dc.contributor.author
Garza, Luis de la
dc.contributor.author
Veit, Johannes
dc.contributor.author
Szolek, Andras
dc.contributor.author
Roettig, Marc
dc.contributor.author
Aiche, Stephan
dc.contributor.author
Gesing, Sandra
dc.contributor.author
Reinert, Knut
dc.contributor.author
Kohlbacher, Oliver
dc.date.accessioned
2018-06-08T04:13:45Z
dc.date.available
2016-04-14T12:02:10.112Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/16854
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-21035
dc.description.abstract
Background Reproducibility is one of the tenets of the scientific method.
Scientific experiments often comprise complex data flows, selection of
adequate parameters, and analysis and visualization of intermediate and end
results. Breaking down the complexity of such experiments into the joint
collaboration of small, repeatable, well defined tasks, each with well defined
inputs, parameters, and outputs, offers the immediate benefit of identifying
bottlenecks, pinpoint sections which could benefit from parallelization, among
others. Workflows rest upon the notion of splitting complex work into the
joint effort of several manageable tasks. There are several engines that give
users the ability to design and execute workflows. Each engine was created to
address certain problems of a specific community, therefore each one has its
advantages and shortcomings. Furthermore, not all features of all workflow
engines are royalty-free —an aspect that could potentially drive away members
of the scientific community. Results We have developed a set of tools that
enables the scientific community to benefit from workflow interoperability. We
developed a platform-free structured representation of parameters, inputs,
outputs of command-line tools in so-called Common Tool Descriptor documents.
We have also overcome the shortcomings and combined the features of two
royalty-free workflow engines with a substantial user community: the Konstanz
Information Miner, an engine which we see as a formidable workflow editor, and
the Grid and User Support Environment, a web-based framework able to interact
with several high-performance computing resources. We have thus created a free
and highly accessible way to design workflows on a desktop computer and
execute them on high-performance computing resources. Conclusions Our work
will not only reduce time spent on designing scientific workflows, but also
make executing workflows on remote high-performance computing resources more
accessible to technically inexperienced users. We strongly believe that our
efforts not only decrease the turnaround time to obtain scientific results but
also have a positive impact on reproducibility, thus elevating the quality of
obtained scientific results.
en
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
Interoperability
dc.subject.ddc
500 Naturwissenschaften und Mathematik
dc.title
From the desktop to the grid
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation
BMC Bioinformatics. - 17 (2016), Artikel Nr. 127
dc.title.subtitle
scalable bioinformatics via workflow conversion
dcterms.bibliographicCitation.doi
10.1186/s12859-016-0978-9
dcterms.bibliographicCitation.url
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0978-9
refubium.affiliation
Mathematik und Informatik
de
refubium.mycore.fudocsId
FUDOCS_document_000000024370
refubium.note.author
Der Artikel wurde in einer Open-Access- Zeitschrift publiziert.
refubium.resourceType.isindependentpub
no
refubium.mycore.derivateId
FUDOCS_derivate_000000006282
dcterms.accessRights.openaire
open access