Clarrhmos is a description language and simulator for myocardial structure and electrophysiology. Input to the program is a model file specifying types of cells, action potential shape, refractory period, 3D placement of the cells, relation of parameters to other functions, pacing, electrode placement. Output is a file describing depolarisation and repolarisation of the myocardium and electrograms. A graphic tool for interactive inspection of the output file is also included.
OIO is a Web-based metadata/data management front-end which is built using Zope and works with Postgresql. No programming is required to build and manage Web-forms or to perform data mining/analysis on the collected data. It is in production at the Harbor/UCLA Medical Center for clinical outcomes management and research data. Forms created with OIO and hosted on any OIO server can be downloaded as XML files. Once downloaded from the "Forms library" and imported into an OIO server, the necessary database tables are automatically recreated and the imported forms become immediately available to the users of that OIO server.
The VP7 Way Kool Project is a GTK application which simulates a laboratory experiment with radioactive nuclei. The user can choose between many predefined radioactive sources or create new ones. The number of decayed nuclei and the activity of the source can be determined with a built-in counter. The beam can be attenuated with shields of paper, aluminium, and/or lead.
FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another. FixDCD is a tiny utility to modify the header of an X-PLOR DCD file to make it readable by programs expecting Charmm DCD files, at the expense of a Timestep size value in the header.
MatDCD is a Matlab package for reading/writing DCD-formatted molecular dynamics trajectory files. It supports Charmm and xplor-format DCD files, it can read both big- and little-endian storage formats, and it can specify which atom indices to load without having to load the entire file.
Mol_Volume calculates the volume of a macromolecule by a method somewhat akin to the Monte Carlo method, namely, by measuring how many vertices of a dense regular grid happen to be within the probe radius of the molecule's atoms. The volume is then calculated as V = V_grid * N_near / N_total = N_near * V_per_node.
PDBCat can be used to manipulate and process PDB files using commonly available text-processing tools such as Perl, awk, etc. The Brookhaven Protein Data Bank stores atomic coordinate information for protein structures in a column-based format which is designed to be read easily read by FORTRAN programs. PDBCat converts the ATOM and HETATM records of PDB files from this column-based format to a field-based one that is more easily processed by standard Unix tools.