Settings

Each change saves the moment you toggle, type, or pick a new option. A small “Saving…” indicator near the page title flips to a green “Saved” for about a second, then disappears. The “Saved” state reflects the write to your users/<you>/settings.json file in the connected data folder.

Rail search

A search bar at the top of the left rail filters the list of sections down to whatever matches your typed text. Type notification and only the Notifications item stays visible. Type trash and the rail narrows to Trash & history. Clear the bar to restore the full list. The currently open section always stays loaded in the pane even when the search filters it out of the rail.

Groups and sections

The rail is divided into four groups. You, Usage & billing, Workspace, and Data. Lab accounts add a fifth Lab group. A lab head's Lab group moves to the top of the rail so the most-used controls lead.

You

Three sections about your identity in the app.

• Profile & appearance - your display name, avatar color and gradient, tinted header toggle, ORCID, affiliation, researcher profile, and the public-profile card. Also shows your account and keys (sharing identity, fingerprint, recovery code). This folds in everything that used to live on the separate /profile route.
• Account & security - who you are signed in as, a Switch user button that opens the same picker as the app login screen, and the password gate for this account. The password wraps your keys with Argon2id (a deliberately slow, memory-hard function) before anything is written to disk. Setting a password gives you a one-time recovery code to store somewhere safe.
• Add a free account (solo users only) - a gentle one-card explainer of the features a free cloud account unlocks (BeakerBot AI, cloud storage, email and phone notifications, Companion pairing, and sharing). If you already have a cloud account this card is hidden and Usage & billing appears instead.

Usage & billing

Because a free account is required to use ResearchOS, this section is available to everyone once you are signed in. It surfaces your cloud and AI usage so you always know where you stand.

• AI usage - your live BeakerBot token balance, recent task costs, and three prepaid top-up packs ($10, $25, $50). During the beta period, when billing enforcement is off, the section instead shows the “AI is free during the beta” framing. Token amounts for each pack come from the live rate, so the numbers stay accurate as rates change. A link to the pricing page shows the current per-token rate. Flagged with a “new” pill.
• Cloud storage - how much of your cloud storage cap you have used, what tier you are on, and a link to the pricing page for upgrade options. Flagged with a “new” pill.

Workspace

Controls for how the app looks and behaves for you day to day.

Appearance & motion

Three sections under one rail item.

• Appearance - three tiles (Light, Dark, System) that set the app theme. System follows your device. This is a per-device preference and does not sync between computers. The welcome page always stays light.
• Animation - a grid of celebration themes for the animation that plays when you complete a task. Ten themes plus a None tile to skip the animation entirely. Click a tile for a live preview. Separately, a BeakerBot animations toggle governs streak and milestone celebrations. The two controls are independent.
• Professional mode - one switch that silences the streak badge, the per-task animation, and BeakerBot personality at once. Turning it back off does not re-enable those automatically; you restore each one from its own panel.

Defaults

Four dropdowns and one toggle for the starting view on the two biggest pages. None of these lock you in. Flipping the view inside a page overrides the default for that session; reopening brings the default back.

• GANTT default range - 1 week, 2 weeks, 3 weeks, 1 month, 3 months, 6 months, 1 year, or All.
• Calendar default view - Month, Week, or Day.
• Date format - MM/DD/YYYY (US), DD/MM/YYYY (EU), or YYYY-MM-DD (ISO).
• Time format - 12-hour (1:30 PM) or 24-hour (13:30).
• Show shared content by default - when on, GANTT and other views include tasks shared with you, not only your own.

Sidebar & tabs

Two controls under one section.

Tabs is a grid of checkboxes for every tab in the header. The full list is Home, Workbench, GANTT, Methods, Sequences, Chemistry, Data Hub, Phylogenetics, Figures, Inventory, Purchases, Calendar, and Links. Home is always on. Uncheck any other tab to hide it from your header. Below the grid, a Default landing tab dropdown picks where the app opens on load. It only lists tabs you have visible, so you can't land on a hidden tab.

Sidebar has two toggles for the left sidebar that appears on every page except Calendar. The Tasks toggle shows your due, overdue, and upcoming tasks for today. The Calendar events toggle adds events from any ICS feeds you have subscribed to. When Calendar events is on, a How much calendar to show dropdown lets you pick Today only, or Today plus the next 3, 7, 14, or 30 days. If you uncheck both toggles, an amber warning appears to tell you the sidebar will be empty on non-calendar pages.

Companion

The Companion section is where you pair your phone to the ResearchOS Companion app and adjust two push preferences.

• Open Companion hub - a button that opens the Companion hub popup (Connect, Info, and Settings tabs) from inside Settings. This is the escape hatch when the header Companion button is hidden, because the popup's own Settings tab is still reachable here.
• Show Companion button on Home - toggles the phone icon in the app header. Off hides it from the header; Companion is still reachable from this Settings section.
• Auto-publish snapshots to paired phones - when on, the laptop pushes today, inventory, and notebook snapshots to your paired phones. Off stops the push.

Below the toggles, the paired devices list (from DevicesSection) shows every phone you have linked with a QR code, along with its last-seen time and an option to unpair it.

Notifications

A 5x4 routing matrix. Five notification categories (rows) crossed with four delivery channels (columns). Every cell is an independent toggle.

The five categories are:

• Shared & assigned to me - a task, method, or project shared with you, or a task assigned or flagged for your review.
• Comments & mentions - someone comments on your work or @-mentions you.
• Lab announcements - your PI posts a lab-wide announcement.
• Purchases & orders - an order you requested is placed or approved, or one is assigned to you.
• Reminders & schedule changes - calendar reminders, and when a shared task's date shifts.

The four channels are:

• Bell - the in-app notification bell. Always on; collects everything.
• Laptop - desktop pop-ups on your computer.
• Phone - push notifications to your paired Companion phone (account required).
• Email - email delivery (account required).

Phone and Email channels require a cloud account. Solo users without an account see a gentle upsell in those columns instead of dead controls.

AI Helper

Generates a schema-aware prompt you can paste into Claude, ChatGPT, Gemini, or Microsoft Copilot to turn it into a support assistant that understands your ResearchOS data model. The section has three parts, a size picker, a copy button, and one-click open-in buttons.

The size picker is a three-option radio group. Token counts are read live from the AI Helper manifest at runtime, so they reflect the current build rather than a hardcoded figure.

• Lean - fits most chat windows including free-tier context limits.
• Full (recommended) - best for big-context models like Claude Sonnet, GPT-5, or Gemini 2.5 Pro.
• Minimal - for tiny windows or local models.

The Copy prompt to clipboard button copies the selected size's markdown. The Open in your AI row has four buttons (Claude, ChatGPT, Gemini, Copilot). Each one copies the prompt and opens that provider in a new tab.

When the prompt served by the app is older than the running code, an amber stale-prompt callout appears with a Pull latest from research-os-xi.vercel.app trapdoor. Clicking it fetches the current manifest and prompt from the live deploy cross-origin. A freshness footer below the buttons shows the date the prompt was built and the commit it came from.

Behavior

Two toggles. Confirm destructive actions shows an “Are you sure?” prompt before you delete a task, project, or similar object. Switching it off skips the prompt. Spell-check in the editor underlines likely misspellings as you write notes. It is off by default because bench shorthand (gene names, reagents, abbreviations) reads as misspelled. The dictionary already knows common lab terms; you can add any flagged word to your own dictionary.

Streaks & PTO

Tracks how many workdays in a row you have saved something in ResearchOS. Streak data is stored in a per-user sidecar and is visible only to you.

The section has a single Enable streak tracking toggle. Disabling it pauses tracking but preserves your existing count so you can re-enable later without losing your history. When enabled, a stat trio appears below the toggle showing your current streak, personal best (always preserved even after a reset), and the date the current run began.

The Reset streak button (red) zeros the current count. A confirmation modal shows your count and asks whether you also want to clear celebrations seen (so milestone animations can re-fire). Click Cancel to back out.

Below the reset, the PTO subsection lets you mark planned days off so the streak counter skips them.

Tips

Two cards. What's new opens the release notes modal listing the most recent feature additions. Explore demo launches the app in demo mode with a pre-seeded folder so you can try any feature without touching your real data.

Data

Controls for your connected folder, local data inventory, and import or maintenance tasks.

• Data folder - the folder this app currently reads and writes. A Connect or switch folder button re-points the app at a different folder. Switching never moves or deletes any files.
• Inventory & export - a read-only transparency panel. Files on disk lists every file path the app has written to your folder, grouped by top-level directory. Browser IndexedDB keys lists the four known keys the app keeps in your browser (the folder access handle, handle metadata, current user, and main user). External calls lists every destination the browser contacts when using ResearchOS: the /api/calendar-feed proxy, Vercel anonymous analytics (va.vercel-scripts.com and vitals.vercel-insights.com), and the live deploy domain (research-os-xi.vercel.app) when you pull the latest AI Helper prompt.
• Trash & history - the cleanup window radio picks how long deleted records stay recoverable (a fixed number of days, or never auto-purge). An Open trash link takes you to the trash page to restore or permanently delete items.
• Maintenance - an Import experiment button for bringing in a -raw.zip bundle another ResearchOS user exported, and a Format upgrades row that shows how many background format checks have run. A Re-run all checks button replays the whole set for support or power-user cases. Format upgrades now run automatically at folder-connect time.
• Lab archives - the LabArchives import wizard. A single card with an Open import button that lets you bring a LabArchives Offline Notebook ZIP into ResearchOS, mapping each notebook page to a task and each folder to a project. See the LabArchives integration page for the full walkthrough.
• Offline & sync - a Block calls to our server toggle that disables the /api/calendar-feed proxy route. An amber notice confirms which features are paused while the toggle is on.

Lab group (lab accounts)

Lab accounts see a Lab group in the rail. For a lab head, this group moves to the top of the rail. Lab members see only the Members section; the PI-only sections (Audit trail, Retention registry, and Department routing) stay hidden.

• Members - a unified view of the cloud lab roster (invite link, pending join requests) and the folder roster (archive and restore for a legacy multi-user folder). If there are pending join requests, the Members rail item shows a red count pill and an attention dot so a PI can see it at a glance without opening the section.
• Lab settings - the Account type tile (Member vs PI) that reshapes your nav and available controls, plus, for a lab head, the lab identity card (name, PI title, optional logo) and the membership agreement (mode, visibility, approval policy). Clicking a non-current Account type tile opens a confirmation dialog before writing anything, and a 10-second Switch back toast lets you undo.
• Audit trail (PI only) - a read-only log of every field change you saved to a member's record as the lab head. An Open audit trail button launches the viewer with a member picker. This surface never edits anything.
• Retention registry (PI only) - configure per-funder and per-member retention policy and run a folder manifest for compliance records.
• Department routing (PI only) - opt in to the purchase routing module. Add department and HR contacts, and edit the draft email template that the Send to department button on a purchase populates. Drafts open in your own mail app, so they send from your real address with no stored credentials.