Related Work - User-Level Workflow Design: A Bioinformatics Perspective - page 166

applicable subsequent services based on the outputs of the already executed
services.
GenePattern
GenePattern [263] is a web-based platform maintained at the BROAD Insti-
tute, which focuses on the analysis of genomic data via reproducible in silico
experiments. Therefore, it provides access to more than 125 specialized tools
and general data processing tasks and supports the definition and execution
of simple analysis workflows (pipelines).
Proteomatic
Proteomatic [291] is a recently released framework specializing in workflows
for tandem mass spectra (MS/MS) data analysis, which has been developed
at the Institute of Plant Biology and Biotechnology, University of Munster.
Workflow building blocks in Proteomatic are simply scripts that access lo-
cally installed tools for particular proteomics analyses. Workflows can be
constructed and executed from the command line or via a graphical user
interface.
RSEQtools
RSEQtools [123] is a software suite targeted at the analysis of data from RNA
sequencing (transcriptome profiling) experiments. that has been developed
in the scope of a joint project of computer science, bioinformatics, molecular
biology and medical research groups at Yale, Harvard and Stanford. The
tools in the suite are provided in a form that allows for the easy invocation
via a command line interface and thus also enables the creation of simple,
customizable workflows using standard scripting languages.
SeaLife Argumentation Interface
The SeaLife project [277] aims at establishing a Semantic Web browser for the
life sciences (currently especially for the study of infectious diseases) based
on Semantic Web technologies and the available eScience infrastructure of
the field. One example of the context-based information integration that is
envisaged by the project is the SeaLife Argumentation Interface [313], where
meaningful terms from the gene expression domain are recognized in the text
of a web page and used for the formulation of higher-level goals, which are,
together with web services that are linked to the terms, given to an HTN
(Hierarchical Task Network) planner [231, 284] that then creates workflows
that are suitable within the current context.