repo holding code for an ephys rig and a database for scientific data

Do these things
Measure these things
In this order
And if you do
You will find
What I found.

This repository has been opened, as-is, in hopes that someone might find some of the ideas explored here useful. This project was not finished and many comments reflect this. This was also my first large python project and there are significant issues with complexity management. Documentation is spotty and much of the code was written for python 3 running on windows XP with specific assumptions about other pieces of software and hardware being connected to the computer, no abstraction layer was implemented so the code probably wont run.

This repository has 3 parts, the database, the rig, and analysis.

• analysis not particularly interesting since it holds scripts for analysing specific data which is not publically accessible.
• rig contains considerable, if scattered, effort to build an integrated interface for controlling an electrophysiology rig and collecting data and metadata about experiments. The most useful code here provides a python interface for Clampex and MultiClampCommander and has already been made publically available via inferno.
• database contains an SQLAlchemy specification for a database for storing experimental data and metadata. It also contains an attempt to create a abstraction for specifying and running protocols on an electrophysiology rig, including everything from the breeding of mice all the way through tracking the serial number of the headstage a specific datafile was collected on.

• >= python 3.X (may run on 2.7.X but untested and may have hidden gotchas)
• >= sqlalchemy-0.8
• psycopg2
• docopt
• numpy
• scipy
• matplotlib
• ipython
• python-neo
• pyserial
• requests
• rpdb2 (debug)
• tom's personal utils (debug, tgplot) >_< bettered fix that

Oh man, don't even get started on this one.