Maxima aims at Mathematica, descends from Macsyma
"Open source satellite control"
biopython, bioperl, biojava, scipy (accomodates Fortran and C++), Octave, Scilab, R, ...
Numerical Python. Note such related resources as enthought, Eric Jones' scipy presentation, ...
clustering ...
Lush
Bil Kleb's paper, "paperComputational Simulations and the Scientific Method" addresses component tests, model management, and publication of test fixtures. "Extreme Programming in a Research Environment" does some of the same.