Database Reference
In-Depth Information
workflow system; a bazaar for sharing, reusing, and repurposing workflows; a
gateway to other established environments, for example, depositing into data
repositories and journals; and a platform to launch workflows, whatever their
system.
In comparison with existing workflow repositories, myExperiment goes the
next step: It aims to cross project, community, and product boundaries; it
emphasizes social networking around the workflows; it gateways to other envi-
ronments; and it forms the foundation of a personal or laboratory workbench.
It also transcends individual workflow systems, envisaging a multiworkflow
environment in which scientists will use whatever workflow is appropriate for
their applications — finding workflows and experiments that they can run
across multiple systems.
The design of the myExperiment software is completely user-centric. In or-
der to bootstrap the system, both in terms of content and community, the
initial user community comprised users of one particular scientific workflow
management system — the Taverna workbench. Developed by the myGrid
project,
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Taverna is used extensively across a range of Life Science prob-
lems: gene and protein annotation; proteomics, phylogeny, and phenotypical
studies; microarray data analysis and medical image analysis; high-throughput
screening of chemical compounds and clinical statistical analysis. Importantly,
Taverna has been designed to operate in the open wild world of bioinformat-
ics. Rather than large-scale, closed collaborations that own resources, Taverna
is used to enable individual scientists to access the many open resources avail-
able on the Web. Consequently it has a distributed and decoupled community
of users who obtain immediate benefit from sharing workflows through my-
Experiment.
Released in November 2007, myExperiment was supporting 500 users within
10 weeks and now provides a unique public collection of several hundred work-
flows from multiple workflow systems.
myExperiment has been designed and built following the mores of Web 2.0
and a set of principles for designing software for adoption by scientists that
were established through the Taverna development.
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It is a Web-based application built on the Ruby on Rails platform and
is not just a single site, like Facebook, YouTube, and others, but rather a
software package that can be installed independently and separately in a lab-
oratory, supporting the exchange of content between other Web applications
and different installations of myExperiment. It reuses other services as far as
possible, and it provides simple APIs so that others can make use of it — to
make it easy to bring myExperiment functionality into the scientists' existing
environment rather than obliging them to come to myExperiment.
Although initially focused on sharing workflows, myExperiment deals not
in workflows or scripts per se but in scientific objects — this allows sharing of
documents, presentations, service descriptions, notes, ontologies, plans, and so
forth. More generally, myExperiment can be used to glue together heteroge-
neous collections like distributed experimental data or, for example, packages
