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DockVision — Roadmap

Phase 0 — Scaffolding (week 0)

  • SvelteKit project with TypeScript, ESLint, Vitest
  • Postgres set up on www0 (or RDS if we decide that early)
  • Auth.js with email magic link + Google OAuth working
  • Postgres schema migrations (see ARCHITECTURE.md)
  • S3 bucket dockvision-prod + IAM policy (per-prefix scoping)
  • RunPod account + API key in /etc/dockvision/env
  • Stripe account in test mode + Customer Portal configured
  • DNS: dockvision.doi.bio → www0; nginx + Let's Encrypt
  • pm2 ecosystem file with the 4 processes: web, worker, recon, msa
  • Repo public on GitHub under AGPL-3.0
  • CI: lint, typecheck, unit tests on PRs

Deliverable: empty SvelteKit app live at dockvision.doi.bio; signup → login → empty /app works.

Phase 1 — GNINA end-to-end (week 1)

  • xterm.js CLI shell at /app
  • CLI commands: whoami, cost, tools, tool gnina, topup
  • Stripe Checkout for prepay → balance increments via webhook
  • S3 upload flow: upload <file>, presigned PUT from browser
  • FS commands: ls, cat, cd, pwd, du, pin, unpin, rm, mv, cp
  • GNINA Docker image + RunPod endpoint configured
  • Handler returns {output_s3_keys, cost_seconds, gpu, error}
  • pg-boss job worker: submit → poll RunPod → debit balance → S3 outputs
  • Pre-flight estimate displayed before submit
  • Hard balance cap at submit (balance >= estimated × 1.2)
  • Job commands: jobs, status, cancel, log
  • WebSocket balance ticker + job status updates

Deliverable: a paying user can run GNINA on real CASP inputs, pay real money, get real outputs.

Phase 2 — Boltz + Protenix (week 2)

  • MSA service: pm2 process for MMseqs2 + ColabFold DB on EBS volume on www0
  • S3-backed MSA cache by sequence sha256
  • Boltz-2 Docker image (weights on RunPod network volume)
  • Protenix Docker image (weights baked, ~5 GB)
  • Adapters for both tools, ported from ~/data/vaults/casp/inputs/adapters/
  • run boltz2, run protenix end-to-end
  • Per-tool pre-flight estimate calibration cron (recompute from p50 of last 100 successful runs)

Deliverable: catalog of three tools, all billed correctly, MSA caching working with measurable hit rate.

Phase 3 — Viewer + polish + CLI shim (week 3)

  • Mol* viewer integration (view <file.cif>) — port from casp-viewer/
  • Wizard mode (wizard <tool>) — form fallback
  • Tab-completion in xterm (commands + path-completion via API)
  • API key issuance (keys create, keys revoke)
  • Public CLI shim: npm install -g @dockvision/cli — dvk binary
  • Reconciliation worker (pm2 process)
  • Daily storage debit cron
  • Marketing landing at / with pricing
  • Public docs site (this directory rendered with mdsvex)

Deliverable: production-feeling product. Reproduces a user's CASP run end-to-end. dvk works from a laptop.

Phase 4 — Soft launch (week 4)

  • Invite ~5 CASP-affiliated scientists for feedback
  • Monitor reconciliation drift; tune the 1.5× markup if needed
  • Status page: dockvision.doi.bio/status (queue depth, recent failures)
  • Announce on r/MachineLearning, Mastodon biotech, BioStars
  • CASP17 timing alignment: ship before CASP17 ligand round

Deliverable: external users running real workloads. First $100 of revenue.

Out of scope (v2+)

  • Teams / orgs / shared workspaces
  • Public REST API (just internal API + the @dockvision/cli shim)
  • DynamicBind (license review)
  • Chai-1 (license review; Chai's free playground is competitive pressure)
  • AlphaFold3 (Google license blocker — likely permanent)
  • IntelliFold
  • Leaderboards / sharing
  • Pose refinement (meta_pose, etc.)
  • MD trajectories
  • Free tier
  • Native mobile apps
  • Multi-region S3

Risks tracked

Risk Likelihood Mitigation
RunPod GPU shortage at peak High Vast.ai fallback wired in worker; queue depth alerts
Cold start > 2 min on Boltz High Network volume w/ baked weights; 1 Active worker if traffic warrants
Stripe chargeback on $10 prepay Medium Require email verification; flag suspicious top-ups
Tool license changes mid-flight Medium Nightly CI checks upstream LICENSE files; alert on diff
Reconciliation drift > $1/day Medium Page on drift; freeze submits until reconciled
User uploads malware as "input" Low ClamAV on every S3 upload; strict file-type allowlist
OOM on user-provided huge ligand Medium Per-tool input size caps enforced at submit time
www0 EC2 dies Medium Daily Postgres backup to S3; runbook for cold restore
MSA index corruption Low Quarterly re-download of ColabFold DB; checksums
S3 egress bill spike from public sharing Medium No public sharing in v1; rate-limit downloads per user