Bio-recipes (Bioinformatics recipes) in Darwin

Bio-recipes are a collection of Darwin example programs.  They show how to solve standard problems in Bioinformatics. Each bio-recipe consists of an introduction, explanations, graphs, figures, and most importantly, Darwin commands (the input commands and the output that they produce) that solve the given problem.

Darwin is an interactive language of the same lineage as Maple designed to solve problems in Bioinformatics. It relies on a simple language for the interactive user, plus the infrastructure necessary for writing object oriented libraries, plus very efficient primitive operations. The primitive operations of Darwin are the most common and time consuming operations typical of bioinformatics, including linear algebra operations. Darwin can be downloaded free of charge from here.

The reasons behind this particular format are the following.

1. It is much easier to understand an algorithm or a procedure or even a theorem, when it is illustrated with a running example.
2. The procedures, as written, may be run on different data and hence serve a useful purpose.
3. It is an order of magnitude easier to modify a correct, existing program, than to write a new one from scratch. This is particularly true for non-computer scientists.
4. The full examples show some features of the language and of the system that may not known to the casual user of the Darwin, hence they serve a tutorial purpose.

Each problem is organized in a separate recipe which corresponds to an html file. These files can be accessed by clicking on the links above. Each recipe contains Darwin statements shown in green, Darwin output in red and comments in black. The comments include a short description about the problem that is solved in the recipe, and about the algorithm that is used to produce the solution.

The intended method of usage for the Bio-recipes is that after reading the explanatory text, the Darwin statments can be copied (cut and paste) to a Darwin prompt. The Darwin output can then be compared to what is given as output in the recipe. If you have to solve a slightly different task from what is shown in the recipe, you can always copy the Darwin statements into a text editor. There you can modify the statements such that your specific problem can be solved.

CBRG

Last updated on Tue Jul 8 04:11:35 CEST 2003 by GhG