The Manual recommends mysqldump as @RomainC suggests:
mysqldump -h [mysqlhost] -u[username] -p[password] --opt ccnet-db > /backup/databases/ccnet-db.sql.`date +"%Y-%m-%d-%H-%M-%S"`
mysqldump -h [mysqlhost] -u[username] -p[password] --opt seafile-db > /backup/databases/seafile-db.sql.`date +"%Y-%m-%d-%H-%M-%S"`
mysqldump -h [mysqlhost] -u[username] -p[password] --opt seahub-db > /backup/databases/seahub-db.sql.`date +"%Y-%m-%d-%H-%M-%S"`
For those using the Pro version, however, there is a real-time backup tool as well.
I suppose if you are willing (and able) to stop your server you could do a backup using rsync and even grab an occasional bare metal image.
There are a few previous discussions on backup that you might want to reference. Some examples are here and here.