PhyloMosaic

Help

Short answers to the questions that come up. Each how-to deck below walks one option step by step with the screen for each step.

Data and backups

Where is my data?

In this browser, on this computer, in the browser's own storage (IndexedDB). Nothing is sent to a server. Another browser, another computer or a private window does not see it. The backup file you download from Data and settings is the copy that travels.

My workspace is gone after a few weeks in Safari.

Safari deletes a site's stored data after seven days of Safari use without a visit to that site. Two protections: download the workspace file after every session (the home page reminds you when a backup is due), and add the app to the Home Screen or the Dock, which Safari exempts from that cleanup. Chrome, Edge and Firefox do not delete on a timer; use "Ask the browser to keep it" in Data and settings and they will not evict the data under storage pressure either.

Autosave stopped and a message says the browser is out of room.

Photos take most of the space. Download the workspace file now, then remove the largest images from artifacts you no longer need the picture for (the text and tags stay). Data and settings shows how much of the browser's allowance the site uses.

How do I move to a new laptop?

Download the workspace file on the old machine (locked or plain), open the app on the new one, go to Data and settings and load the file. A locked file asks for its passphrase. Then delete the workspace on the old machine from Data and settings.

Can two people edit the same workspace?

Not at the same time in this version. One person holds the workspace; others contribute through the check-in link, the slip form on a tablet, or by sending files to import. Hosted shared editing is on the roadmap.

Does anything go to a server?

No. The app runs in your browser, stores in your browser, and the only network requests are for the two Google Fonts, which fall back to system fonts when offline. The check-in link opens your mail app; the slip form keeps answers on the tablet and downloads a CSV. The AI loop is work you do outside the app with files you export and import.

Passphrase lock

I forgot the passphrase.

Nobody can recover it, including STEMsaic. The lock encrypts the workspace with a key made from the passphrase and keeps nothing that could open it another way. A plain backup file (Data and settings, "Download plain copy") is the only other way in. Delete the locked workspace from the unlock screen and load the plain file.

What does the lock protect?

The workspace and every photo in this browser's storage, and the locked backup file. Someone with the laptop and no passphrase sees nothing readable. It does not protect a plain backup file you downloaded, so keep those where the data pathway allows.

Collecting

The check-in link does nothing on a partner's device.

The link ends with "Send by email", which opens the device's mail app. On a locked-down device with no mail app, use "Copy as text" and paste into any message, or "Download file" and send the file. Import either one on the AI loop page.

How do I rename a partner or fix a category?

Partners page, Edit on the row. Check-ins, artifacts and links follow the record, so nothing else needs changing.

Why is a group hidden on a dashboard?

Groups under the suppression threshold (5 or 10, set by the data pathway) are hidden, and a second group is hidden when it would reveal the first by subtraction. The count of hidden groups shows on the figure.

Can I bring in past data?

Yes: check-ins, artifacts, responses and partners from CSV (Data and settings, Bulk import), a sociogram file (Sociogram page), a REFI-QDA project or codebook from another QDA tool (Data and settings), and the JSON an AI agent returns (AI loop). Every import shows its rows for review before anything is saved.

Sharing and exports

The report lost its shading in Word.

Download the report as HTML and open it in a browser, then print to PDF; the shading holds. Word drops some table styling when it opens HTML. Markdown works in any editor.

Can an evaluator use NVivo or MAXQDA with this data?

Yes. Data and settings, "Download project (.qdpx)" writes a REFI-QDA project with every artifact and check-in as a source, the codebook as codes, partners as cases and each tag application as a coding with its quote. Those tools and others (ATLAS.ti, QualCoder) open it. Their codebooks and codings come back the same way.

How does the AI loop work without an API key?

The app writes the schema, the codebook and the prompts (AI loop, "Download AI kit"). You run them in Claude or any agent with your material, save the JSON it returns, and load it in step 3. Every row is shown before it is saved and carries the agent as its coder. A tag the agent used that is not in the codebook is offered as a new tag you can accept or skip.

How-to decks

One deck per option, with a demo workspace you can open in the app with one click from the overview page.

Something else

Data and settings has a "Copy diagnostics" button. It copies the app version, browser, storage use, pathway and the last ten page errors, and no workspace data. Paste that into your message to STEMsaic Research Impacts.