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2. A Chimeric ORF Fusion Phenotypic Reporter for Cryptococcus neoformans.

Author

Phillips-Rose, Louis S., Yu, Chendi K., West, Nicholas P., and Fraser, James A.

Subjects
*GENE expression, *CRYPTOCOCCUS neoformans, *FLUORESCENT proteins, *GENE fusion, *FUNGAL proteins
Abstract

The plethora of genome sequences produced in the postgenomic age has not resolved many of our most pressing biological questions. Correlating gene expression with an interrogatable and easily observable characteristic such as the surrogate phenotype conferred by a reporter gene is a valuable approach to gaining insight into gene function. Many reporters including lacZ, amdS, and the fluorescent proteins mRuby3 and mNeonGreen have been used across all manners of organisms. Described here is an investigation into the creation of a robust, synthetic, fusion reporter system for Cryptococcus neoformans that combines some of the most useful fluorophores available in this system with the versatility of the counter-selectable nature of amdS. The reporters generated include multiple composition and orientation variants, all of which were investigated for differences in expression. Evaluation of known promoters from the TEF1 and GAL7 genes was undertaken, elucidating novel expression tendencies of these biologically relevant C. neoformans regulators of transcription. Smaller than lacZ but providing multiple useful surrogate phenotypes for interrogation, the fusion ORF serves as a superior whole-cell assay compared to traditional systems. Ultimately, the work described here bolsters the array of relevant genetic tools that may be employed in furthering manipulation and understanding of the WHO fungal priority group pathogen C. neoformans. [ABSTRACT FROM AUTHOR]

Published
2024
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6. The Petri-Nets to Statecharts Transformation Case

Author

Van Gorp, Pieter and Rose, Louis M.

Subjects
Computer Science - Programming Languages, I.2.2, F.4.3
Abstract

This paper describes a case study for the sixth Transformation Tool Contest. The case is based on a mapping from Petri-Nets to statecharts (i.e., from flat process models to hierarchical ones). The case description separates a simple mapping phase from a phase that involves the step by step destruction Petri-Net elements and the corresponding construction of a hierarchy of statechart elements. Although the focus of this case study is on the comparison of the runtime performance of solutions, we also include correctness tests as well as bonus criteria for evaluating transformation language and tool features., Comment: In Proceedings TTC 2013, arXiv:1311.7536

Published
2013
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7. Proceedings Sixth Transformation Tool Contest

Author

Van Gorp, Pieter, Rose, Louis M., and Krause, Christian

Subjects
Computer Science - Software Engineering, Computer Science - Programming Languages, F.4.3, I.2.8, D.3.3
Abstract

The aim of the Transformation Tool Contest (TTC) series is to compare the expressiveness, the usability and the performance of graph and model transformation tools along a number of selected case studies. Participants want to learn about the pros and cons of each tool considering different applications. A deeper understanding of the relative merits of different tool features will help to further improve graph and model transformation tools and to indicate open problems. TTC 2013 involved 18 offline case study solutions: 6 solutions to the FlowGraphs case, 9 solutions to the Petri Nets to Statecharts case and 3 solutions to the Restructuring case. 13 of the 18 solutions have undergone a non-blind peer review before the workshop and were presented and evaluated during the workshop in Budapest. This volume contains the submissions that have passed an additional (post-workshop, blind) reviewing round.

Published
2013
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8. Saying Hello World with Epsilon - A Solution to the 2011 Instructive Case

Author

Rose, Louis M., García-Domínguez, Antonio, Williams, James R., Kolovos, Dimitrios S., Paige, Richard F., and Polack, Fiona A. C.

Subjects
Computer Science - Software Engineering
Abstract

Epsilon is an extensible platform of integrated and task-specific languages for model management. With solutions to the 2011 TTC Hello World case, this paper demonstrates some of the key features of the Epsilon Object Language (an extension and reworking of OCL), which is at the core of Epsilon. In addition, the paper introduces several of the task-specific languages provided by Epsilon including the Epsilon Generation Language (for model-to-text transformation), the Epsilon Validation Language (for model validation) and Epsilon Flock (for model migration)., Comment: In Proceedings TTC 2011, arXiv:1111.4407

Published
2011
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9. Proceedings Fifth Transformation Tool Contest

Author

Van Gorp, Pieter, Mazanek, Steffen, and Rose, Louis

Subjects
Computer Science - Software Engineering, Computer Science - Programming Languages, D3.2, D3.4
Abstract

The aim of the Transformation Tool Contest (TTC) series is to compare the expressiveness, the usability and the performance of graph and model transformation tools along a number of selected case studies. Participants want to learn about the pros and cons of each tool considering different applications. A deeper understanding of the relative merits of different tool features will help to further improve graph and model transformation tools and to indicate open problems. TTC 2011 involved 25 offline case study solutions: 12 solutions to the Hello World case, 2 solutions to the GMF Model Migration case, 5 solutions to the Compiler Optimization case, and 7 solutions to the Reengineering (i.e., Program Understanding) case. This volume contains the submissions that have passed an additional (post-workshop) reviewing round., Comment: EPTCS 74, 2011

Published
2011
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12. Structures and processes for managing model-metamodel co-evolution

Author

Rose, Louis M., Paige, Richard F., and Polack, Fiona A. C.

Subjects
005.3
Abstract

Software changes over time. During the lifetime of a software system, unintended behaviour must be corrected and new requirements satisfied. Because software changes are costly, tools for automatically managing change are commonplace. Contemporary software development environments can automatically perform change management tasks such as impact analysis, refactoring and background compilation. Increasingly, models and modelling languages are first-class citizens in software development. Model-Driven Engineering (MDE), a state-of-the-art approach to software engineering, prescribes the use of models throughout the software engineering process. In MDE, modelling tools and task-specific language are used to generate an ultimate artefact, such as simulation models or working code. Contemporary MDE environments provide little support for managing a type of evolution termed model-metamodel co-evolution, in which changes to a modelling language are propagated to models. This thesis demonstrates that model-metamodel co-evolution occurs often in MDE projects, and that dedicated structures and processes for its management can increase developer productivity. Structures and processes for managing model-metamodel co-evolution are proposed, developed, and then evaluated by comparison to existing structures and processes with quantitative and qualitative techniques.

Published
2011

17. Property Access Traces for Source Incremental Model-to-Text Transformation

Author

Ogunyomi, Babajide, Rose, Louis M., Kolovos, Dimitrios S., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Taentzer, Gabriele, editor, and Bordeleau, Francis, editor

Published
2015
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18. On the Use of Signatures for Source Incremental Model-to-text Transformation

Author

Ogunyomi, Babajide, Rose, Louis M., Kolovos, Dimitrios S., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Dingel, Juergen, editor, Schulte, Wolfram, editor, Ramos, Isidro, editor, Abrahão, Silvia, editor, and Insfran, Emilio, editor

Published
2014
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19. A Framework to Benchmark NoSQL Data Stores for Large-Scale Model Persistence

Author

Shah, Seyyed M., Wei, Ran, Kolovos, Dimitrios S., Rose, Louis M., Paige, Richard F., Barmpis, Konstantinos, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Dingel, Juergen, editor, Schulte, Wolfram, editor, Ramos, Isidro, editor, Abrahão, Silvia, editor, and Insfran, Emilio, editor

Published
2014
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23. Model Management in the Wild

Author

Paige, Richard F., Kolovos, Dimitrios S., Rose, Louis M., Matragkas, Nikos, Williams, James R., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Lämmel, Ralf, editor, Saraiva, João, editor, and Visser, Joost, editor

Published
2013
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24. Solving Acquisition Problems Using Model-Driven Engineering

Author

Burton, Frank R., Paige, Richard F., Rose, Louis M., Kolovos, Dimitrios S., Poulding, Simon, Smith, Simon, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Vallecillo, Antonio, editor, Tolvanen, Juha-Pekka, editor, Kindler, Ekkart, editor, Störrle, Harald, editor, and Kolovos, Dimitris, editor

Published
2012
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25. A Plug-in Based Approach for UML Model Simulation

Author

Radjenovic, Alek, Paige, Richard F., Rose, Louis M., Woodcock, Jim, King, Steve, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Vallecillo, Antonio, editor, Tolvanen, Juha-Pekka, editor, Kindler, Ekkart, editor, Störrle, Harald, editor, and Kolovos, Dimitris, editor

Published
2012
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26. A Lightweight Approach for Managing XML Documents with MDE Languages

Author

Kolovos, Dimitrios S., Rose, Louis M., Williams, James, Matragkas, Nicholas, Paige, Richard F., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Vallecillo, Antonio, editor, Tolvanen, Juha-Pekka, editor, Kindler, Ekkart, editor, Störrle, Harald, editor, and Kolovos, Dimitris, editor

Published
2012
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27. EUnit: A Unit Testing Framework for Model Management Tasks

Author

García-Domínguez, Antonio, Kolovos, Dimitrios S., Rose, Louis M., Paige, Richard F., Medina-Bulo, Inmaculada, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Whittle, Jon, editor, Clark, Tony, editor, and Kühne, Thomas, editor

Published
2011
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28. Identifying Desirable Game Character Behaviours through the Application of Evolutionary Algorithms to Model-Driven Engineering Metamodels

Author

Williams, James R., Poulding, Simon, Rose, Louis M., Paige, Richard F., Polack, Fiona A. C., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Cohen, Myra B., editor, and Ó Cinnéide, Mel, editor

Published
2011
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29. Taming EMF and GMF Using Model Transformation

Author

Kolovos, Dimitrios S., Rose, Louis M., Abid, Saad Bin, Paige, Richard F., Polack, Fiona A. C., Botterweck, Goetz, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Petriu, Dorina C., editor, Rouquette, Nicolas, editor, and Haugen, Øystein, editor

Published
2010
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30. A Comparison of Model Migration Tools

Author

Rose, Louis M., Herrmannsdoerfer, Markus, Williams, James R., Kolovos, Dimitrios S., Garcés, Kelly, Paige, Richard F., Polack, Fiona A. C., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Petriu, Dorina C., editor, Rouquette, Nicolas, editor, and Haugen, Øystein, editor

Published
2010
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31. Model Migration with Epsilon Flock

Author

Rose, Louis M., Kolovos, Dimitrios S., Paige, Richard F., Polack, Fiona A. C., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Tratt, Laurence, editor, and Gogolla, Martin, editor

Published
2010
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32. Constructing and Navigating Non-invasive Model Decorations

Author

Kolovos, Dimitrios S., Rose, Louis M., Drivalos Matragkas, Nikolaos, Paige, Richard F., Polack, Fiona A. C., Fernandes, Kiran J., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Tratt, Laurence, editor, and Gogolla, Martin, editor

Published
2010
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33. A Reflective Approach to Model-Driven Web Engineering

Author

Clowes, Darren, Kolovos, Dimitris, Holmes, Chris, Rose, Louis, Paige, Richard, Johnson, Julian, Dawson, Ray, Probets, Steve, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Kühne, Thomas, editor, Selic, Bran, editor, Gervais, Marie-Pierre, editor, and Terrier, François, editor

Published
2010
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34. Concordance: A Framework for Managing Model Integrity

Author

Rose, Louis M., Kolovos, Dimitrios S., Drivalos, Nicholas, Williams, James R., Paige, Richard F., Polack, Fiona A. C., Fernandes, Kiran J., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Kühne, Thomas, editor, Selic, Bran, editor, Gervais, Marie-Pierre, editor, and Terrier, François, editor

Published
2010
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35. FPTC: Automated Safety Analysis for Domain-Specific Languages

Author

Paige, Richard F., Rose, Louis M., Ge, Xiaocheng, Kolovos, Dimitrios S., Brooke, Phillip J., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, and Chaudron, Michel R. V., editor

Published
2009
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37. The Epsilon Generation Language

Author

Rose, Louis M., Paige, Richard F., Kolovos, Dimitrios S., Polack, Fiona A. C., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Schieferdecker, Ina, editor, and Hartman, Alan, editor

Published
2008
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38. Constructing Models with the Human-Usable Textual Notation

Author

Rose, Louis M., Paige, Richard F., Kolovos, Dimitrios S., Polack, Fiona A. C., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Czarnecki, Krzysztof, editor, Ober, Ileana, editor, Bruel, Jean-Michel, editor, Uhl, Axel, editor, and Völter, Markus, editor

Published
2008
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