I've authored or contributed to a number of open-source software packages in the field of computational statistics and physics.
The SCov2-MD database
Allowing the evolution-structure-dynamics-phenotype multidimensional analysis on SARS-CoV-2 genomes. Described in the paper SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions, published in Nucleic Acid Research.
Enabling PLUMED2 Collective Variables (CVs) and arbitrary functions to be defined and auto-differentiated in the Python language. Described in the paper PYCV: a PLUMED 2 Module Enabling the RapidPrototyping of Collective Variables in Python
Providing packages and information on an extensive array of DTW-style algorithms in both R and Python. The DTW algorithm computes the time axis stretch which optimally maps one timeseries (query) onto another (reference). The packages provide the most complete, freely-available (GPL) implementation of Dynamic Time Warping-type (DTW) algorithms up to date. They are described in the paper Computing and Visualizing Dynamic Time Warping Alignments in R: the dtw Package.
Online calculator for A clinical-molecular prognostic model to predict survival in patients with post polycythemia vera and post essential thrombocythemia myelofibrosis. Leukemia 31, 2726–2731 (2017) doi:10.1038/leu.2017.169
Protein preparation: proteinPrepare deals with titration and optimization of the H bonding network preliminary to simulation.
Prepare a protein extracted from PDB and make it ready to build a system and run molecular dynamics simulations. The preparation includes titration of the protonation states using PROPKA 3.1 and overall optimization of the H-network using PDB2PQR 2.1. Choices can be overridden via software or in a 3D webGL viewer. Available online, as part of Playmolecule's ProteinPrepare, and in HTMD (High Throughput Molecular Dynamics), See also the introductory talk at the 3rd HTMD workshop. doi:10.1021/acs.jcim.7b00190
METAGUI extends VMD with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by long-scale molecular dynamics. It is described in doi:10.1016/j.cpc.2017.04.009
The PLUMED2 Metric in HTMD
The MetricPlumed2 class allows the use of arbitrary PLUMED2 collective variables in the construction of Markov models within HTMD. See the introductory talk at the 3rd HTMD workshop.
The MEMBPLUGIN membrane plugin analysis suite for VMD.
MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers. It is described in the paper MEMBPLUGIN: studying membrane complexity in VMD.
VMD plugin provides convenient access to the extensive set of collective variables (CV) defined in the PLUMED software. It allows the use of PLUMED syntax to conduct analysis on MD trajectories, and a convenient interface to prepare the metadynamics CV definitions. It is described in the paper Plumed-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts.
The Density Profile Tool is a VMD analysis plugin that computes 1-D projections of various atomic densities. It's described in the paper Computing 1-D atomic densities in macromolecular simulations: The density profile tool for VMD.
An analysis plugin for VMD that computes one, two or three-dimensional diffusion coefficients during a loaded trajectory based on average mean square displacements. Described in Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD
The RBoinc system (distributed computing as a virtual supercomputer)
RBoinc extends the Berkeley Open Infrastructure for Network Computing (BOINC), the open-source middleware for distributed computing projects, with mechanisms to submit and manage large-scale distributed computations from individual workstations. It is described in the paper Tools to run and manage large-scale BOINC simulations(2010).
a collection of TCL-VMD functions and iterators that support extraction of structural data from large-scale simulations. They provide simple semantics to iterate a block of code over frames or trajectory files, functions to compute the number of native contacts, distance matrices, and more.
a modeling plugin which copies the coordinates of a selection A from another selection B, preserving A's topology. Coordinates of A's atoms will be copied verbatim when an unambiguous match exists in B; otherwise, the new coordinates will be guessed with a local fit.
A multivariate dataset obtained recording the stretch of various segments of the fabric of a sensorized garment while executing several rehabilitation exercises. Open data at Zenodo.
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.
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