The Structural Proteomics Application Development Environment (SPADE) provides a community suite for developing and sharing protein structure and sequence tools. It includes a custom molecular viewer, sequence alignment editor, many reusable tools, and a chemical probing suite to support experimental verification of predicted structural models.
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Theano features tight integration with numpy, transparent use of a GPU, efficient symbolic differentiation, speed and stability optimizations, dynamic C code generation, and extensive unit-testing and self-verification. Theano has been powering large-scale computationally intensive scientific investigations since 2007. But it is also approachable enough to be used in the classroom (IFT6266 at the University of Montreal).