AIPOCH Open-Science v0.35.1

AIPOCH Open-Science v0.35.1

A reach-and-polish release: the connector catalog grows GWAS summary statistics discovery, InterProScan sequence submission, and IEDB receptor evidence searches, the workspace start experience gets a cleaner surface with a common-actions session menu, and Requesty joins the official provider picker.

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.

v0.35.1 widens connector reach and tightens the daily workspace. In the connector catalog, the human genetics connector gains GWAS summary statistics discovery for locating complete study files and reference genome information, InterProScan gains bounded sequence submission to close the submit → status → results loop, and the IEDB connector adds TCR and BCR receptor evidence searches. The new-conversation screen now keeps research starters one click away while drafting, and the session header groups common actions — edit, pin, side chat, fork, export, archive — behind one menu. Requesty joins the official provider picker with a curated, verified model catalog and built-in connection validation. Underneath, fixes preserve composer context across session binding, keep imported sessions read-only, protect replay follow-ups, and harden PDF, notebook, and workspace reliability.

✨ Highlights

• Connector reach. GWAS summary statistics discovery joins the human genetics connector, InterProScan gains sequence submission, and the IEDB connector adds receptor evidence searches. (#3278, #3280, #3304)
• A better start. The new-conversation screen unifies research starters with the composer, and the session header gains a common-actions menu. (#3297, #3267)
• Requesty provider. Requesty joins the official provider picker with a curated model catalog. (#3114)

🚀 New Features

• GWAS summary statistics discovery in the human genetics connector: locate complete summary-statistics files, metadata, and reference genome information for a study. (#3278)
• InterProScan connector gains bounded sequence submission, completing the submit → status → results workflow without manual job creation. (#3280)
• IEDB connector gains TCR and BCR receptor evidence searches alongside epitope and assay search. (#3304)
• New conversation start experience: research starters stay one click away while drafting, with a compact package import option. (#3297)
• Session header menu groups common actions: edit and pin the session, start a side chat or fork, export the conversation, session package, or diagnostics, and archive. (#3267)
• Requesty provider in the official provider picker, with curated model catalog and built-in connection validation. (#3114)

🔧 Improvements

• Side chat tabs and toolbar follow the compact workspace layout. (#3275)
• OpenRouter and Requesty model catalogs are refreshed. (#3276)

🐛 Bug Fixes

• Replay and sessions — follow-up scrolling and recorded file questions are preserved in replay (#3292); imported sessions keep their historical interactions read-only (#3269); the composer keeps its context when a session binding changes (#3306).
• Notebook and runtimes — cross-language notebook file lineage is projected correctly (#3296); corrupt run documents are isolated without blocking recovery (#3294); R environments are preserved when project paths contain spaces (#3290).
• PDF and preview — literature layout extraction is hardened for complex external papers (#3286); PDF context persists before the first prompt is admitted (#3270); verified PDF notes are unified across projects (#3264); persistent reader notices are reduced (#3274).
• Agents and permissions — shared-login settings are isolated by default (#3289); unattended Claude permission denials are explained in the workspace (#3287).
• Workspace and reliability — the titlebar stays above overlays and outside portaled surfaces (#3285, #3307); side chat composer and reading icons align (#3301); session header icons no longer overlap (#3279); unresolved bookmarks are handled and preview highlights clear (#3272); expired artifact transactions are retried (#3295); quoted punctuation no longer trips credential false positives (#3271); bookmark creation failures are diagnosed with their failure stage (#3273).

📦 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 v0.35.0, plus: GWAS summary statistics discovery in the human genetics connector; InterProScan sequence submission; IEDB TCR/BCR receptor evidence searches; the refreshed conversation start experience with a common-actions session menu; and the Requesty provider.
• 🚧 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, @nasus2002, @Korrz777, @Thibaultjaigu, @imjszhang, and everyone in Discord, X, and Discussions.

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Full Changelog: https://github.com/aipoch/open-science/commits/v0.35.1