Information Technology Reference
In-Depth Information
BioSPICE Dashboard
The BioSPICE project [100], launched in 2001 as a collaborative initiative be-
tween the Lawrence Berkeley National Laboratory (LBNL), the University of
California at Berkeley (UCB), the Stanford Research Institute International
(SRI) and others, focused on the development of computational models for
intracellular processes. Besides the provision of mere “access to the most
current computational tools for biologists” [100], the work also aimed at inte-
grating the services into a convenient graphical user environment, called the
BioSPICE Dashboard.
BioSPICE builds upon the Open Agent Architecture (OAA) [67], a dele-
gated computing architecture developed at SRI, for the integration of services
and for the data transfer between the services during workflow execution. For
the workflow definition, a NetBeans-based graphical user interface is provided.
This interface also provides a simple but useful feature building upon basic
semantic information about services, namely the categorization of services
according to different criteria (in particular according to location, provider,
function, or I/O type).
Discovery Net
The Discovery Net system [107], developed in the early 2000s in the scope
of the UK e-Science Programme, is one of the earliest workflow systems that
have been designed specifically for scientific purposes. As several of its fea-
tures (such as the graphical interface and access to remote Web and Grid
services) were considered novel at that time, it served as a role model for the
development of other scientific workflow systems in the following years [106].
The system has been used in a number of bioinformatics projects, especially
in the UK (cf., e.g., [108, 76]).
Discovery Net has been designed for workflow management in a grid com-
puting environment, and thus provides the means for integrating and orches-
trating distributed resources and for deploying workflows for execution on
grid infrastructures. As for its functional range, Discovery Net can be classi-
fied as a closed-world system [106], since it provides a dedicated set of com-
ponents for data mining tasks, but is not prepared for integrating (arbitrary)
new services. In [75] an approach for the formal verification of Discovery Net
models based on temporal logic is proposed. However, these analyses are car-
ried out on a state model that is extracted from the actual workflow model,
rather than directly within the workflow environment, as it is the case in
Bio-jETI (cf. Section 2.2).
Galaxy
Galaxy [114, 45] is a web-based workflow system targeted at data-intensive
bioinformatics analyses. It has been developed jointly by the Center of Com-
parative Genomics and Bioinformatics at Pennsylvania State University and
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