Computing
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Programming Principles
General
- Keep code and data strictly separate.
- Be aware of whether your programming creates executable content.
- When using random number generators, seed them explicitly to keep your results reproducible.
Debugging
- Computers are deterministic machines. All bugs can be reproduced.
Object Oriented Programming
- An instance in a computing process must represent exactly one instance in the modelling domain.
- Use random number generator objects where possible.
Databases
- Identification and description must be kept separate.
- Primary keys should be generated where reasonably possible.
Software
An incomplete list of software that I use.
- The R statistical computing language and system
- Python, a scripting language with a very decent level of support for object oriented programming
- The editors emacs for larger edits, and vi for smaller edits (yes, I use both)
- Java
- PostgreSQL, a free SQL database management system
- the transsys simulator for regulatory gene networks (which I've written myself)