Coarse-grain DNA parameter construction scripts and datasets

A visualisation tool for studying parameter dependence of the space of helical equilibria of elastic rods

Software to compute the shape of sequence-dependant DNA under constraints.

A C++ library for 3D transformations using vectors, matrices, quaterions and Cayley vectors

A visualization tool for studying the eigenmodes of a coarse-grained model of DNA

Curve and knot manipulation, analysis and visualization toolkit

A Python library for solving boundary value problems of differential algebraic equations with advanced and retarded (forward and backward) delays.

VBM is a visualization tool developed at the Laboratory for Computation and Visualization in Mechanics, formerly at the University of Maryland and currently at the Ecole Polytechnique Federal de Lausanne. The unifying themes in VBM are to use visualization and special projections of the bifurcation diagram to facilitate efficient computation of the solution set, organize and allow easy access to the large data sets that arise, and most of all to generate mathematical understanding of the features and properties of the solution set.

DataViewer is an object oriented toolkit for creating visualization applications. DataViewer has both standard and user definable OO data-structures, provides generic viewing facilities (rotation, zoom, etc. through either mouse, key-bindings or 6D controller), bitmap copy to file (PPM), VRML output, animation, stereo viewing, etc. DataViewer is analogous to the widely distributed GeomView program, but the data structures and implementation are more oriented toward interactive high-performance computing.

Snake

Tracking DNA on pairs of stereo-images

Slinky is a package built to interactively explore solutions of an initial value problem for a system of ordinary differential equations describing an elastic ribbon. The ODE system governs the shape of an elastic rod that is used as a model of DNA.