AIPOCH Open-Science v0.35.0

AIPOCH Open-Science v0.35.0

A replay-and-reach release: session replay arrives to step through and discuss recorded sessions, the connector catalog grows Cellosaurus and Monarch alongside GEO matrix discovery, uploaded PDFs gain structure extraction, and Windows gets native titlebar menus.

AIPOCH Open-Science is an open-source, local-first, model-agnostic AI research workbench for scientists and researchers. It enables reproducible, inspectable research across models with scientific AI agents, Python and R execution, scientific data connectors, and cross-platform support for macOS, Windows, and Linux.

v0.35.0 puts recorded work in motion. Session replay lets you step through a recorded session, inspect what happened at each point, and discuss the recorded steps with your agent. The connector catalog keeps growing: a new Cellosaurus connector identifies cell lines and their quality annotations, a new Monarch connector surfaces phenotype association evidence across model organisms, and the omics connector gains GEO expression-matrix discovery with download preflight. Structure extraction now works on uploaded PDFs as well as generated ones, with faster bounded parallel figure and table analysis. The model catalog expands with more OpenCode Zen entries and Jev classification, settings gain continuous usage-chart inspection, and the workspace accepts file drops anywhere in the conversation. Windows users get native titlebar application menus, alongside fixes that harden Windows notebook runtimes, unify permission grants, and make session outcomes durable.

✨ Highlights

• Session replay. Replay recorded sessions step by step and discuss the recorded steps with your agent. (#3140)
• Connector growth. New Cellosaurus and Monarch connectors arrive, and GEO matrix discovery joins the omics connector. (#3230, #3227, #3238)
• Uploaded PDF structure extraction. Structure extraction now works on uploaded PDFs, not only generated ones. (#3222)
• Native Windows titlebar menus. The Windows app gains proper application menus in the titlebar. (#3201)

🚀 New Features

• Session replay: replay recorded sessions with previews and playback interactions, browse replay history, and discuss recorded steps with your agent. (#3140, #3215, #3218)
• Cellosaurus connector: cell-line identity and quality tools — look up cell lines, their identities, and quality annotations. (#3230)
• Monarch connector: phenotype association evidence across model organisms — gene/variant-to-phenotype associations with supporting evidence. (#3227)
• GEO matrix discovery and preflight tools in the omics connector: find GEO expression matrices and preflight downloads. (#3238)
• Expanded OpenCode Zen model catalog with Jev classification. (#3239)
• PDB structures connector gains protein sequence search: find experimental structures by amino-acid sequence with identity, E-value, and coverage filters. (#3250)
• IEDB connector: immunology evidence tools — search epitopes, antigens, and T-cell, B-cell, and MHC assays with source publications. (#3261)
• Continuous usage chart inspection in settings: zoom and inspect usage over time. (#3236)
• Drag and drop files anywhere across the conversation to attach them. (#3224)
• Structure extraction for uploaded PDFs, alongside the existing generated-PDF support. (#3222)
• Windows titlebar application menus for native window management. (#3201)
• Network access rules separate public automation from reviewed private services: private grants bind to an exact hostname, port, and reviewed address set, with DNS rechecked before saving. (#3249)

🔧 Improvements

• Figure and table analysis in PDFs now runs bounded parallel work, speeding up large documents. (#3228)
• Dependencies updated to resolve known vulnerable transitive packages. (#3190)
• Workspace and settings chrome is more compact, including message tool cards, sidebar navigation padding, and the network status card. (#3226, #3225, #3214)
• The workspace import hint gains contrast for accessibility. (#3205)

🐛 Bug Fixes

• Replay and sessions — notebook state is preserved and generated galleries stabilized in replay (#3219); turn outcomes and operation failures persist reliably (#3171); ask-user waits survive app restarts (#3223).
• Notebook and runtimes — Windows REPL startup and cleanup are hardened (#3173); system parent ACL grants are blocked from the Windows sandbox (#3256); Windows runtime compatibility confirmation and its diagnostics are hardened (#3255); Windows sandbox launches no longer stall on repeated ACL rebuilds (#3257); WSL distro folders picked from Explorer map without spawning subprocesses (#3254); isolated Windows runtime execution is repaired (#3105); pip-generated entry points are matched (#3237); scientific I/O paths and loader uncertainty are retained (#3216); contextual folder access grants are offered when needed (#3220); parent traversal for managed paths is granted without directory enumeration (#3246).
• PDF and preview — outline navigation aligns with section positions (#3234); unavailable outlines are clarified and narrow navigation floats (#3232); the notes sidebar floats in narrow readers (#3229); native figure and table content is preserved across varied paper layouts (#3217); literature layout extraction is hardened for complex papers (#3247).
• Agents and permissions — granted folders are exposed to Codex sessions (#3209); ACP grant matching is unified with diagnosis of fallback approvals (#3189); native OpenCode skill updates correlate correctly (#3198); raw folder permission recovery is surfaced in the workspace (#3235).
• Workspace and packages — identical .science objects are deduplicated (#3206); provider and Project drafts are protected and action feedback clarified (#3182); background errors are dismissible (#3203); long skill descriptions truncate to a single line with the full text on hover (#3253).

📦 Install

Requirements: macOS 12+ (Apple Silicon or Intel), Linux x64 or ARM64, or Windows 10/11 x64. On first run, the onboarding wizard checks the environment and can install and configure an app-managed agent runtime. Once installed, the app can update itself in place.

Download the appropriate package from the Assets section below, or from the official download page:

Platform	Package
macOS (Apple Silicon)	DMG for ARM64
macOS (Intel)	DMG for x64
Linux	AppImage or Debian package for x64 / ARM64
Windows	Code-signed installer for x64

macOS — first launch. Official release builds are Developer ID signed and notarized by Apple, so they open like other trusted applications. A locally built copy is notarized differently and may require approval through macOS Privacy & Security.

Windows — first launch. Official release builds are code-signed; Windows recognizes the publisher and no SmartScreen warning appears. Verify that the package came from the official release page before continuing.

Build from source instead:

npm install
npm run build:mac   # or: build:linux / build:win

🧭 What's in this release (maturity)

• ✅ Implemented: everything shipping in v0.34.1, plus: session replay with step-through playback and discussion; the Cellosaurus and Monarch connectors; GEO matrix discovery in the omics connector; structure extraction for uploaded PDFs; continuous usage-chart inspection; and native Windows titlebar menus.
• 🚧 Partial: provider choice remains constrained by the active framework's endpoint compatibility; remote compute covers direct SSH and Slurm (cloud-GPU submission is not built yet); WSL2 Bash remains an opt-in Windows x64 preview; the skills commons ships marketplace discovery but not cross-machine forking or user-facing version pinning; reproducibility ships replayable per-version verification, session replay, and RO-Crate packaging, while solver-exact equivalence remains open; conditional package restore is an exported script workflow; and review is opt-in and record-scoped.
• 🗺️ Roadmap: a unified model gateway, cross-machine skill forking and version pinning, cloud-GPU execution, stronger sandboxing and credential isolation, and collaborative research workflows.

🐢 Known Limitations

• Replay reproduces recorded steps, it does not re-execute them. Solver-exact equivalence guarantees remain open; replayable verification remains the deterministic check, and starting a check from the web client currently requires the desktop app.
• Sensitive package evidence is opt-in. Session diagnostics include sensitive package evidence only after explicit confirmation, and the export stays local until you share it.
• Imported .science sessions are read-only. They stay inspectable and referenceable, and forking them into a writable continuation remains available; execution and continuation remain disabled on the import itself.
• Bookmarks belong to a single session. They do not follow branch switches, join .science package exports, or sync across machines — forking copies them into the new session with fresh identities.
• PDF annotations are bound to the file version they annotate. Notes follow the file across projects and sessions where that version is shared, but they do not sync across machines.
• WSL2 Bash is a preview. It is opt-in on Windows x64 only; PowerShell remains the default shell runtime.
• Remote compute covers direct SSH and Slurm. Cloud-GPU submission is not built yet.
• Editable artifacts cover text formats. Binary formats stay read-only, and editing always publishes new versions.
• Network sandboxing covers the app's notebook and compute runtimes, not the whole system. On Windows, the boundary applies only after the sandbox's one-time administrator setup.
• Provider choice is per framework, not one unified gateway. The available protocol depends on the selected agent backend, and remote endpoints must use HTTPS.
• Code reconstruction is LLM-generated. It does not replace deterministic reproduction; replayable verification is the deterministic check.
• The reviewer is opt-in and record-scoped. It does not replace domain-specific validation of citations, units, statistics, or methods.
• No local GPU compute backend.
• No multi-user real-time collaboration.

🙏 Acknowledgements

Thanks to @ewen-poch, @wen2zhou, @nasus2002, @Harbor404, @imjszhang, @Korrz777, and everyone in Discord, X, and Discussions.

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Full Changelog: https://github.com/aipoch/open-science/commits/v0.35.0