BehavFlow: automating aspects of rodent behavior testing

Setup

• Use a relational database (SQLite) to store animal records, experimental treatment, and metadata.
• Use cloud storage to synchronize experimental schedules and data files across all computers
• Create a local user on Windows to install Dropbox and run MedPC so that it is not specific to one technician
• Use a Linux Server on campus to run services that monitor dropbox folders to convert file formats, run analysis, and generate notifications.
• Use an off campus server (outside of firewall) to work with a messaging system (Slack) to convert user input into data in standard format and send notifications

Services

• Convert Spreadsheet to MedPC macros for each session and all individual rats. A pdf file is also generated for record keeping
• Generate notifications when each operant run is finished
• Extract MedPC data into Spreadsheet, add session number
• Generate notifications when change in operant schedules are needed (e.g. dose, extinction, reinstatement)
• Generate warnings on exceptions (e.g body weight loss, unrealistic body weights, multiple animals have exactly same body weights).
• Generate daily schedule changes in the format that can be pasted into the Spreadsheet.
• Generate “notes” that can be pasted into slack once some procedures are done (e.g. Baytril).
• Generate reminders for starting experiments (until the experiment is started, i.e, data files exist)
• Generate reminders for missing data in database (e.g. DOW, assignment of experiment treatment)
• Update database when certain procedures are done (e.g. Brevital test)
• Maintain a log of periodic tasks (prepare drugs, cleaning chambers, etc.)
• We still have one manually maintained Spreadsheet for experiment planning.

Advantages

• Reducing experimental error
• Convert user friendly format (Spreadsheet) to machine loadable exp file in MedPC.
• “Macros” and pdf files are archived automatically.
• Use foreign key in database
• Check against existing animal ID in the /note app
• Automatic reminder of schedule change
• Automatic check against common errors
• Automatic check for missing information
• Automatic database entry from notes entered in browser
• Standardized experimental record for miscellaneous notes for each animal
• Entered on a computer or smartphone
• Animal ID verified.
• Name of technician and dates are automatically recorded

Disadvantages

• Somewhat fragile (many components)
• Need backup plan when system is down
• Need programming skills
• Still several manual processes (e.g. schedule change still needs to be copy-pasted).