Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry
Identifieur interne : 000488 ( Ncbi/Merge ); précédent : 000487; suivant : 000489Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry
Auteurs : Junaid Arshad ; Alexander Hoffmann [Allemagne] ; Sandra Gesing [États-Unis] ; Richard Grunzke [Allemagne] ; Jens Krüger [Allemagne] ; Tamas Kiss ; Sonja Herres-Pawlis [Allemagne] ; Gabor TerstyanszkySource :
- Journal of Cheminformatics [ 1758-2946 ] ; 2016.
Abstract
In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows.
Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows.
We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository. Meta-workflows and embedded workflows in the template representation
The online version of this article (doi:10.1186/s13321-016-0169-8) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13321-016-0169-8
PubMed: 27818709
PubMed Central: 5073744
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows.</p>
</sec>
<sec><title>Significance</title>
<p>Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows.</p>
</sec>
<sec><title>Conclusions</title>
<p>We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.<fig position="anchor" id="Figa"><label>Graphical Abstract</label>
<caption><p>Meta-workflows and embedded workflows in the template representation</p>
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<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s13321-016-0169-8) contains supplementary material, which is available to authorized users.</p>
</sec>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Cheminform</journal-id>
<journal-id journal-id-type="iso-abbrev">J Cheminform</journal-id>
<journal-title-group><journal-title>Journal of Cheminformatics</journal-title>
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<issn pub-type="epub">1758-2946</issn>
<publisher><publisher-name>Springer International Publishing</publisher-name>
<publisher-loc>Cham</publisher-loc>
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<article-meta><article-id pub-id-type="pmid">27818709</article-id>
<article-id pub-id-type="pmc">5073744</article-id>
<article-id pub-id-type="publisher-id">169</article-id>
<article-id pub-id-type="doi">10.1186/s13321-016-0169-8</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Methodology</subject>
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<title-group><article-title>Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry</article-title>
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</address>
<xref ref-type="aff" rid="Aff4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Krüger</surname>
<given-names>Jens</given-names>
</name>
<address><email>krueger@informatik.uni-tuebingen.de</email>
</address>
<xref ref-type="aff" rid="Aff5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kiss</surname>
<given-names>Tamas</given-names>
</name>
<address><email>T.Kiss@westminster.ac.uk</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-4354-4353</contrib-id>
<name><surname>Herres-Pawlis</surname>
<given-names>Sonja</given-names>
</name>
<address><email>sonja.herres-pawlis@ac.rwth-aachen.de</email>
</address>
<xref ref-type="aff" rid="Aff2">2</xref>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Terstyanszky</surname>
<given-names>Gabor</given-names>
</name>
<address><email>g.z.terstyanszky@westminster.ac.uk</email>
</address>
<xref ref-type="aff" rid="Aff1">1</xref>
</contrib>
<aff id="Aff1"><label>1</label>
Centre for Parallel Computing, School of Computer Science, University of Westminster, 115 New Cavendish Street, London, W1W 6UW UK</aff>
<aff id="Aff2"><label>2</label>
Institut für Anorganische Chemie, Lehrstuhl für Bioanorganische Chemie, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany</aff>
<aff id="Aff3"><label>3</label>
University of Notre Dame, 123 Information Technology Center, Notre Dame, IN 46556 USA</aff>
<aff id="Aff4"><label>4</label>
Center for Information Services and High Performance Computing, Technische Universität Dresden, Zellescher Weg 12-14, 01062 Dresden, Germany</aff>
<aff id="Aff5"><label>5</label>
Applied Bioinformatics Tübingen, University of Tübingen, Sand 14, 72076 Tübingen, Germany</aff>
</contrib-group>
<pub-date pub-type="epub"><day>20</day>
<month>10</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>20</day>
<month>10</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection"><year>2016</year>
</pub-date>
<volume>8</volume>
<elocation-id>58</elocation-id>
<history><date date-type="received"><day>14</day>
<month>2</month>
<year>2016</year>
</date>
<date date-type="accepted"><day>4</day>
<month>10</month>
<year>2016</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2016</copyright-statement>
<license license-type="OpenAccess"><license-p><bold>Open Access</bold>
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<abstract id="Abs1"><sec><title>Background</title>
<p>In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows.</p>
</sec>
<sec><title>Significance</title>
<p>Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows.</p>
</sec>
<sec><title>Conclusions</title>
<p>We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.<fig position="anchor" id="Figa"><label>Graphical Abstract</label>
<caption><p>Meta-workflows and embedded workflows in the template representation</p>
</caption>
<graphic position="anchor" xlink:href="13321_2016_169_Figa_HTML" id="MO1"></graphic>
</fig>
</p>
</sec>
<sec><title>Electronic supplementary material</title>
<p>The online version of this article (doi:10.1186/s13321-016-0169-8) contains supplementary material, which is available to authorized users.</p>
</sec>
</abstract>
<kwd-group xml:lang="en"><title>Keywords</title>
<kwd>Scientific workflows</kwd>
<kwd>Workflow repository</kwd>
<kwd>Quantum chemistry</kwd>
<kwd>Meta-workflow</kwd>
<kwd>Atomic workflow</kwd>
</kwd-group>
<funding-group><award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100001659</institution-id>
<institution>Deutsche Forschungsgemeinschaft</institution>
</institution-wrap>
</funding-source>
<award-id>FOR1405</award-id>
<award-id>MASi (NA711/9-1)</award-id>
<principal-award-recipient><name><surname>Herres-Pawlis</surname>
<given-names>Sonja</given-names>
</name>
</principal-award-recipient>
</award-group>
<award-group><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100004963</institution-id>
<institution>Seventh Framework Programme</institution>
</institution-wrap>
</funding-source>
<award-id>283481 (SCI-BUS)</award-id>
<award-id>no 312579 (ER-flow)</award-id>
</award-group>
</funding-group>
<custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name>
<meta-value>© The Author(s) 2016</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Allemagne</li>
<li>États-Unis</li>
</country>
<region><li>Bade-Wurtemberg</li>
<li>District de Cologne</li>
<li>District de Dresde</li>
<li>District de Tübingen</li>
<li>Indiana</li>
<li>Rhénanie-du-Nord-Westphalie</li>
<li>Saxe (Land)</li>
</region>
<settlement><li>Aix-la-Chapelle</li>
<li>Dresde</li>
<li>Tübingen</li>
</settlement>
<orgName><li>Université technique de Dresde</li>
</orgName>
</list>
<tree><noCountry><name sortKey="Arshad, Junaid" sort="Arshad, Junaid" uniqKey="Arshad J" first="Junaid" last="Arshad">Junaid Arshad</name>
<name sortKey="Kiss, Tamas" sort="Kiss, Tamas" uniqKey="Kiss T" first="Tamas" last="Kiss">Tamas Kiss</name>
<name sortKey="Terstyanszky, Gabor" sort="Terstyanszky, Gabor" uniqKey="Terstyanszky G" first="Gabor" last="Terstyanszky">Gabor Terstyanszky</name>
</noCountry>
<country name="Allemagne"><region name="Rhénanie-du-Nord-Westphalie"><name sortKey="Hoffmann, Alexander" sort="Hoffmann, Alexander" uniqKey="Hoffmann A" first="Alexander" last="Hoffmann">Alexander Hoffmann</name>
</region>
<name sortKey="Grunzke, Richard" sort="Grunzke, Richard" uniqKey="Grunzke R" first="Richard" last="Grunzke">Richard Grunzke</name>
<name sortKey="Herres Pawlis, Sonja" sort="Herres Pawlis, Sonja" uniqKey="Herres Pawlis S" first="Sonja" last="Herres-Pawlis">Sonja Herres-Pawlis</name>
<name sortKey="Kruger, Jens" sort="Kruger, Jens" uniqKey="Kruger J" first="Jens" last="Krüger">Jens Krüger</name>
</country>
<country name="États-Unis"><region name="Indiana"><name sortKey="Gesing, Sandra" sort="Gesing, Sandra" uniqKey="Gesing S" first="Sandra" last="Gesing">Sandra Gesing</name>
</region>
</country>
</tree>
</affiliations>
</record>
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