ collaboration with bioconductor: https://docs.google.com/document/d/1b453zyuwQnmatjfzRJcSOk5fWs3HFqkR9qplJjoCuOY/edit?disco=AAAAg66oJWo - [ ] In the response * Timeline * Thursday next week # 2022-10-11 *Attendees: GS, AG, IV* ## Agenda * Ecosystem * Template * When * Paper ## Notes * Template * Cruft is last PR * Lukas was going to review, is on Holiday * Runs from inside project * IV: Do we want centralized control of bot? * GS probably too much work * Maybe when we centralize for testing * Adam: write tweet * Ecosytem * https://github.com/scverse/ecosystem-packages * https://docs.google.com/document/d/1jcuDTHDY27Ga_COLYwDFdS0z5L1WJsO-IBjWU1UTDzo/edit * README ready to merge * For the paper: whats on the ecosystem listing is different than the ecosystem * `Yaml` * Website * table * AG: Learn page should show more of ecosystem * Paper TODO: * Package inclusion: * Ecosystem packages # 2022-10-04 *Attendees: IV, AG, GS, GP, DB* ## Agenda * Advisory meeting * SCG * Announcements * `cookie-cutter` * `SpatialData` * Package listing (https://docs.google.com/document/d/1jcuDTHDY27Ga_COLYwDFdS0z5L1WJsO-IBjWU1UTDzo/edit#) * Paper * Innsbruck Hackathon (https://docs.google.com/document/d/1qEX8-qz--cQjfdJgg44FMt8zwMu-310wDhHF2Ra5oz8/edit) ## Notes * Advisory meeting – Presentations * What are we * Paper * Things we've been doing * Governance * Community efforts * SpatialData * Grants * Goals of the meeting? * Time for feedback from the Advisory committee * Future directions * We would like to get input/ opportunities from them * How can we sustain this? * How do they think we can use this? * Current problems * Money * Are the problems that we're addressing the right ones? * Adam – How this could work * 15 min what we've been doing * How do we want to grow, funding * How we're trying to get these things done * Isaac – Scientific work * We should say what we're trying to achieve on scientific topics * Topics to discuss * Giovanni – SpatialData * Gregor – nf-core/ TCR, BCR * Danila – Epigenetics * Genomic ranges, collaboration * Goverance, funding * Topic for anndata scaling * TODO: Google slides for next tuesday * SCG * Conflicts with meeting * SpatialData blog post (Giovanni) * Roadmap + technical docs * Also slide from Fabian * Adam: https://newlimit.notion.site/ * https://scib-metrics.readthedocs.io/en/latest/index.html * GP: Announce cookie-cutter? * Should be one afternoon of work * `cruft`: should be last thing * AG: flake8-docstring problems * Private repos * pre-commit, codecov don't work on private * Document how to turn off * Package listing * As reponse: * Ecosystem website + number of dependents * Website * Structure of YAML file * PR template for submission * Structure of yaml (https://docs.google.com/document/d/1jcuDTHDY27Ga_COLYwDFdS0z5L1WJsO-IBjWU1UTDzo/edit#) * Tags * GS: Tags from scrnatools database * GP: Controlled vocab important * Non python packages * Mandatory: docs, tutorials, tests * Who is following up: Isaac, Gregor, Adam(?) * Website work * Danila – some time next week, react component * Paper: * Rebuttal: Giovanni * Innsbruck 8th-9th * Fixing tasks, who to invite * 15-20 probable, maybe 25 * Add people here: https://docs.google.com/document/d/1qEX8-qz--cQjfdJgg44FMt8zwMu-310wDhHF2Ra5oz8/edit # 2022-09-06 *Attendees:* IV, LH, GS ## Agenda * SCOG event * Grant 😢 * hackathon * Stale issues * Governance meeting alternative time slot * UDMs and newsletter * (users & developers meetings) * HiWis ## Notes * SCOG: * Core projects + people * Goals * Future value * Workshops * Hackathon – maybe not? * Spatial * Regulatory genomics * Grant * Could review? * Hackathon * Innsbruck possible? * Some money if it touches e-learning? * Topics: * Tutorials * Try and figure out at least 6 weeks before * We will discuss in more detail at next meeting (Gregor) * Stale issues * There is a bot in the debug mode * Action that labels and action that closes * New time? * User developer meetings * End of september * Next meeting: move to 27th? # 2022-08-23 *Attendees:* Isaac, Gregor, Lukas, Giovanni ## Agenda * bits-in-bio Q&A * community * scverse hackathon for SCOG - is this really happening now or not * Can we get better at closing issues and merging PRs * e.g. stale bot * a clean issue board serves as a public road map * if we want outside contributions we'd better be good at reviewing and merging PRs timely * Meeting with advisory board - SAVE THE DATE -> 24.10 from 5 to 6pm CEST ## Notes * Close old issues for hackathon (See also [list of hackathon ideas](https://github.com/scverse/governance/issues/32)) * https://github.com/scverse/scanpy/issues/1600 * https://docs.google.com/spreadsheets/d/17rIvO3K8pKaRBaUar56YCH-eonryaDT3SkJmO-M68Ck/edit?usp=drive_web&ouid=102785425634284408370 * TODO: * Specification * "needs info" tag * Implementation * Org level labels: * "needs info", "stale" * Hackathon * Need alternatives! * Over next two weeks, collect these, then vote! *
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scverse community meeting notes

scverse community meetings have an open agenda. Feel free to add any points you’d like to discuss ahead of or during the meeting! We usually start off with a ~5min flash talk about new ecosystem packages or other recent developments in the community. If you would liketo present at the meeting, please reach out to Gregor Sturm via the scverse Zulip.

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