Abstract
State-of-the-art research in a variety of natural sciences depends
heavily on methods of computational chemistry, for example, the calculation
of the properties of materials, proteins, catalysts, and drugs. Applications
providing such methods require a lot of expertise to handle their
complexity and the usage of high-performance computing. The MoSGrid
(molecular simulation grid) infrastructure relieves this burden from
scientists by providing a science gateway, which eases access to
and usage of computational chemistry applications. One of its cornerstones
is the molecular simulations markup language (MSML), an extension
of the chemical markup language. MSML abstracts all chemical as well
as computational aspects of simulations. An application and its results
can be described with common semantics. Using such application, independent
descriptions users can easily switch between different applications
or compare them. This paper introduces MSML, its integration into
a science gateway, and its usage for molecular dynamics, quantum
chemistry, and protein docking.
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