Maxima aims at Mathematica, descends from Macsyma
"Open source in the lab"
"Open source satellite control"
biopython, bioperl, biojava, scipy (accomodates Fortran and C++), Octave, Scilab, R, ...
"Fortran, at home on Linux"
Numerical Python. Note such related resources as enthought, Eric Jones' scipy presentation, ...
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.