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42 results on '"Meijer, Jeroen"'

1. NORMAN guidance on suspect and non-target screening in environmental monitoring

Author

Hollender, Juliane, Schymanski, Emma L., Ahrens, Lutz, Alygizakis, Nikiforos, Béen, Frederic, Bijlsma, Lubertus, Brunner, Andrea M., Celma, Alberto, Fildier, Aurelie, Fu, Qiuguo, Gago-Ferrero, Pablo, Gil-Solsona, Ruben, Haglund, Peter, Hansen, Martin, Kaserzon, Sarit, Kruve, Anneli, Lamoree, Marja, Margoum, Christelle, Meijer, Jeroen, Merel, Sylvain, Rauert, Cassandra, Rostkowski, Pawel, Samanipour, Saer, Schulze, Bastian, Schulze, Tobias, Singh, Randolph R., Slobodnik, Jaroslav, Steininger-Mairinger, Teresa, Thomaidis, Nikolaos S., Togola, Anne, Vorkamp, Katrin, Vulliet, Emmanuelle, Zhu, Linyan, and Krauss, Martin

Published
2023
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3. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment

Author

Tkalec, Žiga, Antignac, Jean-Philippe, Bandow, Nicole, Béen, Frederic M., Belova, Lidia, Bessems, Jos, Le Bizec, Bruno, Brack, Werner, Cano-Sancho, German, Chaker, Jade, Covaci, Adrian, Creusot, Nicolas, David, Arthur, Debrauwer, Laurent, Dervilly, Gaud, Duca, Radu Corneliu, Fessard, Valérie, Grimalt, Joan O., Guerin, Thierry, Habchi, Baninia, Hecht, Helge, Hollender, Juliane, Jamin, Emilien L., Klánová, Jana, Kosjek, Tina, Krauss, Martin, Lamoree, Marja, Lavison-Bompard, Gwenaelle, Meijer, Jeroen, Moeller, Ruth, Mol, Hans, Mompelat, Sophie, Van Nieuwenhuyse, An, Oberacher, Herbert, Parinet, Julien, Van Poucke, Christof, Roškar, Robert, Togola, Anne, Trontelj, Jurij, and Price, Elliott J.

Published
2024
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5. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Published
2022
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6. Symbolic Reachability Analysis of B through ProB and LTSmin

Author

Bendisposto, Jens, Koerner, Philipp, Leuschel, Michael, Meijer, Jeroen, van de Pol, Jaco, Treharne, Helen, and Whitefield, Jorden

Subjects
Computer Science - Software Engineering
Abstract

We present a symbolic reachability analysis approach for B that can provide a significant speedup over traditional explicit state model checking. The symbolic analysis is implemented by linking ProB to LTSmin, a high-performance language independent model checker. The link is achieved via LTSmin's PINS interface, allowing ProB to benefit from LTSmin's analysis algorithms, while only writing a few hundred lines of glue-code, along with a bridge between ProB and C using ZeroMQ. ProB supports model checking of several formal specification languages such as B, Event-B, Z and TLA. Our experiments are based on a wide variety of B-Method and Event-B models to demonstrate the efficiency of the new link. Among the tested categories are state space generation and deadlock detection; but action detection and invariant checking are also feasible in principle. In many cases we observe speedups of several orders of magnitude. We also compare the results with other approaches for improving model checking, such as partial order reduction or symmetry reduction. We thus provide a new scalable, symbolic analysis algorithm for the B-Method and Event-B, along with a platform to integrate other model checking improvements via LTSmin in the future.

Published
2016

7. Bandwidth and Wavefront Reduction for Static Variable Ordering in Symbolic Model Checking

Author

Meijer, Jeroen and van de Pol, Jaco

Subjects
Computer Science - Software Engineering, Computer Science - Logic in Computer Science
Abstract

We demonstrate the applicability of bandwidth and wavefront reduction algorithms to static variable ordering. In symbolic model checking event locality plays a major role in time and memory usage. For example, in Petri nets event locality can be captured by dependency matrices, where nonzero entries indicate whether a transition modifies a place. The quality of event locality has been expressed as a metric called (weighted) event span. The bandwidth of a matrix is a metric indicating the distance of nonzero elements to the diagonal. Wavefront is a metric indicating the degree of nonzeros on one end of the diagonal of the matrix. Bandwidth and wavefront are well studied metrics used in sparse matrix solvers. In this work we prove that span is limited by twice the bandwidth of a matrix. This observation makes bandwidth reduction algorithms useful for obtaining good variable orders. One major issue we address is that the reduction algorithms can only be applied on symmetric matrices, while the dependency matrices are asymmetric. We show that the Sloan algorithm executed on the total graph of the adjacency graph gives the best variable orders. Practically, we demonstrate that our work allows to call standard sparse matrix operations in Boost and ViennaCL, computing very good static variable orders in milliseconds. Future work is promising, because a whole new spectrum of more off-the-shelf algorithms, including metaheuristic ones, become available for variable ordering., Comment: preprint

Published
2015

8. Dioxin(-like)-Related Biological Effects through Integrated Chemical-wide and Metabolome-wide Analyses

Author

IRAS OH Epidemiology Chemical Agents, IRAS – One Health Chemical, Zhao, Yujia, Meijer, Jeroen, Walker, Douglas I, Kim, Juni, Portengen, Lützen, Jones, Dean P, Saberi Hosnijeh, Fatemeh, Vlaanderen, Jelle, Vermeulen, Roel, IRAS OH Epidemiology Chemical Agents, IRAS – One Health Chemical, Zhao, Yujia, Meijer, Jeroen, Walker, Douglas I, Kim, Juni, Portengen, Lützen, Jones, Dean P, Saberi Hosnijeh, Fatemeh, Vlaanderen, Jelle, and Vermeulen, Roel

Published
2024

9. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment

Author

European Commission, 0000-0003-4518-3923, 0000-0001-5718-0733, 0000-0002-3680-4786, 0000-0003-0527-1136, 0000-0001-8189-1826, 0000-0001-9705-167X, 0000-0002-4660-274X, 0000-0002-8818-5307, 0000-0002-6421-0344, 0000-0002-0362-4244, 0000-0002-7373-7738, 0000-0002-4551-6823, 0000-0003-0087-6910, 0000-0002-3063-1853, 0000-0002-5393-1533, 0000-0002-2558-1425, Tkalec, Žiga, Antignac, Jean-Philippe, Bandow, Nicole, Béen, Frederic M., Belova, Lidia, Bessems, Jos, Le Bizec, Bruno, Brack, Werner, Cano-Sancho, German, Chaker, Jade, Covaci, Adrian, Creusot, Nicolas, David, Arthur, Debrauwer, Laurent, Dervilly, Gaud, Duca, Radu Corneliu, Fessard, Valérie, Grimalt, Joan O., Guerin, Thierry, Habchi, Baninia, Hecht, Helge, Hollender, Juliane, Jamin, Emilien L., Klánová, Jana, Kosjek, Tina, Krauss, Martin, Lamoree, Marja, Lavison-Bompard, Gwenaelle, Meijer, Jeroen, Moeller, Ruth, Mol, Hans, Mompelat, Sophie, Van Nieuwenhuyse, An, Oberacher, Herbert, Parinet, Julien, Van Poucke, Christof, Roškar, Robert, Togola, Anne, Trontelj, Jurij, Price, Elliott J., European Commission, 0000-0003-4518-3923, 0000-0001-5718-0733, 0000-0002-3680-4786, 0000-0003-0527-1136, 0000-0001-8189-1826, 0000-0001-9705-167X, 0000-0002-4660-274X, 0000-0002-8818-5307, 0000-0002-6421-0344, 0000-0002-0362-4244, 0000-0002-7373-7738, 0000-0002-4551-6823, 0000-0003-0087-6910, 0000-0002-3063-1853, 0000-0002-5393-1533, 0000-0002-2558-1425, Tkalec, Žiga, Antignac, Jean-Philippe, Bandow, Nicole, Béen, Frederic M., Belova, Lidia, Bessems, Jos, Le Bizec, Bruno, Brack, Werner, Cano-Sancho, German, Chaker, Jade, Covaci, Adrian, Creusot, Nicolas, David, Arthur, Debrauwer, Laurent, Dervilly, Gaud, Duca, Radu Corneliu, Fessard, Valérie, Grimalt, Joan O., Guerin, Thierry, Habchi, Baninia, Hecht, Helge, Hollender, Juliane, Jamin, Emilien L., Klánová, Jana, Kosjek, Tina, Krauss, Martin, Lamoree, Marja, Lavison-Bompard, Gwenaelle, Meijer, Jeroen, Moeller, Ruth, Mol, Hans, Mompelat, Sophie, Van Nieuwenhuyse, An, Oberacher, Herbert, Parinet, Julien, Van Poucke, Christof, Roškar, Robert, Togola, Anne, Trontelj, Jurij, and Price, Elliott J.

Abstract

The chemical burden on the environment and human population is increasing. Consequently, regulatory risk assessment must keep pace to manage, reduce, and prevent adverse impacts on human and environmental health associated with hazardous chemicals. Surveillance of chemicals of known, emerging, or potential future concern, entering the environment-food-human continuum is needed to document the reality of risks posed by chemicals on ecosystem and human health from a one health perspective, feed into early warning systems and support public policies for exposure mitigation provisions and safe and sustainable by design strategies. The use of less-conventional sampling strategies and integration of full-scan, high-resolution mass spectrometry and effect-directed analysis in environmental and human monitoring programmes have the potential to enhance the screening and identification of a wider range of chemicals of known, emerging or potential future concern. Here, we outline the key needs and recommendations identified within the European Partnership for Assessment of Risks from Chemicals (PARC) project for leveraging these innovative methodologies to support the development of next-generation chemical risk assessment.

Published
2024

10. Presentation of the 9th Edition of the Model Checking Contest

Author

Amparore, Elvio, Berthomieu, Bernard, Ciardo, Gianfranco, Dal Zilio, Silvano, Gallà, Francesco, Hillah, Lom Messan, Hulin-Hubard, Francis, Jensen, Peter Gjøl, Jezequel, Loïg, Kordon, Fabrice, Le Botlan, Didier, Liebke, Torsten, Meijer, Jeroen, Miner, Andrew, Paviot-Adet, Emmanuel, Srba, Jiří, Thierry-Mieg, Yann, van Dijk, Tom, Wolf, Karsten, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Beyer, Dirk, editor, Huisman, Marieke, editor, and Kordon, Fabrice, editor

Published
2019
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11. Multi-core On-The-Fly Saturation

Author

van Dijk, Tom, Meijer, Jeroen, van de Pol, Jaco, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Vojnar, Tomáš, editor, and Zhang, Lijun, editor

Published
2019
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12. Inter-laboratory mass spectrometry dataset based on passive sampling of drinking water for non-target analysis

Author

Schulze, Bastian, van Herwerden, Denice, Allan, Ian, Bijlsma, Lubertus, Etxebarria, Nestor, Hansen, Martin, Merel, Sylvain, Vrana, Branislav, Aalizadeh, Reza, Bajema, Bernard, Dubocq, Florian, Coppola, Gianluca, Fildier, Aurélie, Fialová, Pavla, Frøkjær, Emil, Grabic, Roman, Gago-Ferrero, Pablo, Gravert, Thorsten, Hollender, Juliane, Huynh, Nina, Jacobs, Griet, Jonkers, Tim, Kaserzon, Sarit, Lamoree, Marja, Le Roux, Julien, Mairinger, Teresa, Margoum, Christelle, Mascolo, Giuseppe, Mebold, Emmanuelle, Menger, Frank, Miège, Cécile, Meijer, Jeroen, Moilleron, Régis, Murgolo, Sapia, Peruzzo, Massimo, Pijnappels, Martijn, Reid, Malcolm, Roscioli, Claudio, Soulier, Coralie, Valsecchi, Sara, Thomaidis, Nikolaos, Vulliet, Emmanuelle, Young, Robert, and Samanipour, Saer

Published
2021
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17. Do cats mirror their owner?: Paired exposure assessment using silicone bands to measure residential PAH exposure

Author

IRAS OH Epidemiology Chemical Agents, IRAS OH Epidemiology Microbial Agents, Figueiredo, Daniel M, Lô, Serigne, Krop, Esmeralda, Meijer, Jeroen, Beeltje, Henry, Lamoree, Marja H, Vermeulen, Roel, IRAS OH Epidemiology Chemical Agents, IRAS OH Epidemiology Microbial Agents, Figueiredo, Daniel M, Lô, Serigne, Krop, Esmeralda, Meijer, Jeroen, Beeltje, Henry, Lamoree, Marja H, and Vermeulen, Roel

Published
2023

18. Towards evolutionary predictions : current promises and challenges

Author

Wortel, Meike T., Agashe, Deepa, Bailey, Susan F., Bank, Claudia, Bisschop, Karen, Blankers, Thomas, Cairns, Johannes, Colizzi, Enrico Sandro, Cusseddu, Davide, Desai, Michael M., van Dijk, Bram, Egas, Martijn, Ellers, Jacintha, Groot, Astrid T., Heckel, David G., Johnson, Marcelle L., Kraaijeveld, Ken, Krug, Joachim, Laan, Liedewij, Lässig, Michael, Lind, Peter A, Meijer, Jeroen, Noble, Luke M., Okasha, Samir, Rainey, Paul B., Rozen, Daniel E., Shitut, Shraddha, Tans, Sander J., Tenaillon, Olivier, Teotónio, Henrique, de Visser, J. Arjan G. M., Visser, Marcel E., Vroomans, Renske M. A., Werner, Gijsbert D. A., Wertheim, Bregje, Pennings, Pleuni S., Wortel, Meike T., Agashe, Deepa, Bailey, Susan F., Bank, Claudia, Bisschop, Karen, Blankers, Thomas, Cairns, Johannes, Colizzi, Enrico Sandro, Cusseddu, Davide, Desai, Michael M., van Dijk, Bram, Egas, Martijn, Ellers, Jacintha, Groot, Astrid T., Heckel, David G., Johnson, Marcelle L., Kraaijeveld, Ken, Krug, Joachim, Laan, Liedewij, Lässig, Michael, Lind, Peter A, Meijer, Jeroen, Noble, Luke M., Okasha, Samir, Rainey, Paul B., Rozen, Daniel E., Shitut, Shraddha, Tans, Sander J., Tenaillon, Olivier, Teotónio, Henrique, de Visser, J. Arjan G. M., Visser, Marcel E., Vroomans, Renske M. A., Werner, Gijsbert D. A., Wertheim, Bregje, and Pennings, Pleuni S.

Abstract

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.

Published
2023
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19. Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

Author

Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Sub Bioinformatics, van Dijk, Bram, Buffard, Pauline, Farr, Andrew D, Giersdorf, Franz, Meijer, Jeroen, Dutilh, Bas E, Rainey, Paul B, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Sub Bioinformatics, van Dijk, Bram, Buffard, Pauline, Farr, Andrew D, Giersdorf, Franz, Meijer, Jeroen, Dutilh, Bas E, and Rainey, Paul B

Published
2023

20. NORMAN guidance on suspect and non-target screening in environmental monitoring

Author

0000-0002-4660-274X, 0000-0001-6868-8145, 0000-0002-5430-6764, 0000-0002-5727-4999, 0000-0001-5910-3248, 0000-0001-7005-8775, 0000-0002-2801-1751, 0000-0001-9763-8737, 0000-0002-3805-4122, 0000-0002-4227-5948, 0000-0002-5987-0399, 0000-0002-4269-1036, 0000-0003-2293-7913, 0000-0002-4663-8742, 0000-0002-6744-1279, 0000-0001-9725-3351, 0000-0002-7373-7738, 0000-0002-7386-4454, 0000-0002-4551-6823, 0000-0002-9587-2981, 0000-0002-2543-9023, 0000-0001-9778-4283, 0000-0001-8270-6979, 0000-0003-4641-8659, 0000-0002-9744-8914, 0000-0003-4500-3400, 0000-0003-2622-6318, 0000-0001-7809-1529, 0000-0002-4624-4735, 0000-0002-5393-1533, 0000-0002-1131-5687, 0000-0002-6325-1531, 0000-0003-2036-1447, 0000-0002-0362-4244, Hollender, Juliane, Schymanski, Emma L., Ahrens, Lutz, Alygizakis, Nikiforos, Béen, Frederic, Bijlsma, Lubertus, Brunner, Andrea M., Celma, Alberto, Fildier, Aurelie, Fu, Qiuguo, Gago-Ferrero, Pablo, Gil-Solsona, Rubén, Haglund, Peter, Hansen, Martin, Kaserzon, Sarit, Kruve, Anneli, Lamoree, Marja, Margoum, Christelle, Meijer, Jeroen, Merel, Sylvain, Rauert, Cassandra, Rostkowski, Pawel, Samanipour, Saer, Schulze, Bastian, Schulze, Tobias, Singh, Randolph R., Slobodnik, Jaroslav, Steininger-Mairinger, Teresa, Thomaidis, Nikolaos S., Togola, Anne, Vorkamp, Katrin, Vulliet, Emmanuelle, Zhu, Linyan, Krauss, Martin, 0000-0002-4660-274X, 0000-0001-6868-8145, 0000-0002-5430-6764, 0000-0002-5727-4999, 0000-0001-5910-3248, 0000-0001-7005-8775, 0000-0002-2801-1751, 0000-0001-9763-8737, 0000-0002-3805-4122, 0000-0002-4227-5948, 0000-0002-5987-0399, 0000-0002-4269-1036, 0000-0003-2293-7913, 0000-0002-4663-8742, 0000-0002-6744-1279, 0000-0001-9725-3351, 0000-0002-7373-7738, 0000-0002-7386-4454, 0000-0002-4551-6823, 0000-0002-9587-2981, 0000-0002-2543-9023, 0000-0001-9778-4283, 0000-0001-8270-6979, 0000-0003-4641-8659, 0000-0002-9744-8914, 0000-0003-4500-3400, 0000-0003-2622-6318, 0000-0001-7809-1529, 0000-0002-4624-4735, 0000-0002-5393-1533, 0000-0002-1131-5687, 0000-0002-6325-1531, 0000-0003-2036-1447, 0000-0002-0362-4244, Hollender, Juliane, Schymanski, Emma L., Ahrens, Lutz, Alygizakis, Nikiforos, Béen, Frederic, Bijlsma, Lubertus, Brunner, Andrea M., Celma, Alberto, Fildier, Aurelie, Fu, Qiuguo, Gago-Ferrero, Pablo, Gil-Solsona, Rubén, Haglund, Peter, Hansen, Martin, Kaserzon, Sarit, Kruve, Anneli, Lamoree, Marja, Margoum, Christelle, Meijer, Jeroen, Merel, Sylvain, Rauert, Cassandra, Rostkowski, Pawel, Samanipour, Saer, Schulze, Bastian, Schulze, Tobias, Singh, Randolph R., Slobodnik, Jaroslav, Steininger-Mairinger, Teresa, Thomaidis, Nikolaos S., Togola, Anne, Vorkamp, Katrin, Vulliet, Emmanuelle, Zhu, Linyan, and Krauss, Martin

Abstract

Increasing production and use of chemicals and awareness of their impact on ecosystems and humans has led to large interest for broadening the knowledge on the chemical status of the environment and human health by suspect and non-target screening (NTS). To facilitate effective implementation of NTS in scientific, commercial and governmental laboratories, as well as acceptance by managers, regulators and risk assessors, more harmonisation in NTS is required. To address this, NORMAN Association members involved in NTS activities have prepared this guidance document, based on the current state of knowledge. The document is intended to provide guidance on performing high quality NTS studies and data interpretation while increasing awareness of the promise but also pitfalls and challenges associated with these techniques. Guidance is provided for all steps; from sampling and sample preparation to analysis by chromatography (liquid and gas—LC and GC) coupled via various ionisation techniques to high-resolution tandem mass spectrometry (HRMS/MS), through to data evaluation and reporting in the context of NTS. Although most experience within the NORMAN network still involves water analysis of polar compounds using LC–HRMS/MS, other matrices (sediment, soil, biota, dust, air) and instrumentation (GC, ion mobility) are covered, reflecting the rapid development and extension of the field. Due to the ongoing developments, the different questions addressed with NTS and manifold techniques in use, NORMAN members feel that no standard operation process can be provided at this stage. However, appropriate analytical methods, data processing techniques and databases commonly compiled in NTS workflows are introduced, their limitations are discussed and recommendations for different cases are provided. Proper quality assurance, quantification without reference standards and reporting results with clear confidence of identification assignment complete the guidance together with a gloss

Published
2023

21. Towards evolutionary predictions: Current promises and challenges

Author

Wortel, Meike T., primary, Agashe, Deepa, additional, Bailey, Susan F., additional, Bank, Claudia, additional, Bisschop, Karen, additional, Blankers, Thomas, additional, Cairns, Johannes, additional, Colizzi, Enrico Sandro, additional, Cusseddu, Davide, additional, Desai, Michael M., additional, van Dijk, Bram, additional, Egas, Martijn, additional, Ellers, Jacintha, additional, Groot, Astrid T., additional, Heckel, David G., additional, Johnson, Marcelle L., additional, Kraaijeveld, Ken, additional, Krug, Joachim, additional, Laan, Liedewij, additional, Lässig, Michael, additional, Lind, Peter A., additional, Meijer, Jeroen, additional, Noble, Luke M., additional, Okasha, Samir, additional, Rainey, Paul B., additional, Rozen, Daniel E., additional, Shitut, Shraddha, additional, Tans, Sander J., additional, Tenaillon, Olivier, additional, Teotónio, Henrique, additional, de Visser, J. Arjan G. M., additional, Visser, Marcel E., additional, Vroomans, Renske M. A., additional, Werner, Gijsbert D. A., additional, Wertheim, Bregje, additional, and Pennings, Pleuni S., additional

Published
2022
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22. High-Performance Data Processing Workflow Incorporating Effect-Directed Analysis for Feature Prioritization in Suspect and Nontarget Screening

Author

Jonkers, Tim J H, Meijer, Jeroen, Vlaanderen, Jelle J, Vermeulen, Roel C H, Houtman, Corine J, Hamers, Timo, Lamoree, Marja H, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, E&H: Environmental Chemistry and Toxicology, AIMMS, E&H: Environmental Health and Toxicology, IRAS OH Epidemiology Chemical Agents, and dIRAS RA-2

Subjects
Chemistry(all), TTR-binding, General Chemistry, effect-directed analysis, Gas Chromatography-Mass Spectrometry, Mass Spectrometry, Article, Workflow, bioassay, antibiotic, Toxicity Tests, Humans, Environmental Chemistry, Biological Assay, suspect and nontarget screening, environment
Abstract

Effect-directed analysis (EDA) aims at the detection of bioactive chemicals of emerging concern (CECs) by combining toxicity testing and high-resolution mass spectrometry (HRMS). However, consolidation of toxicological and chemical analysis techniques to identify bioactive CECs remains challenging and laborious. In this study, we incorporate state-of-the-art identification approaches in EDA and propose a robust workflow for the high-throughput screening of CECs in environmental and human samples. Three different sample types were extracted and chemically analyzed using a single high-performance liquid chromatography HRMS method. Chemical features were annotated by suspect screening with several reference databases. Annotation quality was assessed using an automated scoring system. In parallel, the extracts were fractionated into 80 micro-fractions each covering a couple of seconds from the chromatogram run and tested for bioactivity in two bioassays. The EDA workflow prioritized and identified chemical features related to bioactive fractions with varying levels of confidence. Confidence levels were improved with the in silico software tools MetFrag and the retention time indices platform. The toxicological and chemical data quality was comparable between the use of single and multiple technical replicates. The proposed workflow incorporating EDA for feature prioritization in suspect and nontarget screening paves the way for the routine identification of CECs in a high-throughput manner., A comprehensive workflow was developed that incorporates effect-directed analysis in suspect and nontarget screening for feature prioritization, allowing for the high-throughput identification of bioactive chemicals of emerging concern.

Published
2022

23. High-Performance Data Processing Workflow Incorporating Effect-Directed Analysis for Feature Prioritization in Suspect and Nontarget Screening

Author

IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Jonkers, Tim J H, Meijer, Jeroen, Vlaanderen, Jelle J, Vermeulen, Roel C H, Houtman, Corine J, Hamers, Timo, Lamoree, Marja H, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, Jonkers, Tim J H, Meijer, Jeroen, Vlaanderen, Jelle J, Vermeulen, Roel C H, Houtman, Corine J, Hamers, Timo, and Lamoree, Marja H

Published
2022

24. The NORMAN Suspect List Exchange (NORMAN-SLE) : facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Taha, Hiba Mohammed, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Feunang, Yannick Djoumbou, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Taha, Hiba Mohammed, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Feunang, Yannick Djoumbou, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Abstract

Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov

Published
2022
Full Text
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25. The NORMAN Suspect List Exchange (NORMAN-SLE): Facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

IRAS OH Epidemiology Chemical Agents, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H, Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E, Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A, Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J, Hale, Sarah E, Hernandez, Felix, Janssen, Elisabeth M-L, Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H, Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M, Martin, Jonathan W, McEachran, Andrew D, McLean, John A, Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A, Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M, Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A, Sims, Kerry, Singer, Heinz, Singh, Randolph R, Sumarah, Mark, Thiessen, Paul A, Thomas, Kevin V, Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P, Vermeulen, Roel C H, Vlaanderen, Jelle J, von der Ohe, Peter C, Wang, Zhanyun, Williams, Antony J, Willighagen, Egon L, Wishart, David S, Zhang, Jian, Thomaidis, Nikolaos S, Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L, IRAS OH Epidemiology Chemical Agents, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H, Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E, Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A, Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J, Hale, Sarah E, Hernandez, Felix, Janssen, Elisabeth M-L, Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H, Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M, Martin, Jonathan W, McEachran, Andrew D, McLean, John A, Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A, Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M, Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A, Sims, Kerry, Singer, Heinz, Singh, Randolph R, Sumarah, Mark, Thiessen, Paul A, Thomas, Kevin V, Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P, Vermeulen, Roel C H, Vlaanderen, Jelle J, von der Ohe, Peter C, Wang, Zhanyun, Williams, Antony J, Willighagen, Egon L, Wishart, David S, Zhang, Jian, Thomaidis, Nikolaos S, Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L

Published
2022

26. The NORMAN Suspect List Exchange (NORMAN-SLE):facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C.H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C.H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Abstract

Background: The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results: The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.

Published
2022

27. Towards evolutionary predictions: Current promises and challenges

Author

Wortel, Meike T. (author), Agashe, Deepa (author), Bailey, Susan F. (author), Bank, Claudia (author), Bisschop, Karen (author), Blankers, Thomas (author), Laan, L. (author), Meijer, Jeroen (author), Tans, S.J. (author), Wortel, Meike T. (author), Agashe, Deepa (author), Bailey, Susan F. (author), Bank, Claudia (author), Bisschop, Karen (author), Blankers, Thomas (author), Laan, L. (author), Meijer, Jeroen (author), and Tans, S.J. (author)

Abstract

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions., BN/Bionanoscience, BN/Liedewij Laan Lab

Published
2022
Full Text
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28. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Ministerio de Ciencia e Innovación (España), European Commission, 0000-0001-7820-4335, 0000-0001-9167-9060, 0000-0002-5727-4999, 0000-0001-9512-9314, 0000-0002-0747-8838, 0000-0003-2724-9183, 0000-0002-8351-9435, 0000-0001-7147-384X, 0000-0001-7005-8775, 0000-0002-5959-6190, 0000-0001-9269-6524, 0000-0001-9763-8737, 0000-0001-5143-0543, 0000-0002-4486-3356, 0000-0002-9932-8609, 0000-0001-9351-6855, 0000-0002-9734-324X, 0000-0001-7850-184X, 0000-0002-9436-9954, 0000-0002-5987-0399, 0000-0003-1112-6867, 0000-0002-0749-3982, 0000-0002-1740-9422, 0000-0003-1997-2750, 0000-0002-3778-4721, 0000-0003-2293-7913, 0000-0002-8295-9738, 0000-0002-7743-9199, 0000-0003-1268-3083, 0000-0002-5475-6730, 0000-0002-6415-6173, 0000-0002-6917-3431, 0000-0002-1043-3278, 0000-0002-0362-4244, 0000-0001-6986-5545, 0000-0002-7373-7738, 0000-0003-1008-8790, 0000-0002-6453-236X, 0000-0001-7893-9876, 0000-0002-4439-9194, 0000-0001-6265-4294, 0000-0003-1423-330X, 0000-0001-8918-6419, 0000-0003-3126-5186, 0000-0002-4551-6823, 0000-0002-1808-8835, 0000-0002-8793-5516, 0000-0002-6942-0594, 0000-0001-6672-8414, 0000-0002-2558-4431, 0000-0002-8501-7789, 0000-0003-2396-2993, 0000-0002-0963-8268, 0000-0001-9336-9656, 0000-0003-3088-9771, 0000-0002-1948-9243, 0000-0002-7344-7044, 0000-0002-9251-0790, 0000-0003-1606-0764, 0000-0001-6974-0224, 0000-0001-9778-4283, 0000-0002-4175-4787, 0000-0001-8604-1732, 0000-0001-8270-6979, 0000-0002-0809-7826, 0000-0002-1553-3868, 0000-0002-9744-8914, 0000-0002-1356-285X, 0000-0001-6273-4083, 0000-0002-8542-3699, 0000-0003-4500-3400, 0000-0003-0977-1656, 0000-0002-1992-2086, 0000-0002-2155-100X, 0000-0001-8881-0793, 0000-0001-6067-8321, 0000-0002-6875-957X, 0000-0003-4082-8163, 0000-0001-7350-8962, 0000-0001-9914-7659, 0000-0002-2668-4821, 0000-0001-7542-0286, 0000-0002-3207-2434, 0000-0002-6192-4632, 0000-0002-4624-4735, 0000-0002-4660-274X, 0000-0003-2622-6318, 0000-0001-6868-8145, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramírez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, Schymanski, Emma L., Ministerio de Ciencia e Innovación (España), European Commission, 0000-0001-7820-4335, 0000-0001-9167-9060, 0000-0002-5727-4999, 0000-0001-9512-9314, 0000-0002-0747-8838, 0000-0003-2724-9183, 0000-0002-8351-9435, 0000-0001-7147-384X, 0000-0001-7005-8775, 0000-0002-5959-6190, 0000-0001-9269-6524, 0000-0001-9763-8737, 0000-0001-5143-0543, 0000-0002-4486-3356, 0000-0002-9932-8609, 0000-0001-9351-6855, 0000-0002-9734-324X, 0000-0001-7850-184X, 0000-0002-9436-9954, 0000-0002-5987-0399, 0000-0003-1112-6867, 0000-0002-0749-3982, 0000-0002-1740-9422, 0000-0003-1997-2750, 0000-0002-3778-4721, 0000-0003-2293-7913, 0000-0002-8295-9738, 0000-0002-7743-9199, 0000-0003-1268-3083, 0000-0002-5475-6730, 0000-0002-6415-6173, 0000-0002-6917-3431, 0000-0002-1043-3278, 0000-0002-0362-4244, 0000-0001-6986-5545, 0000-0002-7373-7738, 0000-0003-1008-8790, 0000-0002-6453-236X, 0000-0001-7893-9876, 0000-0002-4439-9194, 0000-0001-6265-4294, 0000-0003-1423-330X, 0000-0001-8918-6419, 0000-0003-3126-5186, 0000-0002-4551-6823, 0000-0002-1808-8835, 0000-0002-8793-5516, 0000-0002-6942-0594, 0000-0001-6672-8414, 0000-0002-2558-4431, 0000-0002-8501-7789, 0000-0003-2396-2993, 0000-0002-0963-8268, 0000-0001-9336-9656, 0000-0003-3088-9771, 0000-0002-1948-9243, 0000-0002-7344-7044, 0000-0002-9251-0790, 0000-0003-1606-0764, 0000-0001-6974-0224, 0000-0001-9778-4283, 0000-0002-4175-4787, 0000-0001-8604-1732, 0000-0001-8270-6979, 0000-0002-0809-7826, 0000-0002-1553-3868, 0000-0002-9744-8914, 0000-0002-1356-285X, 0000-0001-6273-4083, 0000-0002-8542-3699, 0000-0003-4500-3400, 0000-0003-0977-1656, 0000-0002-1992-2086, 0000-0002-2155-100X, 0000-0001-8881-0793, 0000-0001-6067-8321, 0000-0002-6875-957X, 0000-0003-4082-8163, 0000-0001-7350-8962, 0000-0001-9914-7659, 0000-0002-2668-4821, 0000-0001-7542-0286, 0000-0002-3207-2434, 0000-0002-6192-4632, 0000-0002-4624-4735, 0000-0002-4660-274X, 0000-0003-2622-6318, 0000-0001-6868-8145, Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D'Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O'Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramírez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Abstract

The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for "suspect screening" lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide.

Published
2022

29. Additional file 2 of The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Author

Mohammed Taha, Hiba, Aalizadeh, Reza, Alygizakis, Nikiforos, Antignac, Jean-Philippe, Arp, Hans Peter H., Bade, Richard, Baker, Nancy, Belova, Lidia, Bijlsma, Lubertus, Bolton, Evan E., Brack, Werner, Celma, Alberto, Chen, Wen-Ling, Cheng, Tiejun, Chirsir, Parviel, Čirka, Ľuboš, D’Agostino, Lisa A., Djoumbou Feunang, Yannick, Dulio, Valeria, Fischer, Stellan, Gago-Ferrero, Pablo, Galani, Aikaterini, Geueke, Birgit, Głowacka, Natalia, Glüge, Juliane, Groh, Ksenia, Grosse, Sylvia, Haglund, Peter, Hakkinen, Pertti J., Hale, Sarah E., Hernandez, Felix, Janssen, Elisabeth M.-L., Jonkers, Tim, Kiefer, Karin, Kirchner, Michal, Koschorreck, Jan, Krauss, Martin, Krier, Jessy, Lamoree, Marja H., Letzel, Marion, Letzel, Thomas, Li, Qingliang, Little, James, Liu, Yanna, Lunderberg, David M., Martin, Jonathan W., McEachran, Andrew D., McLean, John A., Meier, Christiane, Meijer, Jeroen, Menger, Frank, Merino, Carla, Muncke, Jane, Muschket, Matthias, Neumann, Michael, Neveu, Vanessa, Ng, Kelsey, Oberacher, Herbert, O’Brien, Jake, Oswald, Peter, Oswaldova, Martina, Picache, Jaqueline A., Postigo, Cristina, Ramirez, Noelia, Reemtsma, Thorsten, Renaud, Justin, Rostkowski, Pawel, Rüdel, Heinz, Salek, Reza M., Samanipour, Saer, Scheringer, Martin, Schliebner, Ivo, Schulz, Wolfgang, Schulze, Tobias, Sengl, Manfred, Shoemaker, Benjamin A., Sims, Kerry, Singer, Heinz, Singh, Randolph R., Sumarah, Mark, Thiessen, Paul A., Thomas, Kevin V., Torres, Sonia, Trier, Xenia, van Wezel, Annemarie P., Vermeulen, Roel C. H., Vlaanderen, Jelle J., von der Ohe, Peter C., Wang, Zhanyun, Williams, Antony J., Willighagen, Egon L., Wishart, David S., Zhang, Jian, Thomaidis, Nikolaos S., Hollender, Juliane, Slobodnik, Jaroslav, and Schymanski, Emma L.

Subjects
Pharmacology, Ecology, 39999 Chemical Sciences not elsewhere classified, FOS: Chemical sciences, FOS: Biological sciences, Computational Biology, Marine Biology, Biochemistry, Molecular Biology, Biotechnology, Cancer
Abstract

Additional file 2: Overview of the NORMAN-SLE website (DOCX format) as of 30 May 2022 [82].

Published
2022
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30. Towards evolutionary predictions: Current promises and challenges

Author

Wortel, Meike T., Agashe, Deepa, Bailey, Susan F., Bank, Claudia, Bisschop, Karen, Blankers, Thomas, Laan, L., Meijer, Jeroen, and Tans, S.J.

Subjects
models, predictability, evolution, population genetics, prediction, evolutionary control, disease modelling
Abstract

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.

Published
2022

31. An annotation database for chemicals of emerging concern in exposome research

Author

Meijer, Jeroen, primary, Lamoree, Marja, additional, Hamers, Timo, additional, Antignac, Jean-Philippe, additional, Hutinet, Sébastien, additional, Debrauwer, Laurent, additional, Covaci, Adrian, additional, Huber, Carolin, additional, Krauss, Martin, additional, Walker, Douglas I., additional, Schymanski, Emma L., additional, Vermeulen, Roel, additional, and Vlaanderen, Jelle, additional

Published
2021
Full Text
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32. An annotation database for chemicals of emerging concern in exposome research

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Environmental Cheminformatics (Schymanski Group) [research center], Fonds National de la Recherche - FnR [sponsor], Meijer, Jeroen, Lamoree, Marja, Hamers, Timo, Antignac, Jean-Philippe, Hutinet, Sébastien, Debrauwer, Laurent, Covaci, Adrian, Huber, Carolin, Krauss, Martin, Walker, Douglas I., Schymanski, Emma, Vermeulen, Roel, Vlaanderen, Jelle, Luxembourg Centre for Systems Biomedicine (LCSB): Environmental Cheminformatics (Schymanski Group) [research center], Fonds National de la Recherche - FnR [sponsor], Meijer, Jeroen, Lamoree, Marja, Hamers, Timo, Antignac, Jean-Philippe, Hutinet, Sébastien, Debrauwer, Laurent, Covaci, Adrian, Huber, Carolin, Krauss, Martin, Walker, Douglas I., Schymanski, Emma, Vermeulen, Roel, and Vlaanderen, Jelle

Published
2021

34. Sound Black-Box Checking in the LearnLib

Author

Meijer, Jeroen, van de Pol, Jaco, Dutle, Aaron, Muñoz, César A., and Narkawicz, Anthony

Subjects
Model checking, Finite-state machine, Theoretical computer science, Computer Applications, Computer science, 0202 electrical engineering, electronic engineering, information engineering, Büchi automaton, 020207 software engineering, 020201 artificial intelligence & image processing, 02 engineering and technology, Equivalence (formal languages), Automaton, Counterexample
Abstract

In Black-Box Checking (BBC) incremental hypotheses of a system are learned in the form of finite automata. On these automata LTL formulae are verified, or their counterexamples validated on the actual system. We extend the LearnLib’s system-under-learning API for sound BBC, by means of state equivalence, that contrasts the original proposal where an upper-bound on the number of states in the system is assumed. We will show how LearnLib’s new BBC algorithms can be used in practice, as well as how one could experiment with different model checkers and BBC algorithms. Using the RERS 2017 challenge we provide experimental results on the performance of all LearnLib’s active learning algorithms when applied in a BBC setting. The performance of learning algorithms was unknown for this setting. We will show that the novel incremental algorithms TTT, and ADT perform the best.

Published
2018

35. Suspect and non-targeted screening of chemicals of emerging concern for human biomonitoring, environmental health studies and support to risk assessment: From promises to challenges and harmonisation issues

Author

Pourchet, Mariane, primary, Debrauwer, Laurent, additional, Klanova, Jana, additional, Price, Elliott J., additional, Covaci, Adrian, additional, Caballero-Casero, Noelia, additional, Oberacher, Herbert, additional, Lamoree, Marja, additional, Damont, Annelaure, additional, Fenaille, François, additional, Vlaanderen, Jelle, additional, Meijer, Jeroen, additional, Krauss, Martin, additional, Sarigiannis, Denis, additional, Barouki, Robert, additional, Le Bizec, Bruno, additional, and Antignac, Jean-Philippe, additional

Published
2020
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38. MCC'2017 - The Seventh Model Checking Contest

Author

Kordon, Fabrice, Garavel, Hubert, Hillah, Lom-Messan, Paviot-Adet, Emmanuel, Jezequel, Loïg, Hulin-Hubard, Francis, Amparore, Elvio Gilberto, Beccuti, Marco, Berthomieu, Bernard, Evrard, Hugues, Jensen, Peter Gjøl, Botlan, Didier Le, Liebke, Torsten, Meijer, Jeroen, Srba, Jirí, Thierry-Mieg, Yann, Pol, Jaco van de, Wolf, Karsten, Koutny, Maciej, Kristensen, Lars Michael, Penczek, Wojciech, Koutny, Maciej, Kristensen, Lars Michael, Penczek, Wojciech, Modélisation et Vérification (MoVe), LIP6, Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Construction of verified concurrent systems (CONVECS), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Grenoble (LIG), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Universität des Saarlandes [Saarbrücken], Université Paris Nanterre (UPN), Université Paris Descartes - Paris 5 (UPD5), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Modeling and Exploitation of Interaction and Concurrency (MEXICO), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Spécification et Vérification [Cachan] (LSV), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Torino (UNITO), Équipe Verification de Systèmes Temporisés Critiques (LAAS-VERTICS), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), Imperial College London, Department of Computer Science [Aalborg], Aalborg University [Denmark] (AAU), Institut für Informatik [Rostock], Universität Rostock, University of Twente [Netherlands], Faculty of Informatics [Brno], Masaryk University, Construction of verified concurrent systems (CONVECS ), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Grenoble (LIG ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Spécification et Vérification [Cachan] (LSV), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Faculty of Informatics [Brno] (FI / MUNI), Masaryk University [Brno] (MUNI), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Università degli studi di Torino = University of Turin (UNITO), Université Toulouse 1 Capitole (UT1), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), and University of Twente

Subjects
Model checking, Model Checking Contest, business.industry, Computer science, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], 020207 software engineering, 02 engineering and technology, Petri net, CONTEST, Competition (economics), Software, 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, Joint (building), [INFO]Computer Science [cs], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Petri Nets, Software engineering, business, LTSmin
Abstract

International audience; Created in 2011, the Model Checking Contest (MCC) is an annual competition dedicated to provide a fair evaluation of software tools that verify concurrent systems using state-space exploration techniques and model checking. This article presents the principles and results of the 2017 edition of the MCC, which took place along with the Petri Net and ACSD joint conferences in Zaragoza, Spain.

Published
2018

40. Bandwidth and Wavefront Reduction for Static Variable Ordering in Symbolic Reachability Analysis

Author

Meijer, Jeroen, van de Pol, Jan Cornelis, Rayadurgam, Sanjai, and Tkachuk, Oksana

Subjects
IR-100721, 02 engineering and technology, Design structure matrix, Sparse matrix, Reduction (complexity), Dependency graph, Bandwidth, Reachability, Wavefront, 0202 electrical engineering, electronic engineering, information engineering, Bandwidth (computing), Symmetric matrix, EWI-27067, METIS-318457, Mathematics, Event locality, 020207 software engineering, Petri net, Decision diagram, Event span, 020201 artificial intelligence & image processing, Profile, Algorithm, Symbolic reachability
Abstract

We investigate the use of bandwidth and wavefront reduction algorithms to determine a static BDD variable ordering. The aim is to reduce the size of BDDs arising in symbolic reachability. Previous work showed that minimizing the (weighted) event span of the variable dependency graph yields small BDDs. The bandwidth and wavefront of symmetric matrices are well studied metrics, used in sparse matrix solvers, and many bandwidth and wavefront reduction algorithms are readily available in libraries like Boost and ViennaCL. In this paper, we transform the dependency matrix to a symmetric matrix and apply various bandwidth and wavefront reduction algorithms, measuring their influence on the (weighted) event span. We show that Sloan’s algorithm, executed on the total graph of the dependency matrix, yields a variable order with minimal event span. We demonstrate this on a large benchmark of Petri nets, Dve, Promela, B, and mcrl2 models. As a result, good static variable orders can now be determined in milliseconds by using standard sparse matrix solvers.

Published
2016

41. Adaptive Learning for Learn-Based Regression Testing

Author

Huistra, David, Meijer, Jeroen, Pol, Jaco van de, Howar, Falk, and Barnat, Jiri

Subjects
Model checking, Computer science, business.industry, 020207 software engineering, 02 engineering and technology, Machine learning, computer.software_genre, Software, Regression testing, 0202 electrical engineering, electronic engineering, information engineering, System property, System level, 020201 artificial intelligence & image processing, Adaptive learning, Artificial intelligence, business, computer
Abstract

Regression testing is an important activity to prevent the introduction of regressions into software updates. Learn-based testing can be used to automatically check new versions of a system for regressions on a system level. This is done by learning a model of the system and model checking this model for system property violations. Learning the model of a large system can take an unpractical amount of time however. In this work we investigate if the concept of adaptive learning can improve the learning speed of a model in a regression testing scenario. We have performed several experiments with this technique on two systems: ToDoMVC and SSH. We find that there can be a large benefit to using adaptive learning. In addition we find three main factors that influence the benefit of adaptive learning. There are however also some shortcomings to adaptive learning that should be investigated further.

Published
2018

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