10 Search Results for "Ebert, Peter"

Document
DOI: 10.4230/DagMan.11.1.1
Climate Change: What is Computing’s Responsibility? (Dagstuhl Perspectives Workshop 25122)

Authors: Bran Knowles, Vicki L. Hanson, Christoph Becker, Mike Berners-Lee, Andrew A. Chien, Benoit Combemale, Vlad Coroamă, Koen De Bosschere, Yi Ding, Adrian Friday, Boris Gamazaychikov, Lynda Hardman, Simon Hinterholzer, Mattias Höjer, Lynn Kaack, Lenneke Kuijer, Anne-Laure Ligozat, Jan Tobias Muehlberg, Yunmook Nah, Thomas Olsson, Anne-Cécile Orgerie, Daniel Pargman, Birgit Penzenstadler, Tom Romanoff, Emma Strubell, Colin Venters, and Junhua Zhao

Published in: Dagstuhl Manifestos, Volume 11, Issue 1 (2025)

Abstract
This Manifesto was produced from the Perspectives Workshop 25122 entitled "Climate Change: What is Computing’s Responsibility?" held March 16-19, 2025 at Schloss Dagstuhl, Germany. The Workshop provided a forum for world-leading computer scientists and expert consultants on environmental policy and sustainable transition to engage in a critical and urgent conversation about computing’s responsibilities in addressing climate change - or more aptly, climate crisis. The resulting Manifesto outlines commitments and directions for future action which, if adopted as a basis for more responsible computing practices, will help ensure that these technologies do not threaten the long-term habitability of the planet. We preface our Manifesto with a recognition that humanity is on a path that is not in agreement with international global warming targets and explore how computing technologies are currently hastening the overshoot of these boundaries. We critically assess the vaunted potential for harnessing computing technologies for the mitigation of global warming, agreeing that, under current circumstances, computing is contributing to negative environmental impacts in other sectors. Computing primarily improves efficiency and reduces costs which leads to more consumption and more negative environmental impact. Relying solely on efficiency gains in computing has thus far proven to be insufficient to curb global greenhouse gas emissions. Therefore, computing’s purpose within a strategy for tackling climate change must be reimagined. Our recommendations cover changes that need to be urgently made to the design priorities of computing technologies, but also speak to the more systemic shift in mindset, with sustainability and human rights providing a necessary moral foundation for developing the kinds of computing technologies most needed by society. We also stress the importance of digital policy that accounts for both the direct material impacts of computing and the detrimental indirect impacts arising from computing-enabled efficiencies, and the role of computing professionals in informing policy making.
Cite as

Bran Knowles, Vicki L. Hanson, Christoph Becker, Mike Berners-Lee, Andrew A. Chien, Benoit Combemale, Vlad Coroamă, Koen De Bosschere, Yi Ding, Adrian Friday, Boris Gamazaychikov, Lynda Hardman, Simon Hinterholzer, Mattias Höjer, Lynn Kaack, Lenneke Kuijer, Anne-Laure Ligozat, Jan Tobias Muehlberg, Yunmook Nah, Thomas Olsson, Anne-Cécile Orgerie, Daniel Pargman, Birgit Penzenstadler, Tom Romanoff, Emma Strubell, Colin Venters, and Junhua Zhao. Climate Change: What is Computing’s Responsibility? (Dagstuhl Perspectives Workshop 25122). In Dagstuhl Manifestos, Volume 11, Issue 1, pp. 1-18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{knowles_et_al:DagMan.11.1.1,
  author =	{Knowles, Bran and Hanson, Vicki L. and Becker, Christoph and Berners-Lee, Mike and Chien, Andrew A. and Combemale, Benoit and Coroam\u{a}, Vlad and De Bosschere, Koen and Ding, Yi and Friday, Adrian and Gamazaychikov, Boris and Hardman, Lynda and Hinterholzer, Simon and H\"{o}jer, Mattias and Kaack, Lynn and Kuijer, Lenneke and Ligozat, Anne-Laure and Muehlberg, Jan Tobias and Nah, Yunmook and Olsson, Thomas and Orgerie, Anne-C\'{e}cile and Pargman, Daniel and Penzenstadler, Birgit and Romanoff, Tom and Strubell, Emma and Venters, Colin and Zhao, Junhua},
  title =	{{Climate Change: What is Computing’s Responsibility? (Dagstuhl Perspectives Workshop 25122)}},
  pages =	{1--18},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2025},
  volume =	{11},
  number =	{1},
  editor =	{Knowles, Bran and Hanson, Vicki L. and Becker, Christoph and Berners-Lee, Mike and Chien, Andrew A. and Combemale, Benoit and Coroam\u{a}, Vlad and De Bosschere, Koen and Ding, Yi and Friday, Adrian and Gamazaychikov, Boris and Hardman, Lynda and Hinterholzer, Simon and H\"{o}jer, Mattias and Kaack, Lynn and Kuijer, Lenneke and Ligozat, Anne-Laure and Muehlberg, Jan Tobias and Nah, Yunmook and Olsson, Thomas and Orgerie, Anne-C\'{e}cile and Pargman, Daniel and Penzenstadler, Birgit and Romanoff, Tom and Strubell, Emma and Venters, Colin and Zhao, Junhua},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.11.1.1},
  URN =		{urn:nbn:de:0030-drops-250724},
  doi =		{10.4230/DagMan.11.1.1},
  annote =	{Keywords: sustainability, climate change, efficiency, supply chain management, climate modelling}
}
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.WABI.2025.14
Human Readable Compression of GFA Paths Using Grammar-Based Code

Authors: Peter Heringer and Daniel Doerr

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

Abstract
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly growing file sizes due to the explicit and repetitive encoding of haplotype paths. In this work, we introduce an extension to the GFA format that enables efficient grammar-based compression of haplotype paths while retaining human readability. In addition, grammar-based encoding provides an efficient in-memory data structure that does not require decompression, but conversely improves the runtime of many computational tasks that involve haplotype comparisons. We present sqz, a method that makes use of the proposed format extension to encode haplotype paths using byte pair encoding, a grammar-based compression scheme. We evaluate sqz on recent human pangenome graphs from Heumos et al. and the Human Pangenome Reference Consortium (HPRC), comparing it to existing compressors bgzip, gbz, and sequitur. sqz scales sublinearly with the number of haplotypes in a pangenome graph and consistently achieves higher compression ratios than sequitur and up to 5 times better compression than bgzip in HPRC graphs and up to 10 times in the graph from Heumos et al.. When combined with bgzip, sqz matches or excels the compression ratio of gbz across all our datasets. These results demonstrate the potential of our proposed extension of the GFA format in reducing haplotype path redundancy and improving storage efficiency for pangenome graphs.
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Peter Heringer and Daniel Doerr. Human Readable Compression of GFA Paths Using Grammar-Based Code. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{heringer_et_al:LIPIcs.WABI.2025.14,
  author =	{Heringer, Peter and Doerr, Daniel},
  title =	{{Human Readable Compression of GFA Paths Using Grammar-Based Code}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{14:1--14:19},
  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.2025.14},
  URN =		{urn:nbn:de:0030-drops-239395},
  doi =		{10.4230/LIPIcs.WABI.2025.14},
  annote =	{Keywords: pangenomics, pangenome graphs, compression, grammar-based code, byte pair encoding}
}
Document
DOI: 10.4230/OASIcs.Manzini.10
Phasing Data from Genotype Queries via the μ-PBWT

Authors: Davide Cozzi, Paola Bonizzoni, Christina Boucher, Ben Langmead, and Yuri Pirola

Published in: OASIcs, Volume 131, The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday (2025)

Abstract
Genotype phasing - the process of reconstructing haplotypes from genotype data - is a fundamental problem in genomics with applications in ancestry inference, imputation, and disease association. Traditional phasing methods rely on statistical models or combinatorial approaches which can be computationally expensive, particularly when applied to large-scale reference panels. In this paper, we present a first exploration of using the μ-PBWT (a run-length encoded Positional Burrows-Wheeler Transform) to solve the genotype phasing problem with a reference panel. Leveraging our previous results on positional substrings, we propose an approach that can explain a query genotype if the corresponding haplotype pair exists in the input panel. Moreover, our method is extended to cases where such a pair does not exist, even though some regions should remain unphased if they cannot be explicitly explained using the reference panel. We implemented this method and compared it against Beagle, a state-of-the-art phasing tool, demonstrating that, in the absence of mutations and recombinations, our approach correctly identifies the haplotype pair that explains a genotype query while using seven times less memory than Beagle. However, we also observe that as mutation rates increase, the quality of the phasing decreases as a result of the growing difficulty of identifying consistent haplotype pairs in the presence of sequence variation. These findings highlight the potential of μ-PBWT as an efficient alternative for genotype phasing, particularly in settings where computational resources are limited. The source code is publicly available at https://github.com/dlcgold/muPBWT/tree/phase.
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Davide Cozzi, Paola Bonizzoni, Christina Boucher, Ben Langmead, and Yuri Pirola. Phasing Data from Genotype Queries via the μ-PBWT. In The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday. Open Access Series in Informatics (OASIcs), Volume 131, pp. 10:1-10:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cozzi_et_al:OASIcs.Manzini.10,
  author =	{Cozzi, Davide and Bonizzoni, Paola and Boucher, Christina and Langmead, Ben and Pirola, Yuri},
  title =	{{Phasing Data from Genotype Queries via the \mu-PBWT}},
  booktitle =	{The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday},
  pages =	{10:1--10:17},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-390-4},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{131},
  editor =	{Ferragina, Paolo and Gagie, Travis and Navarro, Gonzalo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.Manzini.10},
  URN =		{urn:nbn:de:0030-drops-239183},
  doi =		{10.4230/OASIcs.Manzini.10},
  annote =	{Keywords: Positional Burrows-Wheeler Transform, r-index, minimal position substring cover, set-maximal exact matches, genotype phasing}
}
Document
Resource Paper
DOI: 10.4230/TGDK.2.2.7
Whelk: An OWL EL+RL Reasoner Enabling New Use Cases

Authors: James P. Balhoff and Christopher J. Mungall

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract
Many tasks in the biosciences rely on reasoning with large OWL terminologies (Tboxes), often combined with even larger databases. In particular, a common task is retrieval queries that utilize relational expressions; for example, “find all genes expressed in the brain or any part of the brain”. Automated reasoning on these ontologies typically relies on scalable reasoners targeting the EL subset of OWL, such as ELK. While the introduction of ELK has been transformative in the incorporation of reasoning into bio-ontology quality control and production pipelines, we have encountered limitations when applying it to use cases involving high throughput query answering or reasoning about datasets describing instances (Aboxes). Whelk is a fast OWL reasoner for combined EL+RL reasoning. As such, it is particularly useful for many biological ontology tasks, particularly those characterized by large Tboxes using the EL subset of OWL, combined with Aboxes targeting the RL subset of OWL. Whelk is implemented in Scala and utilizes immutable functional data structures, which provides advantages when performing incremental or dynamic reasoning tasks. Whelk supports querying complex class expressions at a substantially greater rate than ELK, and can answer queries or perform incremental reasoning tasks in parallel, enabling novel applications of OWL reasoning.
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James P. Balhoff and Christopher J. Mungall. Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{balhoff_et_al:TGDK.2.2.7,
  author =	{Balhoff, James P. and Mungall, Christopher J.},
  title =	{{Whelk: An OWL EL+RL Reasoner Enabling New Use Cases}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{7:1--7:17},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.7},
  URN =		{urn:nbn:de:0030-drops-225918},
  doi =		{10.4230/TGDK.2.2.7},
  annote =	{Keywords: Web Ontology Language, OWL, Semantic Web, ontology, reasoner}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
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Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.16
All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels

Authors: Sarvesh Nikumbh, Peter Ebert, and Nico Pfeifer

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
Most string kernels for comparison of genomic sequences are generally tied to using (absolute) positional information of the features in the individual sequences. This poses limitations when comparing variable-length sequences using such string kernels. For example, profiling chromatin interactions by 3C-based experiments results in variable-length genomic sequences (restriction fragments). Here, exact position-wise occurrence of signals in sequences may not be as important as in the scenario of analysis of the promoter sequences, that typically have a transcription start site as reference. Existing position-aware string kernels have been shown to be useful for the latter scenario. In this work, we propose a novel approach for sequence comparison that enables larger positional freedom than most of the existing approaches, can identify a possibly dispersed set of features in comparing variable-length sequences, and can handle both the aforementioned scenarios. Our approach, \emph{CoMIK}, identifies not just the features useful towards classification but also their locations in the variable-length sequences, as evidenced by the results of three binary classification experiments, aided by recently introduced visualization techniques. Furthermore, we show that we are able to efficiently retrieve and interpret the weight vector for the complex setting of multiple multi-instance kernels.
Cite as

Sarvesh Nikumbh, Peter Ebert, and Nico Pfeifer. All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 16:1-16:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{nikumbh_et_al:LIPIcs.WABI.2017.16,
  author =	{Nikumbh, Sarvesh and Ebert, Peter and Pfeifer, Nico},
  title =	{{All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{16:1--16:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.16},
  URN =		{urn:nbn:de:0030-drops-76459},
  doi =		{10.4230/LIPIcs.WABI.2017.16},
  annote =	{Keywords: Multiple instance learning, conformal MI kernels, 5C, Hi-C}
}
Document
DOI: 10.4230/OASIcs.VLUDS.2011.25
Visualization and Evolution of Software Architectures

Authors: Taimur Khan, Henning Barthel, Achim Ebert, and Peter Liggesmeyer

Published in: OASIcs, Volume 27, Visualization of Large and Unstructured Data Sets: Applications in Geospatial Planning, Modeling and Engineering - Proceedings of IRTG 1131 Workshop 2011

Abstract
Software systems are an integral component of our everyday life as we find them in tools and embedded in equipment all around us. In order to ensure smooth, predictable, and accurate operation of these systems, it is crucial to produce and maintain systems that are highly reliable. A well-designed and well-maintained architecture goes a long way in achieving this goal. However, due to the intangible and often complex nature of software architecture, this task can be quite complicated. The field of software architecture visualization aims to ease this task by providing tools and techniques to examine the hierarchy, relationship, evolution, and quality of architecture components. In this paper, we present a discourse on the state of the art of software architecture visualization techniques. Further, we highlight the importance of developing solutions tailored to meet the needs and requirements of the stakeholders involved in the analysis process.
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Taimur Khan, Henning Barthel, Achim Ebert, and Peter Liggesmeyer. Visualization and Evolution of Software Architectures. In Visualization of Large and Unstructured Data Sets: Applications in Geospatial Planning, Modeling and Engineering - Proceedings of IRTG 1131 Workshop 2011. Open Access Series in Informatics (OASIcs), Volume 27, pp. 25-42, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@InProceedings{khan_et_al:OASIcs.VLUDS.2011.25,
  author =	{Khan, Taimur and Barthel, Henning and Ebert, Achim and Liggesmeyer, Peter},
  title =	{{Visualization and Evolution of Software Architectures}},
  booktitle =	{Visualization of Large and Unstructured Data Sets: Applications in Geospatial Planning, Modeling and Engineering - Proceedings of IRTG 1131 Workshop 2011},
  pages =	{25--42},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-46-0},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{27},
  editor =	{Garth, Christoph and Middel, Ariane and Hagen, Hans},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.VLUDS.2011.25},
  URN =		{urn:nbn:de:0030-drops-37390},
  doi =		{10.4230/OASIcs.VLUDS.2011.25},
  annote =	{Keywords: Software architecture visualization, software comprehension, software maintenance, software evolution, human perception}
}
Document
DOI: 10.4230/OASIcs.VLUDS.2011.113
Controlling In-Vehicle Systems with a Commercial EEG Headset: Performance and Cognitive Load

Authors: Daniel Cernea, Peter-Scott Olech, Achim Ebert, and Andreas Kerren

Published in: OASIcs, Volume 27, Visualization of Large and Unstructured Data Sets: Applications in Geospatial Planning, Modeling and Engineering - Proceedings of IRTG 1131 Workshop 2011

Abstract
Humans have dreamed for centuries to control their surroundings solely by the power of their minds. These aspirations have been captured by multiple science fiction creations, such as the Neuromancer novel by William Gibson or the Brainstorm cinematic movie, to name just a few. Nowadays, these dreams are slowly becoming reality due to a variety of brain-computer interfaces (BCI) that detect neural activation patterns and support the control of devices by brain signals. An important field in which BCIs are being successfully integrated is the interaction with vehicular systems. In this paper, we evaluate the performance of BCIs, more specifically a commercial electroencephalographic (EEG) headset in combination with vehicle dashboard systems, and highlight the advantages and limitations of this approach. Further, we investigate the cognitive load that drivers experience when interacting with secondary in-vehicle devices via touch controls or a BCI headset. As in-vehicle systems are increasingly versatile and complex, it becomes vital to capture the level of distraction and errors that controlling these secondary systems might introduce to the primary driving process. Our results suggest that the control with the EEG headset introduces less distraction to the driver, probably as it allows the eyes of the driver to remain focused on the road. Still, the control of the vehicle dashboard by EEG is efficient only for a limited number of functions, after which increasing the number of in-vehicle controls amplifies the detection of false commands.
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Daniel Cernea, Peter-Scott Olech, Achim Ebert, and Andreas Kerren. Controlling In-Vehicle Systems with a Commercial EEG Headset: Performance and Cognitive Load. In Visualization of Large and Unstructured Data Sets: Applications in Geospatial Planning, Modeling and Engineering - Proceedings of IRTG 1131 Workshop 2011. Open Access Series in Informatics (OASIcs), Volume 27, pp. 113-122, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@InProceedings{cernea_et_al:OASIcs.VLUDS.2011.113,
  author =	{Cernea, Daniel and Olech, Peter-Scott and Ebert, Achim and Kerren, Andreas},
  title =	{{Controlling In-Vehicle Systems with a Commercial EEG Headset: Performance and Cognitive Load}},
  booktitle =	{Visualization of Large and Unstructured Data Sets: Applications in Geospatial Planning, Modeling and Engineering - Proceedings of IRTG 1131 Workshop 2011},
  pages =	{113--122},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-46-0},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{27},
  editor =	{Garth, Christoph and Middel, Ariane and Hagen, Hans},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.VLUDS.2011.113},
  URN =		{urn:nbn:de:0030-drops-37459},
  doi =		{10.4230/OASIcs.VLUDS.2011.113},
  annote =	{Keywords: Brain-computer interface, EEG neuroheadset, EEG control, driver cog- nitive workload, in-vehicle systems.}
}
Document
DOI: 10.4230/DagSemProc.05402.1
Dagstuhl-Manifest zur Strategischen Bedeutung des Software Engineering in Deutschland

Authors: Manfred Broy, Matthias Jarke, Manfred Nagl, Hans Dieter Rombach, Armin B. Cremers, Jürgen Ebert, Sabine Glesner, Martin Glinz, Michael Goedicke, Gerhard Goos, Volker Gruhn, Wilhelm Hasselbring, Stefan Jähnichen, Stefan Kowalewski, Bernd J. Krämer, Stefan Leue, Claus Lewerentz, Peter Liggesmeyer, Christoph Lüth, Barbara Paech, Helmut A. Partsch, Ilka Philippow, Lutz Prechelt, Andreas Rausch, Willem-Paul de Roever, Bernhard Rumpe, Gudula Rünger, Wilhelm Schäfer, Kurt Schneider, Andy Schürr, Walter F. Tichy, Bernhard Westfechtel, Wolf Zimmermann, and Albert Zündorf

Published in: Dagstuhl Seminar Proceedings, Volume 5402, Perspectives Workshop (2006)

Abstract
Im Rahmen des Dagstuhl Perspektiven Workshop 05402 "Challenges for Software Engineering Research" haben führende Software Engineering Professoren den derzeitigen Stand der Softwaretechnik in Deutschland charakterisiert und Handlungsempfehlungen für Wirtschaft, Forschung und Politik abgeleitet. Das Manifest fasst die diese Empfehlungen und die Bedeutung und Entwicklung des Fachgebiets prägnant zusammen.
Cite as

Manfred Broy, Matthias Jarke, Manfred Nagl, Hans Dieter Rombach, Armin B. Cremers, Jürgen Ebert, Sabine Glesner, Martin Glinz, Michael Goedicke, Gerhard Goos, Volker Gruhn, Wilhelm Hasselbring, Stefan Jähnichen, Stefan Kowalewski, Bernd J. Krämer, Stefan Leue, Claus Lewerentz, Peter Liggesmeyer, Christoph Lüth, Barbara Paech, Helmut A. Partsch, Ilka Philippow, Lutz Prechelt, Andreas Rausch, Willem-Paul de Roever, Bernhard Rumpe, Gudula Rünger, Wilhelm Schäfer, Kurt Schneider, Andy Schürr, Walter F. Tichy, Bernhard Westfechtel, Wolf Zimmermann, and Albert Zündorf. Dagstuhl-Manifest zur Strategischen Bedeutung des Software Engineering in Deutschland. In Perspectives Workshop. Dagstuhl Seminar Proceedings, Volume 5402, pp. 1-16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{broy_et_al:DagSemProc.05402.1,
  author =	{Broy, Manfred and Jarke, Matthias and Nagl, Manfred and Rombach, Hans Dieter and Cremers, Armin B. and Ebert, J\"{u}rgen and Glesner, Sabine and Glinz, Martin and Goedicke, Michael and Goos, Gerhard and Gruhn, Volker and Hasselbring, Wilhelm and J\"{a}hnichen, Stefan and Kowalewski, Stefan and Kr\"{a}mer, Bernd J. and Leue, Stefan and Lewerentz, Claus and Liggesmeyer, Peter and L\"{u}th, Christoph and Paech, Barbara and Partsch, Helmut A. and Philippow, Ilka and Prechelt, Lutz and Rausch, Andreas and de Roever, Willem-Paul and Rumpe, Bernhard and R\"{u}nger, Gudula and Sch\"{a}fer, Wilhelm and Schneider, Kurt and Sch\"{u}rr, Andy and Tichy, Walter F. and Westfechtel, Bernhard and Zimmermann, Wolf and Z\"{u}ndorf, Albert},
  title =	{{Dagstuhl-Manifest zur Strategischen Bedeutung des Software Engineering in Deutschland}},
  booktitle =	{Perspectives Workshop},
  pages =	{1--16},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5402},
  editor =	{Manfred Broy and Manfred Nagl and Hans Dieter Rombach and Matthias Jarke},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05402.1},
  URN =		{urn:nbn:de:0030-drops-5853},
  doi =		{10.4230/DagSemProc.05402.1},
  annote =	{Keywords: Software Engineering, Software Technik, Strategie}
}
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