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8 results on '"Fiedler, Jessika"'

1. Performance Evaluation in High-Speed Networks by the Example of Intrusion Detection

Author

Lukaseder, Thomas, Fiedler, Jessika, and Kargl, Frank

Subjects
Computer Science - Cryptography and Security
Abstract

Purchase decisions for devices in high-throughput networks as well as scientific evaluations of algorithms and technologies need to be based in measurements and clear procedures. Therefore, evaluation of network devices and their performance in high-throughput networks is an important part of research. In this paper, we document our approach and show its applicability for our purpose in an evaluation of two of the most well-known and common open source intrusion detection systems, Snort and Suricata. We used a hardware network testing setup to ensure a realistic environment and documented our testing approach. In our work, we focus on accuracy of the detection especially dependent on bandwidth. We would like to pass on our experiences and considerations.

Published
2018

2. Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

Author

Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D, Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z, Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvočiūtė, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren J, Chia, Burton KH, Denis, Bertrand, Froula, Jeff L, Wang, Zhong, Egan, Robert, Don Kang, Dongwan, Cook, Jeffrey J, Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W, Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Silva, Genivaldo Gueiros Z, Cuevas, Daniel A, Edwards, Robert A, Saha, Surya, Piro, Vitor C, Renard, Bernhard Y, Pop, Mihai, Klenk, Hans-Peter, Göker, Markus, Kyrpides, Nikos C, Woyke, Tanja, Vorholt, Julia A, Schulze-Lefert, Paul, Rubin, Edward M, Darling, Aaron E, Rattei, Thomas, and McHardy, Alice C

Subjects
Biological Sciences, Networking and Information Technology R&D (NITRD), Algorithms, Benchmarking, Metagenomics, Sequence Analysis, DNA, Software, Technology, Medical and Health Sciences, Developmental Biology, Biological sciences
Abstract

Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.

Published
2017

4. Additional file 1 of CAMISIM: simulating metagenomes and microbial communities

Author

Fritz, Adrian, Hofmann, Peter, Majda, Stephan, Dahms, Eik, Drรถge, Johannes, Fiedler, Jessika, Lesker, Till, Belmann, Peter, DeMaere, Matthew, Darling, Aaron, Sczyrba, Alexander, Bremges, Andreas, and McHardy, Alice

Abstract

Supplementary information. Taxonomic profile based community design: BIOM format details, Reference database. De novo community design: Creation of the mapping file. Genome assembly metrics. Methods: iTol, Parameters, PICRUST, Configfile. OTU mapping file. (PDF 146 kb)

Published
2019
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5. CAMISIM: Simulating metagenomes and microbial communities

Author

Fritz, Adrian, primary, Hofmann, Peter, additional, Majda, Stephan, additional, Dahms, Eik, additional, Dröge, Johannes, additional, Fiedler, Jessika, additional, Lesker, Till R., additional, Belmann, Peter, additional, Demaere, Matthew Z., additional, Darling, Aaron E., additional, Sczyrba, Alexander, additional, Bremges, Andreas, additional, and Mchardy, Alice C., additional

Published
2018
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6. Critical Assessment of Metagenome Interpretation:a benchmark of metagenomics software

Author

Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D., Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z., Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvociute, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren Johannes, Chia, Burton K. H., Denis, Bertrand, Froula, Jeff L., Wang, Zhong, Egan, Robert, Kang, Dongwan Don, Cook, Jeffrey J., Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W., Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D., Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Silva, Genivaldo Gueiros Z., Cuevas, Daniel A., Edwards, Robert A., Saha, Surya, Piro, Vitor C., Renard, Bernhard Y., Pop, Mihai, Klenk, Hans-Peter, Göker, Markus, Kyrpides, Nikos C., Woyke, Tanja, Vorholt, Julia A., Schulze-Lefert, Paul, Rubin, Edward M., Darling, Aaron E., Rattei, Thomas, McHardy, Alice C., Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D., Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z., Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvociute, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren Johannes, Chia, Burton K. H., Denis, Bertrand, Froula, Jeff L., Wang, Zhong, Egan, Robert, Kang, Dongwan Don, Cook, Jeffrey J., Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W., Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D., Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Silva, Genivaldo Gueiros Z., Cuevas, Daniel A., Edwards, Robert A., Saha, Surya, Piro, Vitor C., Renard, Bernhard Y., Pop, Mihai, Klenk, Hans-Peter, Göker, Markus, Kyrpides, Nikos C., Woyke, Tanja, Vorholt, Julia A., Schulze-Lefert, Paul, Rubin, Edward M., Darling, Aaron E., Rattei, Thomas, and McHardy, Alice C.

Published
2017

7. Critical assessment of metagenome interpretation − a benchmark of computational metagenomics software

Author

Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Droege, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Sparholt Jorgensen, Tue, Shapiro, Nicole, Blood, Philip D., Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z., Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvociute, Monika, Hestbjerg Hansen, Lars, Sorensen, Soren J., Chia, Burton K. H., Denis, Bertrand, Froula, Jeff L., Wang, Zhong, Egan, Robert, Kang, Dongwan Don, Cook, Jeffrey J., Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W., Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Gueiros Z Silva, Genivaldo, Cuevas, Daniel A., Edwards, Robert A., Saha, Surya, Piro, Vitor C., Renard, Bernhard Y., Pop, Mihai, Klenk, Hans-Peter, Goeker, Markus, Kyrpides, Nikos C., Woyke, Tanja, Vorholt, Julia A., Schulze-Lefert, Paul, Rubin, Edward M., Darling, Aaron E., Rattei, Thomas, McHardy, Alice C., Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Droege, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Sparholt Jorgensen, Tue, Shapiro, Nicole, Blood, Philip D., Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z., Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvociute, Monika, Hestbjerg Hansen, Lars, Sorensen, Soren J., Chia, Burton K. H., Denis, Bertrand, Froula, Jeff L., Wang, Zhong, Egan, Robert, Kang, Dongwan Don, Cook, Jeffrey J., Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W., Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Gueiros Z Silva, Genivaldo, Cuevas, Daniel A., Edwards, Robert A., Saha, Surya, Piro, Vitor C., Renard, Bernhard Y., Pop, Mihai, Klenk, Hans-Peter, Goeker, Markus, Kyrpides, Nikos C., Woyke, Tanja, Vorholt, Julia A., Schulze-Lefert, Paul, Rubin, Edward M., Darling, Aaron E., Rattei, Thomas, and McHardy, Alice C.

Abstract

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions.

Published
2017

8. Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Author

Sczyrba, Alexander, primary, Hofmann, Peter, additional, Belmann, Peter, additional, Koslicki, David, additional, Janssen, Stefan, additional, Dröge, Johannes, additional, Gregor, Ivan, additional, Majda, Stephan, additional, Fiedler, Jessika, additional, Dahms, Eik, additional, Bremges, Andreas, additional, Fritz, Adrian, additional, Garrido-Oter, Ruben, additional, Jørgensen, Tue Sparholt, additional, Shapiro, Nicole, additional, Blood, Philip D., additional, Gurevich, Alexey, additional, Bai, Yang, additional, Turaev, Dmitrij, additional, DeMaere, Matthew Z., additional, Chikhi, Rayan, additional, Nagarajan, Niranjan, additional, Quince, Christopher, additional, Meyer, Fernando, additional, Balvoit, Monika, additional, Hansen, Lars Hestbjerg, additional, Sørensen, Søren J., additional, Chia, Burton K. H., additional, Denis, Bertrand, additional, Froula, Jeff L., additional, Wang, Zhong, additional, Egan, Robert, additional, Kang, Dongwan Don, additional, Cook, Jeffrey J., additional, Deltel, Charles, additional, Beckstette, Michael, additional, Lemaitre, Claire, additional, Peterlongo, Pierre, additional, Rizk, Guillaume, additional, Lavenier, Dominique, additional, Wu, Yu-Wei, additional, Singer, Steven W., additional, Jain, Chirag, additional, Strous, Marc, additional, Klingenberg, Heiner, additional, Meinicke, Peter, additional, Barton, Michael, additional, Lingner, Thomas, additional, Lin, Hsin-Hung, additional, Liao, Yu-Chieh, additional, Silva, Genivaldo Gueiros Z., additional, Cuevas, Daniel A., additional, Edwards, Robert A., additional, Saha, Surya, additional, Piro, Vitor C., additional, Renard, Bernhard Y., additional, Pop, Mihai, additional, Klenk, Hans-Peter, additional, Göker, Markus, additional, Kyrpides, Nikos C., additional, Woyke, Tanja, additional, Vorholt, Julia A., additional, Schulze-Lefert, Paul, additional, Rubin, Edward M., additional, Darling, Aaron E., additional, Rattei, Thomas, additional, and McHardy, Alice C., additional

Published
2017
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