Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry
Identifieur interne : 000022 ( Main/Exploration ); précédent : 000021; suivant : 000023Multi-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
Affiliations:
- Allemagne, États-Unis
- Bade-Wurtemberg, District de Cologne, District de Dresde, District de Tübingen, Indiana, Rhénanie-du-Nord-Westphalie, Saxe (Land)
- Aix-la-Chapelle, Dresde, Tübingen
- Université technique de Dresde
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Le document en format XML
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Sand 14, 72076 Tübingen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Applied Bioinformatics Tübingen, University of Tübingen, Sand 14, 72076 Tübingen</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Tübingen</region><settlement type="city">Tübingen</settlement></placeName></affiliation></author><author><name sortKey="Kiss, Tamas" sort="Kiss, Tamas" uniqKey="Kiss T" first="Tamas" last="Kiss">Tamas Kiss</name><affiliation><nlm:aff id="Aff1">Centre for Parallel Computing, School of Computer Science, University of Westminster, 115 New Cavendish Street, London, W1W 6UW UK</nlm:aff><wicri:noCountry code="subfield">W1W 6UW UK</wicri:noCountry></affiliation></author><author><name sortKey="Herres Pawlis, Sonja" sort="Herres Pawlis, Sonja" uniqKey="Herres Pawlis S" first="Sonja" last="Herres-Pawlis">Sonja Herres-Pawlis</name><affiliation wicri:level="3"><nlm:aff id="Aff2">Institut für Anorganische Chemie, Lehrstuhl für Bioanorganische Chemie, RWTH Aachen University, Landoltweg 1, 52074 Aachen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Anorganische Chemie, Lehrstuhl für Bioanorganische Chemie, RWTH Aachen University, Landoltweg 1, 52074 Aachen</wicri:regionArea><placeName><region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region><region type="district" nuts="2">District de Cologne</region><settlement type="city">Aix-la-Chapelle</settlement></placeName></affiliation></author><author><name sortKey="Terstyanszky, Gabor" sort="Terstyanszky, Gabor" uniqKey="Terstyanszky G" first="Gabor" last="Terstyanszky">Gabor Terstyanszky</name><affiliation><nlm:aff id="Aff1">Centre for Parallel Computing, School of Computer Science, University of Westminster, 115 New Cavendish Street, London, W1W 6UW UK</nlm:aff><wicri:noCountry code="subfield">W1W 6UW UK</wicri:noCountry></affiliation></author></analytic><series><title level="j">Journal of Cheminformatics</title><idno type="eISSN">1758-2946</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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></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></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Castelli, G" uniqKey="Castelli G">G Castelli</name></author><author><name sortKey="Taffoni, G" uniqKey="Taffoni G">G Taffoni</name></author><author><name sortKey="Sciacca, E" uniqKey="Sciacca E">E Sciacca</name></author><author><name sortKey="Becciani, U" 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Schmidt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Neese, F" uniqKey="Neese F">F Neese</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tsipis, Ac" uniqKey="Tsipis A">AC Tsipis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Matyjaszewski, K" uniqKey="Matyjaszewski K">K Matyjaszewski</name></author><author><name sortKey="Davis, Tp" uniqKey="Davis T">TP Davis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hoffmann, A" uniqKey="Hoffmann A">A Hoffmann</name></author><author><name sortKey="Borner, J" uniqKey="Borner J">J Börner</name></author><author><name sortKey="Florke, U" uniqKey="Florke U">U Flörke</name></author><author><name sortKey="Herres Pawlis, S" uniqKey="Herres Pawlis S">S Herres-Pawlis</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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>Pour manipuler ce document sous Unix (Dilib)
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