Computing

Programming Principles

General

• Keep code and data strictly separate.
  • Be aware of whether your programming creates executable content.
• Computers are deterministic machines. All bugs can be reproduced.
  • When using random number generators, seed them explicitly to keep your results reproducible.
  • See "Rediscovering Computational Autopoiesis" by Barry McMullin & Francisco Varela for a very instructive example of possible consequences of complex computing that was not fully reproducible.

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.

User Interface Design

• Computers are symbol processing machines. Hence, symbol based user interfaces are most general and powerful.
  • Symbol based interfaces support reproduction of computing much better than graphical user interfaces. The manuscript Reproducible Econometric Research by Roger Koenker and Achim Zeileis discusses some aspects of this.
  • The article "Semiotics and GUI Design" (a.k.a. "Excessive Realism in GUI Design: Helpful or Harmful?") by Gene Callahan does not seem to be available online anymore (two links that are currently stale are http://www.stgtech.com/staff/gcallah/tech_articles/semiotics.html and http://gwa.municipia.at/files/semiotics.html)
• The claim that graphical user interfaces are easier or more intuitively to use than symbolic interfaces is problematic.
  • It is difficult to state the objective meaning of "intuition". In a reasonable approximation, intuition can be defined as a summarised background of experience that is unconscious or semi-conscious.
  • See The Command Line - The Best Newbie Interface? by Richard Wareham.

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)