SMTP

MIMOSA can send email alerts when genomic clusters grow and meet configured outbreak thresholds. Notifications are disabled by default and require an SMTP server.

SMTP setup

Set the following variables in .env:

NOTIFICATIONS_ENABLED=true
SMTP_HOST=your.smtp.server
SMTP_PORT=587
SMTP_SECURE=false
SMTP_REJECT_UNAUTHORIZED=false
SMTP_FROM=no-reply@example.com

Restart MIMOSA after changing these values. To verify the configuration, send a test email:

GET /api/mail/test

The email is sent to the authenticated user. To send to a different address:

GET /api/mail/test?to=other@example.com

Thresholds

Two independent thresholds control when notifications are sent.

Outbreak threshold (system-wide, in backend/src/config/outbreak-rules.json)

The minimum cluster size for MIMOSA to consider a cluster an outbreak at all. Clusters below this threshold are never surfaced to any user. See Configuration for how to set this per profile.

Notification threshold (per user, in Settings)

The minimum cluster size required before a specific user receives an email. Users set this in their own notification preferences — see Notifications.

Alert visibility

Outbreak alerts appear in the dashboard banner for as long as the cluster remains active. After a period of inactivity (no meaningful growth), alerts are collapsed rather than deleted — they can be expanded at any time by clicking Show older alerts in the banner. The full history is available on the Notifications page.

The following settings in backend/src/config/outbreak-rules.json control this behaviour:

Setting	Default	Description
alertVisibilityDays	14	Days without meaningful growth before an alert is collapsed. Set to null to keep all alerts expanded indefinitely.
alertMinGrowthForRefresh	2	Minimum cumulative increase in cluster size required to reset the visibility timer. With a value of 2, a cluster growing from 5 → 6 does not reset the timer, but a further increase to 7 does.