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jvogan (Jacob Vogan) · GitHub

Overview Repositories 19 Projects Packages Stars 3
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jvogan/README.md

My repositories map

BioTools

  • Motif — a molecular biology workbench for Claude Science
  • BioVoice — talk to your protein structures: voice control for PyMOL, ChimeraX, and more
  • Proteus — structural biology automation: publication-quality figures, movies, and analysis

Orchestration & Agent Infra

  • Ox Driver — orchestrate fleets of OpenRouter Ox Alpha agents through Pi, Claude Code, or Codex
  • A Fable of Codexes — turn Claude Code into a conductor over Codex workers
  • Symphony Linear Starter — give your agent worker teams that plan waves, review, and merge through Linear
  • Symphony Claude Lane — run Claude Code workers alongside Codex in Symphony + Linear workflows
  • NeoCloud Bridge — give your agent guarded cloud workers: artifact proof, cost limits, and cleanup
  • Telegram Codex Bridge — talk to your Codex Desktop session remotely: text, voice, and files over Telegram

BioSymphony

  • Structure Factory — structural biology workflows: design binders, screen candidates, prepare cloud runs
  • Small Molecules — small-molecule design workflows: plan synthesis, dock ligands, check ADMET, and more
  • GeneCluster — genome mining for natural products: search public genomes, compare candidate clusters
  • BioProspector — biosynthetic route exploration: find enzyme and gene candidates for target molecules
  • CryoCore — cryo-EM workflows: build maps and models, compare states, make figures
  • Ferm DoE — closed-loop fermentation runs: design a batch, analyze results, plan the next

Agent Skills

  • Daneel — give your agent a Telegram/Discord chatbot only people you approve can talk to
  • yt-agent — give your agent terminal YouTube search, download, and clip tooling
  • Valar — give your agent a voice: unlimited local TTS, ASR, and MCP bridge for Apple Silicon
  • WhisperHUD — give your agent fast local transcription, or system-wide voice-to-text for macOS

Research

  • VibeThinker-3B J Lens — a Jacobian lens for VibeThinker-3B: watch an answer take shape layer by layer

jvogan.github.io · BioSymphony · Motif · Hugging Face · X · houseofvogan.com

Pinned Loading

  1. biovoice biovoice Public

    Talk to your protein structures. Voice control for PyMOL, ChimeraX, AlphaFold, and Rosetta built on the OpenAI Realtime API with structured tool calling.

    TypeScript

  2. a-fable-of-codexes a-fable-of-codexes Public

    Claude Code skills that make Claude (Fable) the conductor of AI worker fleets: many parallel OpenAI Codex workers plus Opus design agents, organized into campaigns, waves, squads, and review gates.

    Python 46 3

  3. motif motif Public

    An AI-native molecular biology workbench for Claude Science: Claude opens sequence files and prepares analyses on request; you annotate, align, and review them in an interactive workspace.

    TypeScript 47 4

  4. proteus proteus Public

    Structural biology superpowers for AI coding agents: PyMOL, ChimeraX, AlphaFold DB, RCSB PDB, UniProt, and Rosetta workflows.

    Python 10

  5. BioSymphony/structure-factory BioSymphony/structure-factory Public

    AI-agent toolkit for structural biology: design binders, map structures, screen candidates, rank results, and prepare cloud-scale runs.

    Python 5

  6. BioSymphony/bioprospector BioSymphony/bioprospector Public

    Biosynthetic route exploration for target molecules: find enzyme and gene candidates and turn pathway ideas into follow-up searches and experiments.

    Python 2

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