The overarching theme of this proposed E-CAM Transverse Extended Software Development Workshop (ESDW) is the design and control of molecular machines including sensors, enzymes, therapeutics, and transporters built as fusion proteins or nanocarrier-protein complexes, and in particular, the software development and interfacing that this entails. Several immuno-diagnostic companies and molecular biology experimental groups have expressed a strong interest in the projects at the core of this proposal. The proposed ESDW is transverse as it entails the use of methodologies from two E-CAM Scientific Workpackages: WP1 (Advanced MD/rare-events methods) and WP4 (Mesoscale/Multiscale simulation).