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Demo polish: colorblind-safe §6 strand; §5 completion-fold; §1 helix occlusion; §7 score chip; logo SVG; §8 evals refresh
- §6 UMAP: strand palette switched from green/red to Okabe-Ito blue/vermillion so the +/- coloring survives deuteranopia and protanopia (the previous pair collapsed to two near-identical grays under both common CVD types). - §5 Folding: new completion-fold pipeline (75% CDS prompt → 25% predicted → fold the C-term tail with ESMFold); mrna-info row reads the prompt/predict ratio for completion-fold genes, falls back to the original genomic→mRNA→ORF chain for legacy fixtures. genes.json gains the fold_setup / fold_example fields and a sections[] tag to scope the showcase set per panel. - §1 Intro: helix occlusion now splits each strand at depth-zero PEAKS rather than centerline crossings, so the "behind" arcs alternate between upper and lower lobes and rungs occlude correctly under the front strand. Edge-touching arcs render solid (no ghosted 5'/3' label ties). - §7 Tree: agreement-score chip redesigned as a typographic stat block — percentage in Carbon green + raw …f5d37e0
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Intro tab + central-dogma primer + em-dash sweep
- New Intro tab as default landing: release blurb, tab-nav guide (bullet list with banner-style links), and an optional "quick primer in genetics" §1-§5 walkthrough using the existing section--two-col + .demo primitives. - Primer visuals: skeletal-formula SVGs for the four bases, static DNA helix (~10 bp/turn), gene strip (promoter / exons / introns), splice diagram with transcribe arrows, 10-column codon to amino-acid table with peptide-bond chain, and a live 3Dmol.js viewer of human hemoglobin (PDB 1A3N) bundled in assets/data/ for fast first paint. - Lazy-init the 3D viewer via MutationObserver on the panel's .active class, so visitors who deep-link to #demo / #sandbox skip the fetch. - Tabs renamed: Demo to DNA Lab, Model to Carbon Recipe (display labels only; data-tab slugs and URL hashes stay 'demo' / 'model' for backwards-compat). - Banner: add Code placeholder link to banner-links; tab buttons use min-width + nowrap so "Carbon Recipe" stays on one line. - …5ea40ce -
Sandbox card layout, sticky-nav breadcrumb, drop §2/§3 score buttons
- Sandbox: refactor into stacked cards (sb-card with eyebrow/title/hint headers, Input → Output) plus a Connected-to strip up top, replacing the flat wall of controls. - Sticky nav: add a CARBON / huggingfacebio-carbon-3b breadcrumb on the left of the sticky strip so the "you're on the Carbon page" cue stays visible after the hero scrolls out. - §2 (VEP) and §3 (Track): drop the manual ▶ score / score all buttons. §3 tracks are precomputed (logprobs ship in data/genes.json), so the toolbar is just a gene selector now; §2 will auto-score on select. - Misc: app.py, precompute.py, controls.css, layout.css, section-tree.css, banner.js and data/genes.json picked up along the way. - Add social-banner.html. Co-authored-by: Cursor <cursoragent@cursor.com>b64beb5
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§5 Folding: hydrate the section from a precomputed fixture
The Carbon endpoint and the NVIDIA NIM ESMFold call together take 10-20s on a cold start, which leaves the section blank when the visitor first scrolls into it. We now ship a precomputed example (Carbon continuation + both ESMFold structures + stats) inside data/genes.json so the section renders instantly. Clicking ▶ fold still triggers a fresh live run. Notable details: - scripts/precompute.py grows a precompute_folds() step that mirrors the live pipeline: it calls the backend /generate (same left-pad-to-six, same <dna> prefix, same streaming framing as runFold()) and then hits NVIDIA NIM directly to fold both the spliced-mRNA reference and Carbon's spliced mRNA. Genes whose last exon sits past 2.5 kb (TP53, MYC) are skipped — Carbon would need to generate too many bases live. - Temperature is set to 0.9 for the fixture, not 0.7. At T<=0.7 the model collapses into low-complexity sinks on long-context generation (poly-T at T<=0.5, AATC-repeat at T=0.7) — a known autoregr…2c4851e
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Add tabbed Demo / Model / Sandbox page (default = Sandbox)
New /demo route serves a single-page app with three tabs: - Demo: 4 interactive sections (gene completion, VEP, likelihood track, cross-species) plus folding/UMAP placeholders - Model: tokenizer, training objective (CE→FNS), data, architecture - Sandbox: the existing DNA continuation playground (default tab) Server-side: new /score endpoint (echo-logprobs), /genes /variants /species data routes, /img static mount, and left-padding for prompts that aren't a multiple of 6 bases (avoids phantom-A artifacts at the prompt boundary). Includes data fetchers (Ensembl REST) for genes / variants / species and a precompute script that bakes per-token logprobs and ref-vs-alt window scores into the JSON files so the page renders instantly without round-tripping the inference endpoint on first paint. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>971b586