Parameter Sweep Workflows for Modelling Carbohydrate Recognition

Kiss, Tamás; Greenwell, Pamela; Heindl, Hans; Terstyánszky, Gábor; Weingarten, Noam

doi:10.1007/s10723-010-9166-8

Cited by 18 publications

(14 citation statements)

References 40 publications

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“…WS-PGRADE/gUSE is widely used via domain-specific science gateways -over 30 have been built in the SCI-BUS project [49]. Significant results are reported: life sciences (Kiss et al [50] and Shahand et al [51]), and astrophysics Costa et al [52]. Kepler…”

Section: Galaxymentioning

confidence: 99%

Scientific workflows: Past, present and future

Atkinson

Gesing

Montagnat

et al. 2017

Future Generation Computer Systems

102

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International audienceThis special issue and our editorial celebrate 10 years of progress with data-intensive or scientific workflows. There have been very substantial advances in the representation of workflows and in the engineering of workflow management systems (WMS). The creation and refinement stages are now well supported, with a significant improvement in usability. Improved abstraction supports cross-fertilisation between different workflow communities and consistent interpretation as WMS evolve. Through such re-engineering the WMS deliver much improved performance, significantly increased scale and sophisticated reliability mechanisms. Further improvement is anticipated from substantial advances in optimisation. We invited papers from those who have delivered these advances and selected 14 to represent today's achievements and representative plans for future progress. This editorial introduces those contributions with an overview and categorisation of the papers. Furthermore, it elucidates responses from a survey of major workflow systems, which provides evidence of substantial progress and a structured index of related papers. We conclude with suggestions on areas where further research and development is needed and offer a vision of future research directions

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Section: Galaxymentioning

confidence: 99%

Scientific workflows: Past, present and future

Atkinson

Gesing

Montagnat

et al. 2017

Future Generation Computer Systems

102

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“…Two such examples in the field of life sciences are the CancerGrid science gateway developed by SZTAKI and the ProSim science gateway [30] developed by University of Westminster. Here, we show only the CancerGrid science gateway as an example.…”

Section: Ws-pgrade Portalmentioning

confidence: 99%

“…Similar to P-GRADE portal, WS-PGRADE is also a generic purpose portal from which application-specific portals can easily be developed by adding application-specific portlets to the basic set of portlets. Two such examples in the field of life sciences are the CancerGrid science gateway developed by SZTAKI and the ProSim science gateway [30] developed by University of Westminster. Here, we show only the CancerGrid science gateway as an example.…”

Section: Ngs P-grade Portalmentioning

confidence: 99%

P‐GRADE portal family for grid infrastructures

Kacsuk

2010

Concurrency and Computation

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SUMMARY P-GRADE portal is one of the most widely used general-purpose grid portal in Europe. The paper summarizes the most advanced features of P-GRADE, such as parameter sweep workflow execution, multi-grid workflow execution and integration with the DSpace workflow repository. It also shows the NGS P-GRADE portal that extends P-GRADE with the GEMLCA legacy code execution support in Grid systems, as well as with coarse-grain workflow interoperability services. Next, the paper introduces the second generation P-GRADE portal called WS-PGRADE that merges the advanced features of the first generation P-GRADE portals and extends them with new workflow and architecture concepts. Finally, the application-specific science gateway of the CancerGrid project is briefly described to demonstrate that application-specific portals can easily be developed on top of the general-purpose WS-PGRADE portal.

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“…The SHIWA Workflow Repository [ 12 ] follows a workflow-driven approach and allows sharing workflows between major workflow platforms such as Galaxy, Kepler, Pegasus, Taverna, WS-PGRADE, etc. There are several science gateways based on the gUSE framework in the Computational Chemistry community for example the MoSGrid portal [ 30 ], the AutoDock Portal [ 31 ] as well as the AMC Docking Gateway [ 32 ]. As above mentioned, MoSGrid supports the following three domains: Docking, Molecular Dynamics (MD) and Quantum Chemistry (QC), while the AutoDock Portal and the AMC Docking Gateway are concerned with leveraging AutoDock [ 33 ] or AutoDock Vina [ 34 ], respectively, for the Docking community.…”

Section: Introductionmentioning

confidence: 99%

Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry

et al. 2016

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Background 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.SignificanceMany 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.ConclusionsWe 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.Graphical AbstractMeta-workflows and embedded workflows in the template representation Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0169-8) contains supplementary material, which is available to authorized users.

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Parameter Sweep Workflows for Modelling Carbohydrate Recognition

Cited by 18 publications

References 40 publications

Scientific workflows: Past, present and future

Scientific workflows: Past, present and future

P‐GRADE portal family for grid infrastructures

Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry

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