FEniCS (https://fenicsproject.org/): a popular free open-source (LGPLv3) computing platform for solving partial differential equations (PDEs) [en].
Jupyter (http://jupyter.org/): a project to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages [en].
R language (https://en.wikipedia.org/wiki/R_(programming_language)): a free software environment for statistical computing and graphics [en].
OpenDreamKit (https://opendreamkit.org/): a project that brings together a range of projects and associate software to create and strengthen virtual research environments [en].
SageMath (http://www.sagemath.org/index.html): a free open-source mathematics software system [en].
Scilab (https://www.scilab.org/en/): free-libre cross-platform software for numerical computation [en].