8 Search Results for "Shan, Tony"

Document
DOI: 10.4230/LIPIcs.WABI.2025.10
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Authors: Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Determining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [Jain et al., 2019], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5-4x speed-up in query time, 44-340x smaller index size, and 3-50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome. The implementation is available at: https://github.com/cartoonist/diverg
Cite as

Ali Ghaffaari, Alexander Schönhuth, and Tobias Marschall. DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 10:1-10:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{ghaffaari_et_al:LIPIcs.WABI.2025.10,
  author =	{Ghaffaari, Ali and Sch\"{o}nhuth, Alexander and Marschall, Tobias},
  title =	{{DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{10:1--10:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.10},
  URN =		{urn:nbn:de:0030-drops-239369},
  doi =		{10.4230/LIPIcs.WABI.2025.10},
  annote =	{Keywords: Sequence graph, distance index, read mapping, sparse matrix}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2024.22
FaaSLoad: Fine-Grained Performance and Resource Measurement for Function-As-a-Service

Authors: Mathieu Bacou

Published in: LIPIcs, Volume 324, 28th International Conference on Principles of Distributed Systems (OPODIS 2024)

Abstract
Cloud computing relies on a deep stack of system layers: virtual machine, operating system, distributed middleware and language runtime. However, those numerous, distributed, virtual layers prevent any low-level understanding of the properties of FaaS applications, considered as programs running on real hardware. As a result, most research analyses only consider coarse-grained properties such as global performance of an application, and existing datasets include only sparse data. FaaSLoad is a tool to gather fine-grained data about performance and resource usage of the programs that run on Function-as-a-Service cloud platforms. It considers individual instances of functions to collect hardware and operating-system performance information, by monitoring them while injecting a workload. FaaSLoad helps building a dataset of function executions to train machine learning models, studying at fine grain the behavior of function runtimes, and replaying real workload traces for in situ observations. This research software project aims at being useful to cloud system researchers with features such as guaranteeing reproducibility and correctness, and keeping up with realistic FaaS workloads. Our evaluations show that FaaSLoad helps us understanding the properties of FaaS applications, and studying the latter under real conditions.
Cite as

Mathieu Bacou. FaaSLoad: Fine-Grained Performance and Resource Measurement for Function-As-a-Service. In 28th International Conference on Principles of Distributed Systems (OPODIS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 324, pp. 22:1-22:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bacou:LIPIcs.OPODIS.2024.22,
  author =	{Bacou, Mathieu},
  title =	{{FaaSLoad: Fine-Grained Performance and Resource Measurement for Function-As-a-Service}},
  booktitle =	{28th International Conference on Principles of Distributed Systems (OPODIS 2024)},
  pages =	{22:1--22:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-360-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{324},
  editor =	{Bonomi, Silvia and Galletta, Letterio and Rivi\`{e}re, Etienne and Schiavoni, Valerio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2024.22},
  URN =		{urn:nbn:de:0030-drops-225581},
  doi =		{10.4230/LIPIcs.OPODIS.2024.22},
  annote =	{Keywords: cloud, serverless, Function-as-a-Service, measurement, performance, resource utilization, dataset generation, workload injection}
}
Document
DOI: 10.4230/DagSemProc.09021.1
09021 Abstracts Collection – Software Service Engineering

Authors: Frank Leymann, Tony Shan, Olaf Zimmermann, and Willem-Jan van den Heuvel

Published in: Dagstuhl Seminar Proceedings, Volume 9021, Software Service Engineering (2009)

Abstract
From 04.01. to 07.01.2009, the Dagstuhl Seminar 09021 ``Software Service Engineering '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
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Frank Leymann, Tony Shan, Olaf Zimmermann, and Willem-Jan van den Heuvel. 09021 Abstracts Collection – Software Service Engineering. In Software Service Engineering. Dagstuhl Seminar Proceedings, Volume 9021, pp. 1-10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{leymann_et_al:DagSemProc.09021.1,
  author =	{Leymann, Frank and Shan, Tony and Zimmermann, Olaf and van den Heuvel, Willem-Jan},
  title =	{{09021 Abstracts Collection – Software Service Engineering}},
  booktitle =	{Software Service Engineering},
  pages =	{1--10},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9021},
  editor =	{Frank Leymann and Tony Shan and Willen-Jan van den Heuvel and Olaf Zimmermann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09021.1},
  URN =		{urn:nbn:de:0030-drops-20463},
  doi =		{10.4230/DagSemProc.09021.1},
  annote =	{Keywords: Service engineering, software engineering, service-oriented computing, service-oriented analysis and design, SOA, systems engineering, Web engineering}
}
Document
DOI: 10.4230/DagSemProc.09021.3
Cases of Software Services Design in Practice

Authors: Susanne Patig

Published in: Dagstuhl Seminar Proceedings, Volume 9021, Software Service Engineering (2009)

Abstract
During the last years, several approaches for the design of software services in service-oriented architectures (SOA) have been proposed. Often these approaches are too rough or too academic to provide guidance for real world SOA projects. Moreover, since the existing SOA design approaches are often not sufficiently validated, their successfulness in practice can be doubted. The research presented here aims at learning from successful SOA projects. Two cases of such projects are described. In the cases similarities show up that are distinct from existing SOA design approaches (mainly the purely academic ones) and, thus, point to necessary enhancements of these approaches.
Cite as

Susanne Patig. Cases of Software Services Design in Practice. In Software Service Engineering. Dagstuhl Seminar Proceedings, Volume 9021, pp. 1-11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{patig:DagSemProc.09021.3,
  author =	{Patig, Susanne},
  title =	{{Cases of  Software Services Design in Practice}},
  booktitle =	{Software Service Engineering},
  pages =	{1--11},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9021},
  editor =	{Frank Leymann and Tony Shan and Willen-Jan van den Heuvel and Olaf Zimmermann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09021.3},
  URN =		{urn:nbn:de:0030-drops-20473},
  doi =		{10.4230/DagSemProc.09021.3},
  annote =	{Keywords: SOA Design Approaches, Service Design, Case Study}
}
Document
DOI: 10.4230/DagSemProc.09021.2
09021 Executive Summary – Software Service Engineering

Authors: Willem-Jan van den Heuvel, Olaf Zimmermann, Frank Leymann, and Tony Shan

Published in: Dagstuhl Seminar Proceedings, Volume 9021, Software Service Engineering (2009)

Abstract
Service-Oriented Architecture (SOA) constitutes an important, standards-based and technology-independent distributed computing paradigm and architectural style for discovering, binding, assembling, and publishing loosely-coupled and network-available software services. With SOA-enabled applications operating in highly complex, distributed, and heterogeneous execution environments, SOA practitioners encounter the limits of traditional software engineering. In this Dagstuhl seminar, we have discussed and explored the fundamental tenets underpinning the development and maintenance of SOA systems. As a result of our discussions, we position software service engineering as an evolving and converging discipline that embraces the open world assumption. Software service engineering entails a departure from traditional software engineering disciplines such as component-based development, supplementing them with techniques and patterns tailored to service enablement, composition, and management.
Cite as

Willem-Jan van den Heuvel, Olaf Zimmermann, Frank Leymann, and Tony Shan. 09021 Executive Summary – Software Service Engineering. In Software Service Engineering. Dagstuhl Seminar Proceedings, Volume 9021, pp. 1-12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{vandenheuvel_et_al:DagSemProc.09021.2,
  author =	{van den Heuvel, Willem-Jan and Zimmermann, Olaf and Leymann, Frank and Shan, Tony},
  title =	{{09021 Executive Summary – Software Service Engineering}},
  booktitle =	{Software Service Engineering},
  pages =	{1--12},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9021},
  editor =	{Frank Leymann and Tony Shan and Willen-Jan van den Heuvel and Olaf Zimmermann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09021.2},
  URN =		{urn:nbn:de:0030-drops-20412},
  doi =		{10.4230/DagSemProc.09021.2},
  annote =	{Keywords: Service engineering, software engineering, service-oriented computing, service-oriented analysis and design, SOA, systems engineering, Web engineering}
}
Document
DOI: 10.4230/DagSemProc.09021.4
Designing Software Services for Business Agility

Authors: Harald Wesenberg

Published in: Dagstuhl Seminar Proceedings, Volume 9021, Software Service Engineering (2009)

Abstract
This presentation focuses on identifying the right services for a domain. The work is based on 10+ years of experience from StatoilHydro identifying and building services that are stable and useful for many years, even across technology shifts. By focusing on workflows with their activities, events and information usage, a set of reusable services can be identified through little effort (espescially if the workflows already exists) and built/composed from existing services. This approach is especially suitable for agile development practices, as it significantly reduces the amount of up-front analysis compared to traditional service design practices.
Cite as

Harald Wesenberg. Designing Software Services for Business Agility. In Software Service Engineering. Dagstuhl Seminar Proceedings, Volume 9021, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{wesenberg:DagSemProc.09021.4,
  author =	{Wesenberg, Harald},
  title =	{{Designing Software Services for Business Agility}},
  booktitle =	{Software Service Engineering},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9021},
  editor =	{Frank Leymann and Tony Shan and Willen-Jan van den Heuvel and Olaf Zimmermann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09021.4},
  URN =		{urn:nbn:de:0030-drops-20445},
  doi =		{10.4230/DagSemProc.09021.4},
  annote =	{Keywords: Enterprise Architecture, SOA, Domain Driven Design, Business Architecture, Software Service}
}
Document
DOI: 10.4230/DagSemProc.09021.5
On Composing RESTful Services

Authors: Cesare Pautasso

Published in: Dagstuhl Seminar Proceedings, Volume 9021, Software Service Engineering (2009)

Abstract
Composition is one of the central tenets of service oriented computing. This paper discusses how composition can be applied to RESTful services in order to foster their reuse. Given the specific constraints of the REST architectural style, a number of challenges for current service composition languages and technologies are identified to point out future research directions.
Cite as

Cesare Pautasso. On Composing RESTful Services. In Software Service Engineering. Dagstuhl Seminar Proceedings, Volume 9021, pp. 1-7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{pautasso:DagSemProc.09021.5,
  author =	{Pautasso, Cesare},
  title =	{{On Composing RESTful Services}},
  booktitle =	{Software Service Engineering},
  pages =	{1--7},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9021},
  editor =	{Frank Leymann and Tony Shan and Willen-Jan van den Heuvel and Olaf Zimmermann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09021.5},
  URN =		{urn:nbn:de:0030-drops-20433},
  doi =		{10.4230/DagSemProc.09021.5},
  annote =	{Keywords: REST, Web Service Composition, RESTful Service Composition}
}
Document
DOI: 10.4230/DagSemProc.09021.6
Software Service Engineering - Architect's Dream or Developer's Nightmare?

Authors: Gregor Hohpe

Published in: Dagstuhl Seminar Proceedings, Volume 9021, Software Service Engineering (2009)

Abstract
Architectural principles such as loose coupling are the key drivers behind the adoption of service-oriented architectures. Service-oriented architectures promote concepts such as composition, process modeling, protocol design, declarative programming, event-based programming, and object-document mapping. These architectural ideals can be fraught with challenges for developers who are faced with unfamiliar programming models and immature tools. This paper briefly reviews the service-oriented architecture concepts and highlights the most pressing challenges for developers. These challenges suggest several focus areas for tool builders and software service engineering researchers.
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Gregor Hohpe. Software Service Engineering - Architect's Dream or Developer's Nightmare?. In Software Service Engineering. Dagstuhl Seminar Proceedings, Volume 9021, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{hohpe:DagSemProc.09021.6,
  author =	{Hohpe, Gregor},
  title =	{{Software Service Engineering - Architect's Dream or Developer's Nightmare?}},
  booktitle =	{Software Service Engineering},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9021},
  editor =	{Frank Leymann and Tony Shan and Willen-Jan van den Heuvel and Olaf Zimmermann},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09021.6},
  URN =		{urn:nbn:de:0030-drops-20423},
  doi =		{10.4230/DagSemProc.09021.6},
  annote =	{Keywords: Event-based programming, declarative programming, object-document mapping, patterns, process modeling, protocol design, service composition, software}
}
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