A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Gesing, Sandra; Grunzke, Richard; Krüger, Jens; Birkenheuer, Georg; Wewior, Martin; Schäfer, Patrick; Schuller, Bernd; Schuster, Johannes; Herres‐Pawlis, Sonja; Breuers, Sebastian; Balaskó, Ákos; Kozlovszky, Miklós; Fabri, Anna Szikszay; Packschies, Lars; Kacsuk, Péter; Blunk, Dirk; Steinke, Thomas; Brinkmann, André; Fels, Gregor; Müller-Pfefferkorn, R.; Jäkel, René; Kohlbacher, Oliver

doi:10.1007/s10723-012-9247-y

Cited by 40 publications

(19 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As rightly pointed out by Gesing et al [20], both the input and output data of molecular simulations are sensitive and may constitute a valuable intellectual property. Therefore, they need to be stored securely.…”

Section: Discussionmentioning

confidence: 99%

“…Gesing et al [20] report on a very important security issue while carrying out computations in structural bioinformatics, molecular modeling, and quantum chemistry with the use of Molecular Simulation Grid (MoSGrid). MoSGrid is a science gateway that makes use of WS-PGRADE [15] as a user interface, gUSE [30] as a high-level middleware service layer for workload storage, workload execution, monitoring and others, UNICORE [64] as a Grid resources middleware layer, and XtreemeFS [26] as a file system for storage purposes.…”

Section: Related Workmentioning

confidence: 99%

See 1 more Smart Citation

Scaling Ab Initio Predictions of 3D Protein Structures in Microsoft Azure Cloud

2015

View full text Add to dashboard Cite

Computational methods for protein structure prediction allow us to determine a three-dimensional structure of a protein based on its pure amino acid sequence. These methods are a very important alternative to costly and slow experimental methods, like X-ray crystallography or Nuclear Magnetic Resonance. However, conventional calculations of protein structure are time-consuming and require ample computational resources, especially when carried out with the use of ab initio methods that rely on physical forces and interactions between atoms in a protein.Fortunately, at the present stage of the development of computer science, such huge computational resources are available from public cloud providers on a payas-you-go basis. We have designed and developed a scalable and extensible system, called Cloud4PSP, which enables predictions of 3D protein structures in the Microsoft Azure commercial cloud. The system makes use of the Warecki-Znamirowski method as a sample procedure for protein structure prediction, and this prediction method was used to test the scalability of the system. The results of the efficiency tests performed proved good acceleration of predictions when scaling the system vertically and horizontally. In the paper, we show the system architecture that allowed us to achieve such good results, the Cloud4PSP processing model, and the results of the scalability tests. At the end of the paper, we try to answer which of the scaling techniques, scaling out or scaling up, is better for solving such computational problems with the use of Cloud computing.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

Scaling Ab Initio Predictions of 3D Protein Structures in Microsoft Azure Cloud

2015

View full text Add to dashboard Cite

show abstract

“…NBO calculations were accomplished using the program suite NBO 6.0 [86][87][88]. Some of these calculations have been performed within the MoSGrid environment [98][99][100].…”

Section: Computational Detailsmentioning

confidence: 99%

Reactivity of Zinc Halide Complexes Containing Camphor-Derived Guanidine Ligands with Technical rac-Lactide

et al. 2017

Self Cite

View full text Add to dashboard Cite

Abstract:Three new zinc complexes with monoamine-guanidine hybridligands have been prepared, characterized by X-ray crystallography and NMR spectroscopy, and tested in the solvent-free ring-opening polymerization of rac-lactide. Initially the ligands were synthesized from camphoric acid to obtain TMGca and DMEGca and then reacted with zinc(II) halides to form zinc complexes. All complexes have a distorted tetrahedral coordination. They were utilized as catalysts in the solvent-free polymerization of technical rac-lactide at 150 • C. Colorless polylactide (PLA) can be produced and after 2 h conversion up to 60% was reached. Furthermore, one zinc chlorido complex was tested with different qualities of lactide (technical and recrystallized) and with/without the addition of benzyl alcohol as a co-initiator. The kinetics were monitored by in situ FT-IR or 1 H NMR spectroscopy. All kinetic measurements show first-order behavior with respect to lactide. The influence of the chiral complexes on the stereocontrol of PLA was examined. Moreover, with MALDI-ToF measurements the end-group of the obtained polymer was determined. DFT and NBO calculations give further insight into the coordination properties. All in all, these systems are robust against impurities and water in the lactide monomer and show great catalytic activity in the ROP of lactide.

show abstract

“…All interacting bodies need to have a valid certificate including a valid chain of trust down to the root of the CA [22]. In practice this means that all users need to obtain a personal certificate as well as all portal, storage, and compute resources need to have a server certificate.…”

Section: Authentication and Securitymentioning

confidence: 99%