CLINT: A universal interface for driving complex simulation programs

Protein simulation programs require sophisticated input command languages. These command languages drive computationally intensive simulations based on a given set of command parameters. Therefore, erroneous input can needlessly burden the scientist, with single simulations requiring weeks of computation. Command languages for these simulation programs must follow a set of logical rules relating the input parameters of a command within a given simulation. However, most simulation programs are developed ad-hoc, with an emphasis on functionality, rather than a design which provides a comprehensive command language with a semantic relationship between individual input parameters.; Due to the various complexities of these command languages, the barrier for usage can be high for scientists unfamiliar with the software or some of the technical details underlying macromolecular simulations. For example, many molecular dynamics simulation programs use some implementation of the "shake" algorithm to restrain bond lengths and yet, even to a biophysicist who understands the principles behind mechanics and thermodynamics, the Shake tolerance parameter is dubious. With a simple explanation for this single parameter at the click of a button or the hovering of a mouse, a biophysicist could quickly overcome this obstacle and finish setting up commands for a simulation.; To address these problems, we have developed CLINT (Command Language Interface), a universal interface for driving complex simulation software. CLINT enables any command line simulation program driven by an input file or an array of arguments to be run from a Graphical User Interface with a standardized set of menus and forms. Each form is driven by an Encoded Command Language (ECL) document, which is an extension of the Extensible Markup Language (XML). The rules, dependencies and hierarchy inherent to ECL may be utilized to provide abstract syntactical relationships to a simulation program's command language where none exist. A given set of ECL documents comprises the interface to "plug in" any simulation program into CLINT, providing a means to create a workbench of tools for the user to perform analysis on a given macromolecule. The current workbench of tools supported with complete ECL files by CLINT includes SIGMA, DOWSER, FAMBE and SIMS.