Here is the current plan:
Write an implementation of the FIX protocol in Python, with MySQL storing the data as if it were a charting application. I'm working on this with one other programmer, we won't release anything until we have some code. A few programmers have offered to help, we will be doing everything in Python and MySQL.
Quote Protocol
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Interpreted data
Writes to MySQL Database

Order Protocol
FIX 4.4 base
Proprietary Extensions
Generics for handling order types
Can fetch data on position sizes, balance, etc.

Indicators
Written in MySQL (SQL, possibly some Transactional SQL, Possibly stored procedures)
Python Indicator Interface (PyIndicator)
Indicators can also be written in Python
Can be time sensitive and historically time sensitive. (In the past X weeks of data, how many Tuesdays at 8am NY time did the price go up if 8am London time went up?)

Automated Trading
Uses Indicators and Quotes to place orders
Written in Python, makes PyIndicator calls
Sends orders to OrderProtocol
Has internal data structures, objects

Account Information
Fetches information from OrderProtocol
Used to pick lot sizes
Historical performance records
Historical record of trades