HPC-Europa single point of access as a framework for building science gateways

2007 ◽  
Vol 19 (6) ◽  
pp. 851-866 ◽  
Author(s):  
Ariel Oleksiak ◽  
Alisdair Tullo ◽  
Paul Graham ◽  
Tomasz Kuczyński ◽  
Jarek Nabrzyski ◽  
...  
Keyword(s):  
Single Point ◽  
Building Science ◽  
Science Gateways

Building Science Gateways for Humanities

2020 ◽  
Author(s):  
Jun Zhou ◽  
Karen Smith ◽  
Greg Wilsbacher ◽  
Paul Sagona ◽  
David Reddy ◽  
...  
Keyword(s):  
Building Science ◽  
Science Gateways

scholarly journals BUILDING SCIENCE GATEWAYS BY UTILIZING THE GENERIC WS-PGRADE/GUSE WORKFLOW SYSTEM

2013 ◽  
Vol 14 (3) ◽  
pp. 307 ◽  
Author(s):  
Balasko Akos ◽  
Farkas Zoltan ◽  
Kacsuk Peter
Keyword(s):  
Building Science ◽  
Workflow System ◽  
Science Gateways

scholarly journals BUILDING SCIENCE GATEWAYS BY UTILIZING THE GENERIC WS-PGRADE/GUSE WORKFLOW SYSTEM

2013 ◽  
Vol 14 (2) ◽  
pp. 307 ◽  
Author(s):  
Balasko Akos ◽  
Farkas Zoltan ◽  
Kacsuk Peter
Keyword(s):  
Building Science ◽  
Workflow System ◽  
Science Gateways

scholarly journals Building Science Gateways for Analysing Molecular Docking Results Using a Generic Framework and Methodology

2020 ◽  
Vol 18 (3) ◽  
pp. 529-546
Author(s):  
Damjan Temelkovski ◽  
Tamas Kiss ◽  
Gabor Terstyanszky ◽  
Pamela Greenwell
Keyword(s):  
Molecular Docking ◽  
User Interfaces ◽  
Complex Environments ◽  
Building Science ◽  
Science Gateway ◽  
Docking Experiment ◽  
Screening Experiments ◽  
Science Gateways ◽  
Generic Framework ◽  
High Level

Abstract Molecular docking and virtual screening experiments require large computational and data resources and high-level user interfaces in the form of science gateways. While science gateways supporting such experiments are relatively common, there is a clearly identified need to design and implement more complex environments for further analysis of docking results. This paper describes a generic framework and a related methodology that supports the efficient development of such environments. The framework is modular enabling the reuse of already existing components. The methodology, which proposes three techniques that the development team can use, is agile and encourages active participation of end-users. Based on the framework and methodology, two prototype implementations of science-gateway-based docking environments are presented and evaluated. The first system recommends a receptor-ligand pair for the next docking experiment, and the second filters docking results based on ligand properties.

Fine-scale taxonomic and temporal variability in the energy density of invertebrate prey of juvenile Chinook salmon Oncorhynchus tshawytscha

2020 ◽  
Vol 655 ◽  
pp. 185-198
Author(s):  
J Weil ◽  
WDP Duguid ◽  
F Juanes
Keyword(s):  
Energy Density ◽  
Chinook Salmon ◽  
Temporal Variability ◽  
Energy Content ◽  
Single Point ◽  
Single Species ◽  
Fine Scale ◽  
Temporal Differences ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook

Variation in the energy content of prey can drive the diet choice, growth and ultimate survival of consumers. In Pacific salmon species, obtaining sufficient energy for rapid growth during early marine residence is hypothesized to reduce the risk of size-selective mortality. In order to determine the energetic benefit of feeding choices for individuals, accurate estimates of energy density (ED) across prey groups are required. Frequently, a single species is assumed to be representative of a larger taxonomic group or related species. Further, single-point estimates are often assumed to be representative of a group across seasons, despite temporal variability. To test the validity of these practices, we sampled zooplankton prey of juvenile Chinook salmon to investigate fine-scale taxonomic and temporal differences in ED. Using a recently developed model to estimate the ED of organisms using percent ash-free dry weight, we compared energy content of several groups that are typically grouped together in growth studies. Decapod megalopae were more energy rich than zoeae and showed family-level variability in ED. Amphipods showed significant species-level variability in ED. Temporal differences were observed, but patterns were not consistent among groups. Bioenergetic model simulations showed that growth rate of juvenile Chinook salmon was almost identical when prey ED values were calculated on a fine scale or on a taxon-averaged coarse scale. However, single-species representative calculations of prey ED yielded highly variable output in growth depending on the representative species used. These results suggest that the latter approach may yield significantly biased results.

Mill Experiences with Single Point Kappa Analysers

2017 ◽  
Vol 71 (3) ◽  
pp. 289-293
Author(s):  
Yusuke Ishimoto
Keyword(s):  
Single Point

Cupin Variants as Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Miho Yuasa ◽  
Yosuke Nishikawa ◽  
Genji Kurisu ◽  
Shinobu Itoh ◽  
...  
Keyword(s):  
Michael Addition ◽  
In Silico ◽  
Addition Reaction ◽  
Single Point ◽  
Point Mutations ◽  
Unsaturated Ketone ◽  
Michael Addition Reaction ◽  
Beta Barrel ◽  
Cupin Superfamily ◽  
Single Point Mutations

Cupin superfamily proteins (TM1459) work as a macromolecular ligand framework with a double-stranded beta-barrel structure ligating to a Cu ion through histidine side chains. Variegating the first coordination sphere of TM1459 revealed that H52A and H54A/H58A mutants effectively catalyzed the diastereo- and enantio-selective Michael addition reaction of nitroalkanes to an α,β-unsaturated ketone. Moreover, in silico substrate docking signified C106N and F104W single-point mutations, which inverted the diastereoselectivity of H52A and further improved the stereoselectivity of H54A/H58A, respectively.

Optimal Duration of the Preincubation Phase in Enzyme Inhibition Experiments

2020 ◽  
Author(s):  
Petr Kuzmic
Keyword(s):  
Enzyme Inhibition ◽  
Dose Response ◽  
Enzyme Inhibitor ◽  
Single Point ◽  
Association Rate ◽  
Weakly Bound ◽  
Inhibitor Complex ◽  
Dissociation Equilibrium ◽  
Optimal Duration ◽  
Algebraic Formula

This report describes an algebraic formula to calculate the optimal duration of the pre-incubation phase in enzyme-inhibition experiments, based on the assumed range of expected values for the dissociation equilibrium constant of the enzyme–inhibitor complex and for the bimolecular association rate constant. Three typical experimental scenarios are treated, namely, (1) single-point primary screening at relatively high inhibitor concentrations; (2) dose-response secondary screening of relatively weakly bound inhibitors; (3) dose-response screening of tightly-bound inhibitors.

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