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11.1 Molecular Simulations Supported by a Sophisticated
Infrastructure
Nowadays, molecular simulations and docking tools are invaluable computational
methods to gain new insight into molecular structures, their prediction, and the
analysis of their functions. They are applied in numerous research areas like
materials science, structural biology, and computer-aided drug design. The complex
underlying theory is reflected in the tools and, thus, their use requires a lot of
experience to gain meaningful results. Furthermore, researchers mainly process and
analyze data not only via single jobs but via workflows as well. The computing- and
data-intensive applications and workflows demand for distributed computing
infrastructures (DCIs) additionally increase the complexity.
To lower the hurdle of using molecular simulations and docking methods for
inexperienced users and to serve experienced users with advanced workflows, the
MoSGrid project has developed a science gateway to offer easy and intuitive access
to applications on DCIs (Gesing 2012; Grunzke 2013). The science gateway provides
an extensive virtual research environment to the community. The set of gUSE ser-
vices and their flexible user interface WS-PGRADE form the basis for the MoSGrid
science gateway, along with the adapted infrastructure for the needs of the user
community. The following sections go into detail for the extended infrastructure and
the designs, concepts, and implementations accomplished by the MoSGrid project.
11.2 The Extended Infrastructure
The MoSGrid project evaluated and designed the infrastructure for the science
gateway under consideration of the application domain, existing standards, and the
available grid infrastructure (Herres-Pawlis 2014). First of all, the security infra-
structure has been extended (Gesing 2012). The role-based management features of
Liferay (2014) are applied to reflect the diverse roles of users belonging to the
computational chemistry community in the science gateway. Furthermore, SAML
(2002), as a widely-used security standard for trust delegation in federated identity
management systems (e.g., via Shibboleth (Wang 2009)), has been built into the
security infrastructure (Fig.
11.1
). Thus, the science gateway can be easily inte-
grated with diverse authentication systems.
Due to the flexible DCI support, the graphical workflow editor, and the possi-
bility to process parameter sweeps, WS-PGRADE, which was developed on top of
the portal framework Liferay, forms the basis for the science gateway. On the DCI
layer the grid middleware UNICORE 6 (Streit 2010) was chosen because of its
service-oriented and reliable architecture. XtreemFS (Hupfeld 2008) was selected
for distributed data management because of its ef
ciency and reliability in wide-
area networks. The support of UNICORE and XtreemFS in WS-PGRADE and
gUSE has been implemented by the MoSGrid project.
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