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.
Total Number of Pairs of Amino Acids in the SwissProt Database
Basic introduction to programming in Darwin
Chi-square Test for a Contingency Table of Counts
Linear Regressions: 5 Methods to Compute A^t * A
Unbiased selection of sample alignments
Counters: an example of a simple Class
Linear algebra in Darwin
Finding Orthologous sequences and building a phylogenetic tree
Significance assessment of an alignment
Multiple repetitions of a short motif
Sequence Alignments with Special Characteristics
Search your Name in the SwissProt Database
Recognizing Proteins by Weight of their Digested Parts
String Alignment using Dynamic Programming
Linear Classification or Discrimination
Random Distance Trees, analysis of properties
A Class for Discrete Bayesian Networks in Darwin
Phylogenetic tree of the "Nigerian Prince" email scam
The tRNA Pairing Index
The most significant Codon Bias in Yeast
Virus Classification using k-nucleotide Frequencies
Determination of Haplotypes from Genotype information
How to Compute Mutation and Dayhoff Matrices
Introduction to Codon Substitution Matrices
Idealized Mutational Clocks
Back Translation (protein to DNA) in an optimal way
Greedy algorithms for optimization: an example with Synteny
Computing Confidence Levels for Quartets
How to Solve a Number Puzzle
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.
Last updated on Tue Jul 8 04:11:35 CEST 2003 by GhG