Software

I've authored or contributed to a number of open-source software packages in the field of computational statistics and physics.

Past projects

  • Earlier research focused on the modelling of biomolecular recognition in unstructured proteins, a wide class of proteins, whose detailed mechanisms of action are largely undetermined, and on multi-scale simulation and prediction of the drug safety problems related with hERG within the Virtual Physiological Human Network of Excellence.
  • MyHeart's NeuroRehab project (2005-2008) The NR platform supports physicians and therapists in the delivery of personalized exercise plans. The recovery process supports both motor rehabilitation exercises, which are monitored with kinestetic strain-sensor garments, and cognitive rehabilitation. The project involved the creation of the mathematical models, refinement of algorithms, and development of hardware and software, up to the clinical tests of the prototypes. (See videoand publications)
  • AdaRTE dialog management system for the medical domain (lead, 2002-2008) The proposal set forth in my PhD thesis (AdaRTE, a framework to support automated spoken dialogues in telemedicine) was developed into a system which is now used routinely in teaching, research, and to realize dialog systems used in the clinic. (See publications)
  • Formerly, I worked with the APE collaboration in Pisa and DESY-Zeuthen (Berlin), profiling the hardware and compilation chain of the ApeNEXT massively-parallel dedicated super computer during its development.

Superseded software

  • RMSD trajectory tool enhanced with native contacts
    • enables VMD to compute the number of native contacts in a trajectory. It is an extension of the RMSD Trajectory Tool, of which it shares the interface.
  • The PdbTer plugin
    • allows VMD to write PDB files with TER cards separating molecules, as required by the PDB standard and some molecular-manipulation software (notably, tleap and xleap).
  • Full "Save as" for VMD
    • A function to (almost) save the complete state of a VMD session. Saved state includes the view, materials, colors (as with the usual save state menu item), as well as trajectories and topologies. This way, you can save and resume working on an image. Now part of the VMD extension functions.