Skip to content

INDEX.md

Latest commit

 

History

History
529 lines (479 loc) · 33.1 KB

INDEX.md

File metadata and controls

529 lines (479 loc) · 33.1 KB
Raw

INDEX — talks and reusable slides

A catalog of every talk in this repository plus a topic-wise lookup of where to copy slides from when authoring a new deck. Pair this file with SOUL.md (mission/style) and CLAUDE.md (authoring workflow).

Slide IDs use the form <file>#section-<n>[/sub-<m>] where n counts top-level <section> elements in the source file (1-based). When a top-level section has vertical sub-slides, sub-m counts those (1-based). This matches reveal.js's URL-fragment numbering: #/<n-1>/<m-1>.

Per-talk inventory

Shelved drafts and outlines that are not currently being prepared for a venue live under _backdrawer_/ and are listed in the Shelved (backdrawer) section below the active inventory. Cross-references in the per-topic lookup point at the shelved path (_backdrawer_/<TALK-ID>.html).

2026-usrse-con-talk.html — [WiP] Reuse, Compose, Extend, Standardize, Automate: Two Decades of RSEing Open (Neuro)Science at CON (draft)

  • Venue / date: US-RSE'26 (proposal-stage draft; title carries a [WiP] marker in the tab and on the title slide).
  • Spine: the five-verb spine (Reuse / Compose / Extend / Standardize / Automate) plus a "Reuse, in reverse" coda, an Automate section (with the meta-automation handoff), and an HI+AI close.
  • Reusable highlights:
    • Title slide (per SOUL.md §3).
    • "Two decades, five verbs" intro slide (NEW).
    • "When it began for us" verb-tagged timeline (NEW; extension of 2024-distribits-datalad.html § timeline; Automate milestones include 2007 PyMVPA-with-CI, 2016 ReproIn/HeuDiConv, 2019 dandiset auto-mirroring + con/tinuous).
    • Reuse: NeuroDebian + PyMVPA blocks borrowed from 2022-nih-compcore.html; con/citations-collector added as the modern continuation of duecredit.
    • Compose: DataLad sandwich mermaid + extensions diagram from 2024-distribits-datalad.html; registry stats from 2025-distribits-YODA.html; small-units table referencing ReproIn / HeuDiConv / NeuroConv / con/nwb2bids / ReproStim / ReproNim-containers / con/duct.
    • Extend: a NEW "From RUNCMD to BEP028" mermaid summarizing the upstream-lift pattern.
    • Standardize: BIDS slide + BIDS-minder image (from 2023-bids-dicom.html) + LinkML/concepts.datalad.org bullets.
    • Federated archives slide (DANDI + EMBER + OpenNeuro) with DANDI deep-dive borrowed from 2023-brain-dandi.html.
    • "Reuse, in reverse" 3-up table (AnnexTube / mykrok / con/serve).
    • Automate section (NEW): 4 slides — opener + "Where we automate" table (CI / con/tinuous / ReproNim-containers / acquisition / archive mirroring / validation / releases) + "Cost: harnesses, harnesses, harnesses → meta-automation via AI" (with con/skills / con/yolo) + "The five verbs climb the SciOps ladder" mapping (5-verbs ↔ SciOps L1–L5; the SciOps paper itself names BIDS / NWB / DataLad / DANDI / brainlife.io as Level-3 exemplars, and reserves Level 5 — Optimizing — for AI-in-the-loop). Hands off into HI+AI.
    • HI+AI section: opener + "Why every layer matters now" (STAMPED + SciOps) + "HI ↔ AI — every project picks its own policy" (NEW): 4-stance spectrum table (Reject / Accept-with-disclosure / Spec-driven AI-generated / Autonomous) with OSS exemplars + CON projects + SciOps level + STAMPED principle, citing ICMJE Jan 2026 and melissawm/open-source-ai-contribution-policies. Pointing to 2026-ca-origami-retreat-aicoding.html as the deeper-dive companion.
    • MVC mini-section (NEW): 4 slides — opener + Models + Views + Controllers — placed between HI+AI and the Monday checklist. Models row covers BIDS / NWB / DuckDB-hive layouts + LinkML / pydantic / JSON Schema / SHACL metadata schemas + DataLad storage; Views row includes a dedicated Schema-driven UIs row (vjsf → DANDI meditor; shacl-vue → forms and research-group websites; Hanke et al. LinkML workflow ReproTube reference); Controllers row carries the punchline (pick any cell — Model, View, or Controller — and swap it; the rest still works). This block is the seed of the (now shelved) _backdrawer_/202x-mvc-stack.html stub.
    • Standardize section's "Metadata: schemas as first-class citizens" slide (NEW): expanded from a LinkML+concepts.datalad.org one-liner into a multi-language schema overview (LinkML / pydantic / JSON Schema / SHACL); also names OBC (Open Brain Consent) as the consent layer of standardization.
    • Monday checklist: 6 entries (was 5) — added an Automate take-home pointing at con/tinuous.
    • Monday checklist (NEW; 5-action wrap-up).
    • Acknowledgements + Yoda SVG sign-off.
  • Notes: drafted in support of 2026-usrse/talk-proposal-draft.md. Companion files in 2026-usrse/. QR code TBD; uncomment the data-src line in the title slide once the live URL is published.

2026-ca-origami-retreat-aicoding.html — A few words of intro into AI assisted coding

  • Venue / date: CA Origami Retreat 2026.
  • Spine: AI-coding ladder + spec-driven workflow + CON tools.
  • Reusable highlights:
    • Title slide with Avogadro Corp book reference (intro hook).
    • "Reality Check" disclaimer slide (idiocracy GIF).
    • YODA-Beyond-Code-and-Data table (traditional vs. expanded YODA scope).
    • con/serve "The Vault" mermaid diagram (inbound / hub / outbound).
    • AI Coding Maturity Ladder Levels 1–5 (Chat → Mid-loop → In-the-loop → On-the-loop → Multi-agent).
    • 5-Stage Development Loop mermaid.
    • Mapping table: Vibe coding vs. Spec-driven vs. Compound engineering.
    • Spec-driven tools ecosystem table (spec-kit / OpenSpec / Compound / LAD).
    • AI-assisted projects table (mykrok, AnnexTube, con/serve, citations-collector, dandi-cli).
    • Reusable-skills table (con/skills repo).
  • Notes: planning notes in 2026-ca-origami-retreat-aicoding/PLAN.md, rendered checkpoint screenshots in the same directory.

2026-repronim-YODA-BIDS-webinar.html — ReproFlow & YODA: Structure your studies

  • Venue / date: ReproNim Webinar, 2026-02-06.
  • Spine: YODA principle-by-principle deep dive with BIDS framing.
  • Reusable highlights:
    • The full YODA principles canon (yoda-principles-reordered.png).
    • Principle 1: Version control everything — Why version control? table with PhD Comics 1531; VCS-as-experiment slides; datalad run walk-through; datalad rerun; "datalad runs in the wild" registry statistics; git-annex addcomputed; con/duct.
    • Principle 2: Portable compute environments — software-container families; datalad-container; ReproNim/containers; datalad containers-run; clean-record CEREBRA/MRIQC.
    • Principle 3: Modular composition — modules-and-layouts ladder; BIDS as layout; OpenNeuroDerivatives walkthrough.
    • "Look up you must not!" corollary slide (pics/yoda-do-not-look-up.png, pics/depends-on-untracked-file.png).
    • Reality Check / disclaimer slide pattern.
  • Notes: companion materials in 2026-repronim-YODA-BIDS-webinar/{notes,planning}/.

2025-distribits-YODA.html — Pragmatic YODA: principles and their wild life encounters

  • Venue / date: distribits 2025, recorded https://www.youtube.com/watch?v=EuKVapscUQ4.
  • Spine: same YODA spine as the 2026 ReproNim webinar — older but shorter; many slides identical and reused there.
  • Reusable highlights: see ReproNim entry above; this is the parent of that deck. Use either as a source for YODA section material.

2025-ca-origami-retreat.html — A challenge on the way to Neuroscience Nirvana: WORKAROUNDS!

  • Venue / date: CA Origami Retreat 2025.
  • Spine: Nirvana / archives / make-re-use-convenient framing.
  • Reusable highlights:
    • WordNet "nirvana" definition pre block.
    • "Where data go to die / how data are reincarnated" Q-and-A slides (Buddha background).
    • "What makes data re-use INconvenient?" two-slide pair (data bugs; ad-hoc data access; opinionated software) with bug / feed-me cartoons.
    • "What allows to make data re-use convenient?" — Standards (BIDS) and Validation (BIDS).
    • "What if standard does not (yet) fill the bill?"
    • Closing "talk in BIDS" Nirvana slide.

2024-distribits-datalad.html — "What's in the DataLad sandwich" AKA the DataLad ecosystem

  • Venue / date: distribits 2024.
  • Spine: DataLad origin → sandwich layering → ecosystem → CI / health.
  • Reusable highlights:
    • "When it began for us" timeline (git → PyMVPA → GitHub → git-annex → DataLad first commits).
    • First use case: arjlover crawler → website-crawler-born mermaid.
    • "From an email to a proposal" Joey-email screenshot timeline.
    • "More layers to the sandwich" mermaid (datalad → git-annex → git-annex-remote-archives → git-annex → git-annex-remote-datalad).
    • DataLad crawler pipeline gitGraph (incoming → processed → master).
    • DataLad realizations & shortcomings checklist.
    • DataLad extensions mechanism + extension template + initial extension graph.
    • DataLad core "what it is" definition slide with JOSS citation.
    • DataLad Extensions & Their Health (pics/datalad-extensions.png).
    • DataLad Handbook overview (3-row table).
    • "DataLad fulfilled original promise of a Data Distribution" (datasets.datalad.org snapshot).
    • Examples-of-use: OpenNeuro, brainlife, CONP infrastructure use; YODA + ReproNim/containers; DANDI alternative view + Dropbox.
    • "DataLad ecosystem" DataLad-minder.svg figure.
    • CI / testing / monitoring stack: DataLad-all-changes-are-tested, extensions tested daily, git-annex daily, daily-status-email, con/tinuous archives, datalad-installer.
    • Acknowledgements slide with funders + collaborators.

2024-distribits-datalad-name.html — "What's in the DataLad name" AKA How come DataLad?

  • Venue / date: distribits 2024 (lightning).
  • Spine: just the naming history (datagit → ftf → datalad).
  • Reusable highlights: name-history single-slide timeline (good warm-up / origin-story slide).

2023-brain-dandi.html — DANDI: distributed archives for neurophysiology data integration

  • Venue / date: BRAIN Initiative talk, 2023.
  • Spine: archive challenge → DANDI ingredients → standards → testing.
  • Reusable highlights:
    • "Challenge: Develop a BRAIN Initiative Archive" (radial-gradient section divider).
    • "Where data go to die" → DANDI born.
    • "What data is in DANDI" dandi-slide-modalities.svg.
    • "Data chronology and demographics" 20230622-NWB-and-DANDI-tutorial-updates.svg.
    • "Ingredients needed to build an archive" — People / Standards / Technologies / FOSS / Automations.
    • DANDI users by role (submitter / researcher / developer SVGs).
    • DANDI integrates standards (20210421-INCF-dandischema.svg).
    • DANDI ecosystem (DANDI-ecosystem.svg).
    • Testing the entire archive: docker-compose; DataLad-mirroring of dandisets; con/tinuous; webshots; trivial IO across all dandisets (dandisets-healthstatus.png).
    • "DANDI ..." final summary bullets (modular FOSS, integrates, novel-tech adoption, automated QA).

2023-lbl-building-dandi.html — Building an Archive for Large-scale Neuroscience Data

  • Venue / date: LBL talk, 2023.
  • Spine: same as 2023-brain-dandi.html but longer; with a Brief Bio section for general-audience framing.
  • Reusable highlights: see DANDI entries above; this is the larger parent deck. Includes:
    • "Brief Bio" slide (Born in Siberia → Ukraine → US trajectory).
    • "Standard for neurophysiology data: NWB" slide.
    • "Standards make DANDI FAIR for People" slide.
    • DANDI schema deeper-dive (dandi-slide-schema.svg).

2023-bids-dicom.html — BIDS 4 DICOM WG-16

  • Venue / date: DICOM WG-16 meeting, 2023.
  • Spine: BIDS as a meta-standard, and where BIDS ↔ DICOM collaboration could go.
  • Reusable highlights:
    • "Brief Bio" (variant).
    • BIDS-Steering iframe slide.
    • "Standard for neural datasets: BIDS" with the 2016 BIDS Sci Data citation (canonical citation slide).
    • "BIDS ..." features bullets, including "you've seen one BIDS dataset you've seen them all".
    • BIDS-minder upstream-images slide (bids-standard.github.io/.../BIDS-minder.svg).
    • DICOM ↔ BIDS chronology (1982 DICOM → 2014 BIDS).
    • Clunie MICCAI 2017 5-image fragments (data is in pics/2017-Clunie-*.png).
    • "All standards are 'Bad', but some are used" — recurring rhetorical slide.
    • DICOMs in BIDS workflow (sourcedata, .json sidecars, BEP019, PR#1450).

2023-brain-dandi-imgdatasrc.html — short DANDI talk

  • Tiny deck (86 lines), title-only template; safe to ignore as source.

2022-nih-compcore.html — An Integrated and Trusted Scientific and Statistical Computing Core

  • Venue / date: NIH SSCR pitch, 2022.
  • Spine: trust → noise → human IO → standards → FOSS distribution → data management → archive → all the projects in one walk.
  • Reusable highlights:
    • Yarik-goal cartoon (pics/yarik-goal.svg) — the "north star".
    • "Brief Bio" slide (canonical version; reused in 2023 talks).
    • CON principles (con-principles.png) — used in title slides.
    • "Integration & Trust Tiers" ladder (Social / Data acquisition / Methods/Analytics / Software systems / Data management / Services).
    • "Trust is largely a social aspect" framing slides.
    • "How can we minimize unexplained variance?" — minimize-human-IO bullets, simulations, assertions, peer-review, provenance, re-use.
    • 3rd-party / "God-is-at-the-computer" slide (recursive trust).
    • Phantom QA / Nuisance study figure (F1000 2020 citation).
    • ReproNim 5 steps (pics/repronim-5steps.png, http://5steps.repronim.org).
    • OBC (Open Brain Consent) born-in-2014 slide; outcomes; OBC tools.
    • "Challenge: minimize human IO to understand data" → BIDS → BIDS-Apps.
    • ReproIn / HeuDiConv sequence-naming → automated BIDS slides.
    • Beyond ReproIn: ReproStim / ReproEvents / con/noisseur.
    • "Challenge 2007: no ML framework" → PyMVPA features / classification / searchlight / hyperalignment / TRANSFusion; PyMVPA-on-phone deployment punchline.
    • NeuroDebian born-2009 slide; integration figure; user-perspective figure; nd_overview.svg developer view; benefits bullets (Conda-Forge / Fedora / Gentoo handoff, "Containerization comes for free").
    • DataLad-in-one-figure (pics/datalad_process_tuned/00base_preview.png).
    • Provenance capture: 3-step datalad run / datalad containers-run / datalad rerun code blocks.
    • Extend DataLad extensions overview.
    • DataLad CI / health (testing-extensions / git-annex daily / con/tinuous archive).
    • "In DataLad We Trust" + decentralized RDM citation.
    • DANDI-section duplicate (modalities / services / standards / schema / "Webshots of all dandisets").
    • Closing "Integrated and Trusted" bullet manifesto.
  • This deck is the richest single source of reusable CON-history material — borrow heavily for any retrospective talk.

2022-tx-big-neuroscience.html — Towards the Big Data Neuroscience Nirvana

  • Venue / date: ACNN Workshop 2022 (Texas).
  • Spine: Nirvana / archives / making re-use convenient + DataLad CI health quick tour.
  • Reusable highlights: prototype of the Nirvana arc later refined in 2025-ca-origami-retreat.html. Includes "Big Data" section, the largest-Git-repo / datasets.datalad.org snapshot, the for-users / for-developers slide pair, and DataLad / extensions / git-annex daily validation triplet.

0000-zoom-background.html — Zoom background slide template

  • Not a talk; layout source for sharing CON banner during Zoom.

Shelved (backdrawer)

Outline-only stubs and parked drafts. See _backdrawer_/README.md for the convention (filenames preserved so the published URL still works on revival, symlink-into-root pattern for live preview, git mv to promote back to active status).

_backdrawer_/202x-mvc-stack.html — [WiP] MVC at the stack scale: what makes the open-(neuro)science stack compose (shelved stub)

  • Status: Shelved in _backdrawer_/ — outline-only stub, no venue lined up. The MVC framing lives on as a 4-slide mini-section inside 2026-usrse-con-talk.html. If revived: git mv the file back to the root, rename to <YYYY>-<venue>-mvc-stack.html, drop the [WiP] prefix, and regenerate the QR code (the URL changes with the filename).
  • Spine: re-reads the four CON verbs as Model–View–Controller at the stack scale.
  • Authoring seed: the 4-slide MVC mini-section inside 2026-usrse-con-talk.html is the seed; promote each row into its own slide here, plus borrow visuals from the per-topic lookup below.
  • Section openers in place:
    • "One thesis, two parts" — explicit MVC-at-stack-scale claim.
    • "Why 'at the stack scale' is the new word" — classical-vs-stack-MVC contrast.
    • Models: Dataset layout / Per-file / Metadata / Storage (4 stub slides).
    • Views: Browse-the-archive humans / Tabular ad-hoc / Programmatic / External services / Schema-driven UIs (vjsf → DANDI meditor; shacl-vue → forms + research-group websites) / Long-form narrative.
    • Controllers: Acquisition→layout / Reproducible execution / Logistics / Data→derivative / Validation — and a recursive Standardize moment (the latter is now the most fleshed-out slide: con/validation harmonizes bids-validator + HED + pynwb + zarr + nwbinspector + OME-Zarr; deployed in dandi-cli; VisiData for triage).
    • Contrast: the "service-tied UI" pattern section (NEW): four slides walking through the academic anti-pattern (LIMS / ELN / "just a Flask app"), naming the design-pattern literature (Smart UI [Evans], Anemic Domain Model [Fowler], Hexagonal / Ports & Adapters [Cockburn 2005], Adapter / Strategy / Façade [GoF], Service Layer [PoEAA]), and showing CON's static-first contrast (datasets.datalad.org as plain nginx, schema-driven UIs, JAMstack-style decks). Includes a "if your project dies when the server is down for a week..." heuristic.
    • One stack, many lenses section: a table of six lenses (Architectural / Procedural / Sharing / Compositional / Purpose / Maturity) mapping to MVC / STAMPED / FAIR / YODA / project-purpose / AI-ladder. Captured as a recurring framing in SOUL.md §1.
    • "Three things to do this week" closer.
  • TODO markers in-file flag what to fill in.

Topic-wise lookup

Use these as a fast "where do I steal a slide for X?" cheat sheet.

Reuse / upstream contribution / NeuroDebian

  • 2022-nih-compcore.html § "NeuroDebian from user perspective", § "Under-the-hood for a NeuroDebian developer", § Overall benefits.
  • 2024-distribits-datalad.html § "git-annex is built and tested daily", § datalad-installer, § acknowledgements.
  • Asset: pics/neurodebian*.{png,svg}, pics/nd_overview.svg, pics/neuropy_history.svg.

Compose / DataLad ecosystem / sandwich layering

  • 2024-distribits-datalad.html § Sandwich mermaid, § Extensions template, § DataLad ecosystem (DataLad-minder.svg), § "DataLad for developers".
  • 2022-nih-compcore.html § Provenance + extensions list.
  • Asset: pics/DataLad-minder.svg, pics/datalad-extensions.png, pics/tall-burger.png, pics/datalad_process_tuned/.

Compose / small acquisition+compute units (HeuDiConv / ReproStim /

ReproNim-containers / con/duct / ReproMan)

  • 2022-nih-compcore.html § ReproIn / HeuDiConv / Beyond-ReproIn.
  • 2025-distribits-YODA.html § "datalad-container", § "ReproNim/ containers" walkthrough, § ReproMan reference.
  • 2026-repronim-YODA-BIDS-webinar.html § same Principle 2 section.
  • 2025-distribits-YODA.html § con/duct; § "datalad runs in the wild"; § git-annex addcomputed.
  • Asset: pics/webshot-repronim-containers.png, pics/repronim-containers-{workflow,show,yoda-lower}.png, pics/webshot-con-duct.png, pics/screenshot-duct-*.png, pics/duct-mriqc-cerebra.png, pics/borrowed/reproin-logo.jpg.

Extend / standards work / BIDS BEPs

  • 2023-bids-dicom.html § BIDS features, § BIDS-minder, § DICOMs-in-BIDS workflow, § "All standards are bad, but some are used".
  • 2022-nih-compcore.html § Microscopy-BIDS citation.
  • Asset: pics/BIDS-minder.svg, pics/bids-logo-wide.png, pics/bids-yoda.png, pics/bep028-example1.png.

Standardize / data archives / DANDI / OpenNeuro / federation

  • 2023-brain-dandi.html (whole deck) — best DANDI walkthrough.
  • 2023-lbl-building-dandi.html — extended version.
  • 2024-distribits-datalad.html § DANDI alternative-view slide; § OpenNeuro infrastructure use.
  • Asset: pics/dandi-slide-{modalities,services,standards,schema}.svg, pics/DANDI-{ecosystem,FAIR,users-*}.svg, pics/dandiarchive-webshots.png, pics/dandisets-healthstatus.png.

YODA principles + "Look up you must not"

  • 2025-distribits-YODA.html and 2026-repronim-YODA-BIDS-webinar.html — full YODA spine.
  • Asset: pics/yoda*.{png,svg}, pics/principle-{vcs,computeenv, structure}.png, pics/depends-on-untracked-file.png, pics/yoda-hierarchy-with-containers.png, pics/yoda-do-not-look-up.png, pics/yoda-all-the-way-down.png.

Provenance / datalad run / datalad rerun / RUNCMD → BEP028

  • 2025-distribits-YODA.html and 2026-repronim-YODA-BIDS-webinar.html § Principle 1.
  • 2022-nih-compcore.html § Provenance capture (3 code-block slides).
  • 2024-distribits-datalad.html § DataLad crawler gitGraph.

CI / con/tinuous / daily-tested git-annex / health dashboards

  • 2024-distribits-datalad.html § three-image stack of PR-test screenshots; daily-status email iframe; con/tinuous.
  • 2023-brain-dandi.html § identical CI slides re-used for DANDI.
  • 2022-nih-compcore.html § "PART of an answer: AUTOMATION" + 3 testing slides.
  • Asset: pics/con-tinuous-{github,term,term-dandi-cli}.png, pics/datalad-extensions.png, pics/datalad-git-annex.png, pics/webshot-datalad-installer.png, pics/datalad-daily-status-email-subject.png, embed/datalad_git-annex_daily.html.

Trust / accountability / variance / phantom QA / OBC

  • 2022-nih-compcore.html § "Trust is largely social", § Nuisance study, § ReproNim 5 steps, § OBC born/outcomes/tools.
  • Asset: pics/god-is-at-the-computer.jpg, pics/MRI-scanner.png, pics/f1000-webshot-20200930*.png, pics/repronim-5steps.png, pics/OBC_LogoCheck.svg, pics/obc-{main,ultimate,tools}.png.

PyMVPA / "we ported the intent upstream"

  • 2022-nih-compcore.html § PyMVPA Features → searchlight → hyperalignment → TRANSFusion → "phone deployment".
  • Asset: pics/pymvpa*.png/svg, pics/pymvpa_logo_fromfusionposter.svg, pics/pymvpa_on_phone.jpg, pics/uniform_analysis.svg.

"Make re-use convenient" / Nirvana framing

  • 2025-ca-origami-retreat.html — full deck.
  • 2022-tx-big-neuroscience.html — original.
  • 2023-brain-dandi.html § "Where data go to die".

AI angle / HI+AI / AI-coding ladder / con/serve

  • 2026-ca-origami-retreat-aicoding.html — full deck.
  • 2026-repronim-YODA-BIDS-webinar.html § hand-off to AI talk (Appendix-style slide referenced from the AI talk's "Previously on…").
  • Asset: pics/borrowed/ai-ladder-skills.png, pics/borrowed/2026-ai-intensifies.png, pics/surface-depth-v2.jpg, pics/borrowed/idiocracy-fixed.gif.

MVC framing / "why the stack composes"

  • 2026-usrse-con-talk.html § "Why it composes — MVC at the stack scale" (4-slide mini-section: opener + Models + Views + Controllers table).
  • _backdrawer_/202x-mvc-stack.html (stub) — the standalone deck spun out of that mini-section.
  • Asset: re-uses existing tables; no new images required for the seed. When deepening the standalone talk, borrow pics/DataLad-minder.svg (storage model), pics/BIDS-minder.svg (dataset-layout model), and the controllers screenshots from 2025-distribits-YODA.html / 2026-repronim-YODA-BIDS-webinar.html.

Validation harmonization (con/validation)

  • 2026-usrse-con-talk.html § MVC mini-section's Controllers row ("Validation (and harmonization)") names con/validation as the harmonizer for bids-validator (+ HED) / pynwb / zarr / nwbinspector / OME-Zarr / LinkML validators, deployed in dandi-cli.
  • _backdrawer_/202x-mvc-stack.html § Controllers/"Validation — and a recursive Standardize moment" — the long-form treatment: con/validation is the type-checker for your validators; once results are one Model, Views are easy (dashboards, VisiData on the validation TSV).
  • External: https://github.com/con/validation; deployed in https://github.com/dandi/dandi-cli.

Automate / harness / meta-automation

  • 2026-usrse-con-talk.html § Automate (3 slides: opener, "Where we automate" table, "Cost: harnesses, harnesses, harnesses → meta- automation via AI"). Cites con/tinuous as the canonical CI-archival example (highly modular, fits con/serve's archival mission).
  • Older talks with reusable CI/automation slides:
    • 2024-distribits-datalad.html § "DataLad: all changes are tested", "extensions tested daily", "git-annex daily", con/tinuous archive, datalad-installer.
    • 2022-nih-compcore.html § "PART of an answer: AUTOMATION" + the same three testing slides.
    • 2023-brain-dandi.html § "Dandisets converted into DataLad and pushed to GitHub", "Webshots of all dandisets", "Testing trivial IO across all dandisets".
  • Asset: pics/con-tinuous-{github,term,term-dandi-cli}.png, pics/datalad-extensions.png, pics/datalad-git-annex.png, pics/datalad-daily-status-email-subject.png, embed/datalad_git-annex_daily.html, pics/dandiarchive-webshots.png, pics/dandisets-healthstatus.png.
  • Meta-automation framing: harness maintenance is the place where AI assistance becomes most viable for a small RSE center; pair with con/skills and con/yolo (per 2026-ca-origami-retreat-aicoding.html).

HI ⇄ AI policy spectrum (per-project AI-acceptance)

  • 2026-usrse-con-talk.html § "HI ↔ AI — every project picks its own policy" (in the HI+AI section): a 4-row spectrum table mapping policy stance ↔ OSS exemplars ↔ CON project ↔ SciOps level ↔ STAMPED property:
    • Reject — Zig, Krita, Clojure, QEMU; git-annex (Joey Hess's "Feb 30" satirical policy).
    • Accept with disclosure — NumPy, Kubernetes, Linux, Django; DataLad / DANDI with Co-Authored-By trailers, @pytest.mark.ai_generated.
    • Spec-driven AI-generated — AnnexTube, mykrok, con/citations-collector, parts of dandi-cli.
    • Autonomous — con/skills + con/yolo workflows. Common ground per ICMJE Jan 2026: AI cannot be author, humans retain responsibility, disclosure mandatory.
  • External survey: melissawm/open-source-ai-contribution-policies — community-maintained catalog of declared OSS policies; the three+one bucket framework (Accept / Restrict / Reject / Ongoing) is what the slide's 4-stance spectrum is built on.
  • SOUL.md §1 names this as a recurring framing — use it for any deck that touches AI contributions.

Backend-coupled "service-tied UI" anti-pattern / Hexagonal contrast

  • _backdrawer_/202x-mvc-stack.html § "Contrast: the 'service-tied UI' pattern" (4 slides): the anti-pattern in academia, design-pattern names (Smart UI / Anemic Domain Model / Hexagonal-Ports-Adapters / Adapter / Strategy / Façade / Service Layer), CON's static-first counter-pattern.
  • Citations: Cockburn, Hexagonal Architecture, 2005 https://alistair.cockburn.us/hexagonal-architecture/; Evans, Domain-Driven Design, 2003 (Smart UI anti-pattern); Fowler, Patterns of Enterprise Application Architecture (https://martinfowler.com/eaaCatalog/serviceLayer.html; Anemic Domain Model: https://martinfowler.com/bliki/AnemicDomainModel.html); Gamma, Helm, Johnson, Vlissides (GoF), Design Patterns, 1994 (Adapter / Strategy / Façade).
  • Use this slide block when an audience is more enterprise-software- literate than data-archive-literate, or when a critic asks "why don't you just build a portal?".

Five verbs ↔ SciOps maturity levels

  • Mapping (Johnson et al., 2024; https://arxiv.org/abs/2401.00077):
    • L1 Initial — ad-hoc; no CON verb yet.
    • L2 Managed — Compose (lab-local; YODA layout).
    • L3 Defined — Reuse / Compose / Extend / Standardize; FAIR data + FAIR workflows. Paper-cited L3 exemplars: BIDS, NWB, DataLad / git-annex, DANDI, brainlife.io.
    • L4 Scalable — Automate; "SciOps pipelines" (semi-automated continuous workflows).
    • L5 Optimizing — Automate × AI; closing the discovery loop.
  • Slide anchors: 2026-usrse-con-talk.html § Automate's 4th slide ("The five verbs climb the SciOps ladder"); _backdrawer_/202x-mvc-stack.html § Many-lenses Maturity row (now spells out all 5 levels); 2026-usrse-con-talk.html § HI+AI's updated SciOps bullet (STAMPED = per-artifact, SciOps = team-operations).
  • SOUL.md §7 explicitly lists the verb→level mapping; cite it from any future deck that wants to talk about maturity.
  • Practical implication: when you name one of the 5 verbs in a slide, mention which SciOps level it corresponds to — CMM language travels well to RSE audiences.

Multi-dimensional framings ("many lenses, one stack")

  • _backdrawer_/202x-mvc-stack.html § "One stack, many lenses" — table of six lenses (Architectural / Procedural / Sharing / Compositional / Purpose / Maturity) with example axes:
    • Architectural → MVC (this talk's spine)
    • Procedural → STAMPED — Self-containment, Tracking, Actionability, Modularity, Portability, Ephemerality, Distributability (Macdonald et al. 2026, stamped-paper)
    • Sharing → FAIR
    • Compositional → YODA
    • Purpose → acquisition / curation / archive / analysis / governance / sharing / training
    • Maturity → SciOps five-level CMM (Johnson et al. 2024, arXiv:2401.00077) + AI-coding ladder L1–L5 for the agentic-readiness sub-axis. Use this slide when a talk needs to triangulate several patterns at once instead of pitching one.
  • SOUL.md §1 names this as a recurring framing — read it before writing a talk that compares projects/properties along multiple axes.
  • Both STAMPED and SciOps now have entries in SOUL.md §5 (canonical citations), so any future deck can cite them with one-line consistency.

Schema-driven UIs / "the Model materializes the View"

  • 2026-usrse-con-talk.html § Standardize → "Metadata: schemas as first-class citizens" (LinkML / pydantic / JSON Schema / SHACL bullets) and § MVC mini-section's Views slide (vjsf → DANDI meditor; shacl-vue → forms + research-group websites).
  • _backdrawer_/202x-mvc-stack.html (stub) § Models → "Metadata: many languages, one idea" and § Views → "Schema-driven UIs: the View that the Model generates".
  • External reference: M. Hanke et al., LinkML metadata-driven workflow — on ReproTube: https://datasets.datalad.org/repronim/ReproTube/DataLad/web/#/video/oF98hdaph1k?tab=local&wide=1&t=644&q=model&filter=1 (YouTube id oF98hdaph1k, timestamp 644s); cite when borrowing or expanding the schema-driven-UI argument.
  • Suggested screenshots to add later: DANDI meditor at https://gui.dandiarchive.org/; a shacl-vue-rendered website (per psychoinformatics-de's deployments).

CON identity / acknowledgements / funders

  • 2024-distribits-datalad.html final acknowledgements slide is the canonical layout: software → some-slides-origin → Funders → Collaborators.
  • 2022-nih-compcore.html § "Trust ladder" CON banner.
  • Asset: pics/con-{principles,ack-*,webshot-*,logo_*}.{png,svg}, pics/con-ccn-dartmouth-letterhead.svg, pics/borrowed/{nih,nsf*,bmbf_2020,binc,erdf,cbbs_logo,LSA-Logo,fzj_logo, hbp_logo,conp_logo,vbc_logo,repronim_logo,openneuro_logo,cbrain_logo, brainlife_logo,dandi_logo,bannerthanks}.{png,svg,jpg}.

Speaker bio / "Brief Bio" slides

  • 2022-nih-compcore.html, 2023-bids-dicom.html, 2023-lbl-building-dandi.html — three near-identical versions of Yarik's bio + CON-principles r-stack.

Title / opening hook archetypes

  • 2025-ca-origami-retreat.html opens with "WORKAROUNDS!" reveal.
  • 2026-repronim-YODA-BIDS-webinar.html opens with Reality-Check GIF.
  • 2024-distribits-datalad.html opens with QR code + logo strip (canonical template).

Closing slides

  • "Save your questions for the panel discussion" / "Let me know what to fix": 2024-distribits-datalad.html, 2025-distribits-YODA.html, 2026-ca-origami-retreat-aicoding.html ("Let the AI agents be with you", with the Yoda SVG as a sign-off).

How to use this index

  1. Pick a story arc from SOUL.md §7.
  2. Walk the per-talk list above for the arc's parent deck — its slide anchors are your "free" content.
  3. For each section of the new deck, consult the topic-wise lookup to pull supporting slides from sibling decks rather than re-creating them.
  4. When you copy a slide, update relative data-src paths only if the new deck lives in a subdirectory (it shouldn't — keep new decks at the repo root).
  5. Add the new deck to this index when committed.