Computing

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)