JGraph— A Java Based System for Drawing Graphs and Running Graph Algorithms

Bagga, Jay S.; Heinz, Adrian

doi:10.1007/3-540-45848-4_45

Cited by 20 publications

(11 citation statements)

References 1 publication

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“…ArchReco is built on top of the jGraph framework [2] by adding additional functionality to support the recommendations for Design patterns in real time, during the design of Software Architecture Diagrams. The recommendation algorithms and the methods of presenting the recommendation results were built as individual components and integrated with the basic graph editor tool, which exists in the jGraph package.…”

Section: Archreco Prototypementioning

confidence: 99%

ArchReco

Sielis

Tzanavari

Papadopoulos

2015

Proceedings of the 2015 European Conference on Software Architecture Workshops

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This work presents ArchReco, a tool that supports Context Aware Recommendations for Design Patterns while a designer performs a Software Architecture Design. The prototype tool presented in this work takes into consideration the contextual elements that characterize a Software Architecture model and use them for the computation of the most suitable Design Patterns that can be applied during the process of Software Architecture diagram design. The tool currently supports three Context Aware Recommendation methods for the computation of recommendations for the most suitable Design Patterns.

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Section: Archreco Prototypementioning

confidence: 99%

ArchReco

Sielis

Tzanavari

Papadopoulos

2015

Proceedings of the 2015 European Conference on Software Architecture Workshops

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“…The communication analysis has been performed using our own JAVAwritten code, which is based on the JGraph library (25).…”

Section: Communication Analysismentioning

confidence: 99%

Protonation-State-Dependent Communication in Cytochrome c Oxidase

Helabad

Ghane

Reidelbach

et al. 2017

Biophysical Journal

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Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D-and K-channels. For the protein to function as both redox enzyme and proton pump, proton transfer out of either of the channels toward the BNC or into the protein toward a proton loading site, and ultimately through the membrane, must be highly regulated. The O/E intermediate of cytochrome c oxidase is the first redox state in its catalytic cycle, where proton transfer through the K-channel, from K362 to Y288 at the BNC, is important. Molecular dynamics simulations of this intermediate with 16 different combinations of protonation states of key residues in the D-and K-channel show the mutual impact of the two proton-conducting channels to be protonation state-dependent. Strength as well as means of communication, correlations in positions, or connections along the hydrogen-bonded network, change with the protonation state of the K-channel residue K362. The conformational and hydrogen-bond dynamics of the D-channel residue N139 regulated by an interplay of protonation in the D-channel and K362. N139 thus assumes a gating function by which proton passage through the D-channel toward E286 is likely facilitated for states with protonated K362 and unprotonated E286, which would in principle allow proton transfer to the BNC, but no proton pumping until a proton has reached E286.

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“…Path Set uses the global search approach to compute a set of paths which forms a minimal counterexample. GUI provides the possibility to define DTMCs by their underlying graphs and to modify them using the JGraph library [15]. This component is connected both to SccMC and Concretize via Java Native Interface (JNI).…”

Section: The Comics Toolmentioning

confidence: 99%

The COMICS Tool – Computing Minimal Counterexamples for DTMCs

Jansen

Ábrahám

Volk

et al. 2012

Lecture Notes in Computer Science

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This report presents the tool COMICS 1.0, which performs model checking and generates counterexamples for DTMCs. For an input DTMC, COMICS computes an abstract system that carries the model checking information and uses this result to compute a critical subsystem, which induces a counterexample. This abstract subsystem can be refined and concretized hierarchically. The tool comes with a command-line version as well as a graphical user interface that allows the user to interactively influence the refinement process of the counterexample.

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JGraph— A Java Based System for Drawing Graphs and Running Graph Algorithms

Cited by 20 publications

References 1 publication

ArchReco

ArchReco

Protonation-State-Dependent Communication in Cytochrome c Oxidase

The COMICS Tool – Computing Minimal Counterexamples for DTMCs

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