Standards‐based metadata management for molecular simulations

Abstract

SUMMARYState‐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. Copyright © 2013 John Wiley & Sons, Ltd.

Experiences of the Brazilian national high‐performance computing network on the rapid prototyping of science gateways

“…It is worth comparing the data provenance solution described earlier with efforts by other pieces of work, for example, . Our instantiation of the CSBase framework implements a much simpler data provenance solution, which gathers data from the point of view of the user interface (i.e., the input and output arguments passed by the user to the algorithm).…”

“…Our instantiation of the CSBase framework implements a much simpler data provenance solution, which gathers data from the point of view of the user interface (i.e., the input and output arguments passed by the user to the algorithm). In and , data provenance is gathered from the point of view of the binaries or workflows that run in the infrastructure. It is worth mentioning, however, that the new support of our gateway engine to the OSC language and its underlying enactment service (GWO) includes a more comprehensive data provenance solution, based on Open Provenance Model (OPM) , which is rather similar to the one described in .…”

Maintaining a Science Gateway - Lessons Learned from MoSGrid

“…There are no standards or automatisms for handling e.g., a version upgrade of an application. Such a change can affect the configuration of workflow nodes, the MSML template [30] describing the workflow and sometimes even the structure of the workflow graph. If for example a new version of a particular application provides a modified output scheme, it might be necessary to rework the whole workflow including a parsing step to ensure consistent results.…”

Science gateways - leveraging modeling and simulations in HPC infrastructures via increased usability

“…Therefore, the PortletAPI [34] was developed that enables the portal to dynamically create portlets. Based on MSML [36] templates individual and customizable options are available while the usage and appearance remains uniform. Obviously, this approach is beneficial for the users of MoSGrid as they only have to familiarize themselves with the usage MoSGrid once.…”