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1. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Rehm, Heidi L., Page, Angela J.H., Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J.S., Beck, Tim, Beckmann, Jacques S., Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K., Boughtwood, Tiffany F., Bourque, Guillaume, Bowers, Sarion R., Brookes, Anthony J., Brudno, Michael, Brush, Matthew H., Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, L. Jonathan, Dyke, Stephanie O.M., Eddy, James A., Eilbeck, Karen, Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M., Ho, Calvin W.L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jené, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J.M., Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M., Kekesi-Lafrance, Kristina, Kelleher, Jerome, Kerry, Giselle, Khor, Seik-Soon, Knoppers, Bartha M., Konopko, Melissa A., Kosaki, Kenjiro, Kuba, Martin, Lawson, Jonathan, Leinonen, Rasko, Li, Stephanie, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Liyanage, Isuru Udara, Lopez, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Metke-Jimenez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Munoz-Torres, Monica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura A.D., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Rodriguez, Laura Lyman, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos, Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Guimera, Roman Valls, Vamathevan, Jessica, Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, North, Kathryn, and Birney, Ewan

Published
2021
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2. GA4GH Passport standard for digital identity and access permissions

Author

Voisin, Craig, Linden, Mikael, Dyke, Stephanie O.M., Bowers, Sarion R., Alper, Pinar, Barkley, Maxmillian P., Bernick, David, Chao, Jianpeng, Courtot, Mélanie, Jeanson, Francis, Konopko, Melissa A., Kuba, Martin, Lawson, Jonathan, Leinonen, Jaakko, Li, Stephanie, Ota Wang, Vivian, Philippakis, Anthony A., Reinold, Kathy, Rushton, Gregory A., Spalding, J. Dylan, Törnroos, Juha, Tulchinsky, Ilya, Guidry Auvil, Jaime M., and Nyrönen, Tommi H.

Published
2021
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8. Grid Infrastructure Monitoring as Reliable Information Service

Author

Holub, Petr, Kuba, Martin, Matyska, Luděk, Ruda, Miroslav, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, and Dikaiakos, Marios D., editor

Published
2004
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10. EOSC-Life Access and User Management System for Life Science – the blueprint update

Author

Linden, Mikael, Bucik, Dominik Frantisek, Gormanns, Philipp, Haley, Natalie, Heikkinen, Jani, Holub, Petr, Kankaanpää, Pasi, Kouril, Daniel, Kuba, Martin, Licehammer, Slavek, Matyska, Ludek, Nyrönen, Tommi, Prochazka, Michal, Reihs, Robert, Romano, Paolo, Sanderson, Fiona, Shigaval, Athresh, Smith, Callum, and Tedds, Jonathan

Subjects
access management, identity management, Life science AAI, authentication and authorisation service
Abstract

This deliverable is the updated blueprint of the Life Science AAI (LS AAI), a common authentication and authorisation service for the European life science research infrastructures. The Life Science AAI provides a way to coordinate how user identity and access is managed in research services in the (community-specific) federated Infrastructure. The Life Science AAI was launched on 11 April 2022 and the users of ELIXIR AAI were migrated to it. The Life Science AAI service is managed by the life sciences community and operated by the e- infrastructures, including GEANT and EGI. This deliverable is the second update to deliverable D5.1 “Access and User Management System for Life Science – the blueprint” [LIND19] that laid the ground for the production deployment with e- infrastructures. D5.1 was updated for the first time in March 2021 by deliverable D5.3 “Access and User Management System for Life Science – the blueprint update”. In this deliverable and its appendices, only those sections of D5.3 are updated where the requirements have changed or become clearer, while the rest of the document remains unchanged. This deliverable can be read as an independent document, without reading D5.1 or D5.3 first. This deliverable and its appendices first introduce the technical and non-technical requirements for the AAI service, including the components operated by the e-infrastructures, and further clarify how that relates to and integrates with the AAI service components operated by the life sciences research infrastructures. Relevant external work, including the EOSC AAI, is then introduced. Finally, the the deliverable provides an overview of Life Science AAI’s potential relying services within the EOSC-Life project and beyond.

Published
2022
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11. Evidence for direct and indirect benefits of female promiscuity in vertebrates

Author

Kuba, Martin, Albrecht, Tomáš, and Šulc, Michal

Subjects
unfaithful females, extra-pair paternity, infanticide, adaptive explanations, non-adaptive explanations, multi male mating, good genes, genetic complementarity, kin selection, sexual ornamentation
Abstract

Female promiscuous behaviour has been observed in many vertebrate groups but its evolution and potential benefits to promiscuous females remain unclear. To explain female promiscuous behaviour, both adaptive and non-adaptive hypotheses have been proposed. According to adaptive hypotheses, females are promiscuous, because they gain benefits through multiple male copulations. These can further be divided into direct benefits hypotheses, where females are assumed to benefit directly from promiscuity by gaining more resources to themselves and improving their own survival, and indirect (genetic) benefits hypotheses where fitness gains to promiscuous females are through improved quality of their offspring. In contrast, according to non-adaptive hypotheses, females do not gain any benefits from promiscuous behaviour and female promiscuous behaviour is a result of male offensive strategies to gain paternity. Adaptive hypotheses, especially those concerning genetic benefits, are highly debated and existing studies often differ in their conclusions. The aim of this thesis is to provide a review of studies evaluating adaptive and non-adaptive hypotheses to explain female promiscuous behaviour in vertebrates. Key words: Promiscuity, sexual conflict, sperm competition, good genes, genetic complementarity,...

Published
2022

12. CINECA Report on GA4GH Researcher ID D2.2

Author

Linden, Mikael, Kuba, Martin, Izquierdo, Jorge, and Mbiyavanga, Mamana

Subjects
data access, permissions, GA4GH visa, ELIXIR AAI, GA4GH researcher ID, authentication, GA4GH passport
Abstract

GA4GH Passport (a.k.a. GA4GH Researcher ID) is the GA4GH standard for expressing an authenticated researcher’s roles and data access permissions (a.k.a. passport visas). Together with the GA4GH Authentication and Authorisation Infrastructure (AAI) specification, it describes how passport visas are issued and delivered from their authority (such as a Data Access Committee) to the environment where the data access takes place (such as an analysis platform or cloud). The work package has contributed to the Passport and AAI standards which were approved by the GA4GH in October 2019. This deliverable provides an overview of the GA4GH Passport and AAI standards (version 1.0) in general. It then describes in detail how ELIXIR AAI has implemented the specification as a Passport broker service. Some directions of the next version of the GA4GH Passport and AAI standards, which are still in development in the GA4GH DURI workstream, are displayed. Finally, a hands-on experiment presents how passports could alternatively leverage self-sovereign identity, an emerging identity and access management paradigm in the industry.

Published
2021
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14. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Abigail Wexner Research Institute, Academy of Finland, Medical Research Future Fund, BioBank Japan, Canada Foundation for Innovation, Canadian Institutes of Health Research, European Commission, German Research Foundation, Genome Canada, Google, Howard Hughes Medical Institute, Instituto de Salud Carlos III, Japan Agency for Medical Research and Development, Mayo Clinic, Fundación la Caixa, Ministère de l'Économie et de l'Innovation (Québec), Monarch Initiative, National Human Genome Research Institute (US), National University of Singapore, Agency for Science, Technology and Research A*STAR (Singapore), National Health and Medical Research Council (Australia), National Institutes of Health (US), National Institute of General Medical Sciences (US), Swiss Institute of Bioinformatics, State Secretariat for Education, Research and Innovation (Switzerland), Terry Fox Research Institute, Canada Research Chairs, European Molecular Biology Laboratory, Ministry of Research, Innovation and Science (Ontario), Ontario Genomics Institute, Natural Sciences and Engineering Research Council of Canada, Wellcome Trust, National Taiwan University, Rehm, Heidi L., Page, Angela, Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J. S., Beck, Tim, Beckmann, Jacques S., Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Brudno, Michael, Kelleher, Jerome, Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, Kerry, Giselle, Brush,Matthew H., North, Kathryn, Birney, Ewan, Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Khor, Seik-Soon, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Melanie, Cunningham, Fiona, Knoppers, Bartha M., Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, Lewis Jonathan, Dyke, Stephanie O. M., Eddy, James A., Eilbeck, Karen, Konopko, Melissa A., Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Kosaki, Kenjiro, Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Kuba, Martin, Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Lawson, Jonathan, Hendricks-Sturrup, Rachele M., Ho, Calvin W. L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Shujui Hsu, Jacob, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Leinonen, Rasko, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jene, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J. M., Kanitz, Alexander, Kato, Kazuto, Li, Stephanie, Keane, Thomas M., Kekesi-Lafrance, Kristina, Beltran, Sergi, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Udara Liyanage, Isuru, López, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Bernick, David, Metke-Jiménez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Muñoz-Torres, Mónica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Bernier, Alexander, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Wang, Vivian Ota, Paglione, Laura A. D., Bonfield, James K., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Boughtwood, Tiffany F., Lyman Rodríguez, Laura, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Bourque, Guillaume, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Bowers, Sarion R., Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos,Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Valls Guimera, Roman, Brookes, Anthony J., Vamathevan, Jessica, Abigail Wexner Research Institute, Academy of Finland, Medical Research Future Fund, BioBank Japan, Canada Foundation for Innovation, Canadian Institutes of Health Research, European Commission, German Research Foundation, Genome Canada, Google, Howard Hughes Medical Institute, Instituto de Salud Carlos III, Japan Agency for Medical Research and Development, Mayo Clinic, Fundación la Caixa, Ministère de l'Économie et de l'Innovation (Québec), Monarch Initiative, National Human Genome Research Institute (US), National University of Singapore, Agency for Science, Technology and Research A*STAR (Singapore), National Health and Medical Research Council (Australia), National Institutes of Health (US), National Institute of General Medical Sciences (US), Swiss Institute of Bioinformatics, State Secretariat for Education, Research and Innovation (Switzerland), Terry Fox Research Institute, Canada Research Chairs, European Molecular Biology Laboratory, Ministry of Research, Innovation and Science (Ontario), Ontario Genomics Institute, Natural Sciences and Engineering Research Council of Canada, Wellcome Trust, National Taiwan University, Rehm, Heidi L., Page, Angela, Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J. S., Beck, Tim, Beckmann, Jacques S., Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Brudno, Michael, Kelleher, Jerome, Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, Kerry, Giselle, Brush,Matthew H., North, Kathryn, Birney, Ewan, Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Khor, Seik-Soon, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Melanie, Cunningham, Fiona, Knoppers, Bartha M., Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, Lewis Jonathan, Dyke, Stephanie O. M., Eddy, James A., Eilbeck, Karen, Konopko, Melissa A., Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Kosaki, Kenjiro, Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Kuba, Martin, Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Lawson, Jonathan, Hendricks-Sturrup, Rachele M., Ho, Calvin W. L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Shujui Hsu, Jacob, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Leinonen, Rasko, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jene, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J. M., Kanitz, Alexander, Kato, Kazuto, Li, Stephanie, Keane, Thomas M., Kekesi-Lafrance, Kristina, Beltran, Sergi, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Udara Liyanage, Isuru, López, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Bernick, David, Metke-Jiménez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Muñoz-Torres, Mónica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Bernier, Alexander, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Wang, Vivian Ota, Paglione, Laura A. D., Bonfield, James K., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Boughtwood, Tiffany F., Lyman Rodríguez, Laura, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Bourque, Guillaume, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Bowers, Sarion R., Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos,Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Valls Guimera, Roman, Brookes, Anthony J., and Vamathevan, Jessica

Abstract

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Published
2021

16. EOSC-Life Access and user management system for life science – the blueprint

Author

Linden, Mikael, Bucik, Dominik Frantisek, Gormanns, Philipp, Haley, Natalie, Heikkinen, Jani, Holub, Petr, Kankaanpää, Pasi, Kouril, Daniel, Kuba, Martin, Licehammer, Slavek, Matyska, Ludek, Nyrönen, Tommi, Prochazka, Michal, Reihs, Robert, Romano, Paolo, Sanderson, Fiona, Shigaval, Athresh, Smith, Callum, and Tedds, Jonathan

Subjects
access management, ComputingMilieux_COMPUTERSANDEDUCATION, identity management, Life science AAI
Abstract

This deliverable is the blueprint of the Life Science AAI, a common authentication and authorisation service for the European life science research infrastructures. The Life Science AAI provides a way to coordinate the way how user identity and access is managed in research services and data in the (community-specific) federated Infrastructure. The service will be managed by the life sciences community and operated by the e-infrastructures, such as GEANT, EGI and EUDAT. The requirements of the Life Science AAI were initially developed by CORBEL WP5 and piloted with e-infrastructures in the AARC2 project. This deliverable lays the ground for the production deployment with e-infrastructures during the EOSC-Life project. This deliverable and its appendices first introduces the technical and non-technical requirements for the e-infrastructure service offering and further clarifies how that relates to and integrates to the AAI service components operated by the life sciences research infrastructures. Relevant external work is then introduced. Finally, the deliverable provides an overview of Life Science AAI’s potential relying services from EOSC-Life project and beyond.

Published
2019
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18. Common ELIXIR Service for Researcher Authentication and Authorisation

Author

Linden, Mikael, primary, Prochazka, Michal, additional, Lappalainen, Ilkka, additional, Bucik, Dominik, additional, Vyskocil, Pavel, additional, Kuba, Martin, additional, Silén, Sami, additional, Belmann, Peter, additional, Sczyrba, Alexander, additional, Newhouse, Steven, additional, Matyska, Ludek, additional, and Nyrönen, Tommi, additional

Published
2018
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21. Dialog as an image of battle

Author

Kuba, Martin

Subjects
dialog, boj, mediaval Czech literature, Easter, česká středověká literatura, Velikonoce, image, battle
Abstract

Text se pokouší popsat specifika staročeské literární památky Hra o Kristovu zmrtvýchvstání i o jeho oslavení. Na základě analýzy použitých jazykových prostředků s konotací boje a bitvy dále ukazuje na kompozici celého textu jako promyšleného konceptu boje Dobra se Zlem. Pozornost věnuje i mimořádnému zachycení Kristova sestoupení do pekel a jeho textovému ztvárnění z temporálního hlediska. This text describes the specifics of "Play of the Resurrection of Christ and Its Celebration", a Czech medieval Easter play. It attempts to find an explanation for its unusual battle-oriented linguistic and compositional format. It also explores the extraordinary composition of the play´s Hell scene.

Published
2016

23. Content of distinct metals in periprosthetic tissues and pseudosynovial joint fluid in patients with total joint arthroplasty.

Author

Kuba, Martin, Gallo, Jiří, Pluháček, Tomáš, Hobza, Martin, and Milde, David

Abstract

This prospective study examined the content of metals released from total joint arthroplasty into joint fluid, whole blood and periprosthetic tissues. We determined the levels of Ti, V, Nb, Co, Cr, and Mo, using inductively coupled plasma mass spectrometry, in samples from patients who underwent reoperation of total hip or knee arthroplasty. All of the patients (n = 117) included in the study had either metal on polyethylene or ceramic on polyethylene‐bearing pairs. First, our results conclusively showed that the majority of released metals were deposited in periprosthetic tissues. In this context, the bloodstream turned out to be an ineffective biomarker of the effects occurring in local tissues. Second, there was a clear time‐dependent nature of metallic accumulation. Based on our extensive dataset, we found significantly elevated levels of the released metals in joint fluid and periprosthetic tissues originating from loosened implants compared to stable ones, as well as recognizable differences between the groups with stable implants and aseptic loosening. Finally, it was proved that the concentrations of metals decreased dependent on the distance of the tissue from the implant. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 107B: 454–462, 2019. [ABSTRACT FROM AUTHOR]

Published
2019
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24. Sustainable management of river oases along the Tarim River (SuMaRiO) in Northwest China under conditions of climate change

Author

Rumbaur, Christian, Thevs, Niels, Ahlheim, Michael, Disse, Markus, Brieden, Andreas, Cyffka, Bernd, Düthmann, Doris, Feike, Til, Frör, Oliver, Gärtner, Philipp, Halik, Ümüt, Hill, Joachim, Hinnenthal, Marie, Keilholz, Patrick, Kleinschmit, Birgit, Krysanova, Valentina, Kuba, Martin, Mader, Sebastian, Menz, Christoph, Othmanli, Hussein, Pelz, Sonna, Schroeder, Matthias, Siew, Tuck Fatt, Stender, Vivien, Stahr, Karl, Thomas, Frank M., Welp, Martin, Wortmann, Michel, Zhao, Xiaoning, Chen, Xi, Jiang, Tong, Luo, Jing, Yimit, Hamid, Yu, Ruide, Zhang, Xi, Zhao, Chengyi, Rumbaur, Christian, Thevs, Niels, Ahlheim, Michael, Disse, Markus, Brieden, Andreas, Cyffka, Bernd, Düthmann, Doris, Feike, Til, Frör, Oliver, Gärtner, Philipp, Halik, Ümüt, Hill, Joachim, Hinnenthal, Marie, Keilholz, Patrick, Kleinschmit, Birgit, Krysanova, Valentina, Kuba, Martin, Mader, Sebastian, Menz, Christoph, Othmanli, Hussein, Pelz, Sonna, Schroeder, Matthias, Siew, Tuck Fatt, Stender, Vivien, Stahr, Karl, Thomas, Frank M., Welp, Martin, Wortmann, Michel, Zhao, Xiaoning, Chen, Xi, Jiang, Tong, Luo, Jing, Yimit, Hamid, Yu, Ruide, Zhang, Xi, and Zhao, Chengyi

Abstract

The Tarim River basin, located in Xinjiang, NW China, is the largest endorheic river basin in China and one of the largest in all of Central Asia. Due to the extremely arid climate, with an annual precipitation of less than 100 mm, the water supply along the Aksu and Tarim rivers solely depends on river water. This is linked to anthropogenic activities (e.g., agriculture) and natural and semi-natural ecosystems as both compete for water. The ongoing increase in water consumption by agriculture and other human activities in this region has been enhancing the competition for water between human needs and nature. Against this background, 11 German and 6 Chinese universities and research institutes have formed the consortium SuMaRiO (Sustainable Management of River Oases along the Tarim River; http://www.sumario.de), which aims to create a holistic picture of the availability of water resources in the Tarim River basin and the impacts on anthropogenic activities and natural ecosystems caused by the water distribution within the Tarim River basin. On the basis of the results from field studies and modeling approaches as well as from suggestions by the relevant regional stakeholders, a decision support tool (DST) will be implemented that will then assist stakeholders in balancing the competition for water, acknowledging the major external effects of water allocation to agriculture and to natural ecosystems. This consortium was formed in 2011 and is funded by the German Federal Ministry of Education and Research. As the data collection phase was finished this year, the paper presented here brings together the results from the fields from the disciplines of climate modeling, cryology, hydrology, agricultural sciences, ecology, geoinformatics, and social sciences in order to present a comprehensive picture of the effects of different water availability schemes on anthropogenic activities and natural ecosystems along the Tarim River. The second objective is to present the pro

Published
2015

28. Sustainable management of river oases along the Tarim River in North-Western China under conditions of climate change

Author

Rumbaur, Christian, Thevs, Niels, Disse, Markus, Ahlheim, Michael, Brieden, Andreas, Cyffka, Bernd, Doluschitz, Reiner, Düthmann, Doris, Feike, Til, Frör, Oliver, Gärtner, Philipp, Halik, Ümüt, Hill, Joachim, Hinnenthal, Marie, Keilholz, Patrick, Kleinschmit, Birgit, Krysanova, Valentina, Kuba, Martin, Mader, Sebastian, Menz, Christoph, Othmanli, Hussein, Pelz, Sonna, Schroeder, Matthias, Siew, Tuck Fatt, Stender, Vivien, Stahr, Karl, Thomas, Frank M., Welp, Martin, Wortmann, Michel, Zhao, Xiaoning, Chen, Xi, Jiang, Tong, Zhao, Chengyi, Zhang, Xi, Luo, Jing, Yimit, Hamid, Yu, Ruide, Rumbaur, Christian, Thevs, Niels, Disse, Markus, Ahlheim, Michael, Brieden, Andreas, Cyffka, Bernd, Doluschitz, Reiner, Düthmann, Doris, Feike, Til, Frör, Oliver, Gärtner, Philipp, Halik, Ümüt, Hill, Joachim, Hinnenthal, Marie, Keilholz, Patrick, Kleinschmit, Birgit, Krysanova, Valentina, Kuba, Martin, Mader, Sebastian, Menz, Christoph, Othmanli, Hussein, Pelz, Sonna, Schroeder, Matthias, Siew, Tuck Fatt, Stender, Vivien, Stahr, Karl, Thomas, Frank M., Welp, Martin, Wortmann, Michel, Zhao, Xiaoning, Chen, Xi, Jiang, Tong, Zhao, Chengyi, Zhang, Xi, Luo, Jing, Yimit, Hamid, and Yu, Ruide

Abstract

The Tarim River Basin, located in Xinjiang, NW China, is the largest endorheic river basin of China and one of the largest in whole Central Asia. Due to the extremely arid climate with an annual precipitation of less than 100 mm, the water supply along the Aksu and Tarim River solely depends on river water. This applies for anthropogenic activities (e.g. agriculture) as well as for the natural ecosystems so that both compete for water. The on-going increase of water consumption by agriculture and other human activities in this region has been enhancing the competition for water between human needs and nature. Against this background, 11 German and 6 Chinese universities and research institutes formed the consortium SuMaRiO (www.sumario.de), which aims at gaining a holistic picture of the availability of water resources in the Tarim River Basin and the impacts on anthropogenic activities and natural ecosystems caused by the water distribution within the Tarim River Basin. The discharge of the Aksu River, which is the major tributary to the Tarim, has been increasing over the past 6 decades due to enhanced glacier melt. Alone from 1989 to 2011, the area under agriculture more than doubled. Thereby, cotton became the major crop and there was a shift from small-scale farming to large-scale intensive farming. The major natural ecosystems along the Aksu and Tarim River are riparian ecosystems: Riparian (Tugai) forests, shrub vegetation, reed beds, and other grassland. Within the SuMaRiO Cluster the focus was laid on the Tugai forests, with Populus euphratica as dominant tree, because the most productive and species-rich natural ecosystems can be found among those forests. On sites with groundwater distance of less than 7.5 m the annual increments correlated with river runoffs of the previous year. But, the further downstream along the Tarim River, the more the natural river dynamics ceased, which impacts on the recruitment of Populus euphratica. Household surveys revealed

Published
2014

30. Glycerol to acrolein - as fast as possible

Author

Kuba, Martin and Dubois, Jean-Luc

Subjects
Glycerin -- Research, Glycerol -- Research, Catalysis -- Methods, Business, Chemicals, plastics and rubber industries
Published
2009

31. Návrh opatření vedoucích ke zklidnění automobilové dopravy v Náchodě

Author

Ledvinová, Michaela, Sršeň, Jan, Kuba, Martin, Ledvinová, Michaela, Sršeň, Jan, and Kuba, Martin

Abstract

Diplomová práce se zabývá analýzou současného stavu dopravy na území města, dále pak navržením a zhodnocením několika alternativních opatření, která by měla vést k částečnému zklidnění automobilové dopravy na nejvytíženější ulici v Náchodě., This thesis deals with analysis of current transport, propositioning and evaluating of several alternative measures, which should lead to modulation of automobile transport on the busiest street in Nachod., Katedra technologie a řízení dopravy, Student obhájil diplomovou práci a zodpověděl otázky členů zkušební komise., Dokončená práce s úspěšnou obhajobou

Published
2011

32. Prostředky zajišťující bezpečnost letového provozu - systémy a zařízení pro spojení, navigaci a sledování

Author

Šourek, David, Kuba, Martin, Šourek, David, and Kuba, Martin

Abstract

Bakalářská práce se zaměřuje na bezpečnost letového provozu, řízení letového provozu a na prostředky, které tuto bezpečnost zajišťují. Cílem této práce je představit některé používané systémy a zařízení zabezpečovací letecké techniky, vysvětlit jejich funkce, principy používání, a to jak je k řízení letového provozu a zajištění bezpečnosti letového provozu využívá služba řízení letového provozu., The bachelor work is focus to safety of air traffic, air traffic control and resources handling safety of air traffic. The aim of this work is present some systems and equipment for safety of air traffic, explain their functions and using for air traffic control., Katedra technologie a řízení dopravy, Dokončená práce s úspěšnou obhajobou

Published
2009

36. Automated trust negotiation in identity federations using OWL-based abduction of missing credentials.

Author

Kuba, Martin

Abstract

Creating ontologies and access control policies have one thing in common - a lot of work is spent on creating precise definitions like “who is a full time student” and answering difficult questions like “Are unpaid teachers employees?”. Thus ontologies written in OWL and SWRL are a good match for access control policies. However the research in this area always assumed that the semantic information about a user is readily available. But such assumption can be satisfied only in a centralized system, not in decentralized systems enabled by the recent formation of identity federations, in which organizations can authenticate users from other organizations, and make authorization decisions about access to their resources based on user information provided by the other organizations. [ABSTRACT FROM PUBLISHER]

Published
2011

37. Sealed Grid with Downloadable Services.

Author

Priol, Thierry, Vanneschi, Marco, Kuba, Martin, Kouřil, Daniel, and Procházka, Michal

Abstract

In a service-based grid, the data to be processed are usually moved to the service. However this is not always possible for security and data privacy reasons, as in biomedical grids processing patients' data. The other way, moving services to the location of the data, brings challenges in dealing with heterogeneity of deployment environments. A solution for this problem is proposed in this paper, based on services deployed in hardware virtual machines. Such setting allows a user to download all needed grid services into a tightly controlled environment, possibly even disconnected from the network, thus creating a "sealed grid" for processing sensitive data. [ABSTRACT FROM AUTHOR]

Published
2008
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39. Eco-morphological response of floodplain forests ( Populus euphratica Oliv.) to water diversion in the lower Tarim River, northwest China.

Author

Aishan, Tayierjiang, Halik, Ümüt, Kurban, Alishir, Cyffka, Bernd, Kuba, Martin, Betz, Florian, and Keyimu, Maierdang

Subjects
FLOODPLAIN forests, WATER diversion, INLAND navigation, POPLARS, COTTON growing
Abstract

The Tarim River is about 1,320 km long and is one of the longest continental inland waterways in the world. In an undisturbed state, it is accompanied on both sides by floodplain forests of Euphrates poplar ( Populus euphratica Oliv.). The rising water consumption in the upper and middle reaches, and massive hydro-technical interventions in the development of uncultivated land for cotton farming, especially during the last decades, have led to a widespread destruction of the natural ecosystems. This is the case particularly in the lower reaches of the river, where 320 km of the floodplain forests are either highly degraded or dead. Since the year 2000, the Chinese government has made efforts to restore these ecosystems and conducted man-made water diversion project into the affected area. The starting phase of recovering measures needs an efficient and extensive long-term monitoring. A combined approach of remote sensing and terrestrial samples can meet these demands. This study is based on the data from a small-scale ecological monitoring in the past 7 years and combination of QuickBird image information of the floodplain forests along the lower reaches of the Tarim River within the purview of the man-made restoration project. The effects of the artificial water diversion on the dynamics of the groundwater layer and the revitalization of P. euphratica floodplain forests have been analysed in the Arghan transect. The results showed that the groundwater level has risen from 12.6 to 5.5-6.2 m below the surface in the vicinity of the river beds. Some eco-morphological parameters of the P. euphratica trees have different levels of response to the ecological water diversion. To specify, in the vertical direction, the farther the trees are from the river, the weaker the response of ecological indicators. These parameters include tree vitality level, crown diameter, under branch height as well as newly developed crown types of P. euphratica trees. Generally, the floodplain forests within 200 m to the riverbed recovered remarkably, and those between 200 and 800 m from the river showed a medium response to the water transfer, while forests further away than 800 m from the river bed showed less sign of recovery. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

40. Grid Empowered Sharing of Medical Expertise.

Author

Kuba, Martin, Krajíček, Ondřej, Lesný, Petr, Vejvalka, Jan, and Holeček, Tomáš

Abstract

Today, applications for Grids emerge in various scientific fields, each with specific requirements. We present concept and architecture which enables biomedical experts to collaborate and share resources by encapsulating their knowledge and expertise as grid services, with (semi-)formally described semantics. Grid Services allow machine processing of the encapsulated knowledge, while their semantic description provides means for their automated discovery and interaction. This brings new possibilities of building biomedical systems offering machine-driven assistance to the biomedical experts. [ABSTRACT FROM AUTHOR]

Published
2006

41. Genetické algoritmy – Multi-core CPU implementace

Author

Matoušek, Radomil, Kuba, Martin, Studnička, Vladimír, Matoušek, Radomil, Kuba, Martin, and Studnička, Vladimír

Abstract

Cílem diplomové práce je vytvořit co možná nejuniverzálnější knihovnu pro genetické algoritmy v jazyce C++, s určitým počtem implementovaných univerzálních operátorů a následně vytvořenou knihovnu otestovat na příkladech. Musí být implementována podpora více-jádrových procesorů pomocí OpenMP. Knihovna bude testována celkově na třech příkladech. První dva příklady jsou matematické funkce, které se používají právě k testování genetických algoritmů. Dalším testovacím příkladem je problém rozložení n-dam na šachovnici, aby se vzájemně neohrožovali. Nakonec se pokusíme pomocí navrhnutých algoritmů zjistit řešení puzzle s názvem Eternity II, za jehož vyřešení je vypsána odměna 2 milióny dolarů., his diploma thesis deals with creating the most universal library of genetic algorithms in C++, as much as possible, implemented with the certain number of universal operators, and then with testing created library on some examples. Library must support multi-core processors, implementation will be done over OpenMP. The library will be tested on three examples in all. The first two examples are mathematical functions, that are used just for genetic algorithms testing. Last problem for test is N-Queens problem. Finally we will use genetic algorithms to try find solution for Eternity II puzzle, there is declared a 2 million bounty for full solution.

42. Návrh podnikatelského plánu pro vznik a rozvoj společnosti

Author

Konečná, Zdeňka, Kuba, Martin, Kingová, Jana, Konečná, Zdeňka, Kuba, Martin, and Kingová, Jana

Abstract

Obsahem této diplomové práce je návrh podnikatelského plánu pro vznik a rozvoj společnosti. Konkrétně byl vytvořen podnikatelský plan pro zřízení kavárny s názvem Ollie, která je zároveň komunitním místem, dílnou a místem pro práci v Brně Komárov, nedaleko sportovního areálu Komec. První část tvoří teoretická východiska práce, která obsahují vysvětlení pojmů potřebných ke zpracování praktické části diplomové práce. Praktická část obsahuje analýzu současného stavu a vlastní návrh řešení. Metodami, které byly použity k analýzám jsou například metoda PESTLE nebo Porterova analýza., The content of this diploma thesis is a proposal for a business plan for the establishment and development of a company. Specifically, it is a business plan for a café called Ollie, which is also a community center, a workshop and a place to work situated in Brno Komárov, near the Komec sports complex. The first part consists of the theoretical basis of the work containing an explanation of the concepts needed to write the practical part of the thesis. The practical part contains an analysis of the current state and the actual design of the solution. Methods used are for example PESTLE or Porter’s Analysis.

43. Gramatická evoluce – Java

Author

Matoušek, Radomil, Kuba,, Martin, Bezděk, Pavel, Matoušek, Radomil, Kuba,, Martin, and Bezděk, Pavel

Abstract

Předmětem mé diplomové práce je realizace gramatické evoluce v programovacím jazyce Java pro řešení úloh aproximace funkcí a syntézy logických obvodů. Aplikace je prakticky využita pro testování a sběr dat v kontextu s použitím odlišných účelových funkcí a paralelní gramatické evoluce. Data jsou analyzována a vyhodnocena., The object of my thesis is the realization of grammatical evolution in the Java programming language for solving problems of approximation of functions and synthesis of logical circuits. The application is practical used for testing and gathering data in context of using different purpose function and parallel grammatical evolution. The data are analyzed and evaluated.

44. Distribuované výpočty s využitím technologie ActionScript

Author

Matoušek, Radomil, Kuba,, Martin, Minář, Petr, Matoušek, Radomil, Kuba,, Martin, and Minář, Petr

Abstract

Tato diplomová práce se zabývá problematikou návrhu optimalizačního software v jazyku ActionScript 3.0. Navržené aplikace realizují samostatné i distribuované výpočty pomocí implementované optimalizační heuristiky HC12. Pro ověření funkcionality a výkonu byla vybrána sada testovacích úloh. Praktickým výsledkem práce je vytvoření veřejně přístupných klientů v síti internet a zpracovávání dílčích výpočtů s nimi. Klienti jsou trojího druhu dle pravomocí a úloh na nich spočívajících. Práce vznikla při řešení výzkumného záměru Inteligentní systémy v automatizaci podporovaného MŠMT ČR pod registračním číslem MSM 0021630529., This Master thesis deals with designing and realization of optimalization software in ActionScript 3.0 background. The designed applications realized in terms of computation by standalone and distributed variant and by means of chosen heuristic method called HC12. For verification of a function and performance was select set of testing examples. The main purpose of the work was create public clients in the network internet and calculated partial computing by it. The completed clients are selected by competence and carry on tasks. This research has been supported by the Czech Ministry of Education in the frame of MSM 0021630529 Research Intention Intelligent Systems in Automation.

45. Genetické programování - Java implementace

Author

Matoušek, Radomil, Kuba,, Martin, Tomaštík, Marek, Matoušek, Radomil, Kuba,, Martin, and Tomaštík, Marek

Abstract

Tato diplomová práce má za cíl vytvoření programové aplikace v jazyce Java, dále využitelné v oblasti automatického generování modelů, speciálně v úlohách tzv. symbolické regrese. Práce zahrnuje stručný popis genetického programování (GP) a vlastní implementací GP s důrazem na využití pokročilých operátorů (nedestruktivní operace, elitní přistup, zjednodušování výrazů). Pro zvolené datové množiny je technikou symbolické regrese generován matematický model. K ověření funkcionality je využito tzv. testovacích úloh. Pro vybrané parametry GP je hledáno optimální nastavení., This Master´s thesis implements computer program in Java, useful for automatic model generating, specially in symbolic regression problem. Thesis includes short description of genetic programming (GP) and own implementation with advanced GP operands (non-destructive operations, elitism, exptression reduction). Mathematical model is generating by symbolic regression, exacly for choosen data set. For functioning check are used test tasks. Optimal settings is found for choosen GP parameters.

46. Gramatická evoluce – Java

Author

Matoušek, Radomil, Kuba,, Martin, Bezděk, Pavel, Matoušek, Radomil, Kuba,, Martin, and Bezděk, Pavel

Abstract

Předmětem mé diplomové práce je realizace gramatické evoluce v programovacím jazyce Java pro řešení úloh aproximace funkcí a syntézy logických obvodů. Aplikace je prakticky využita pro testování a sběr dat v kontextu s použitím odlišných účelových funkcí a paralelní gramatické evoluce. Data jsou analyzována a vyhodnocena., The object of my thesis is the realization of grammatical evolution in the Java programming language for solving problems of approximation of functions and synthesis of logical circuits. The application is practical used for testing and gathering data in context of using different purpose function and parallel grammatical evolution. The data are analyzed and evaluated.

47. Pokročilé plánování cesty robotu (RRT)

Author

Matoušek, Radomil, Kuba,, Martin, Knispel, Lukáš, Matoušek, Radomil, Kuba,, Martin, and Knispel, Lukáš

Abstract

Tato diplomová práce práce se zabývá plánováním cesty všesměrového mobilního robotu pomocí algoritmu RRT (Rapidly-exploring Random Tree – Rychle rostoucí náhodný strom). Teoretická část popisuje základní algoritmy plánování cesty a prezentuje bližší pohled na RRT a jeho potenciál. Praktická část práce řeší návrh a tvorbu v zásadě multiplatformní C++ aplikace v prostředí Windows 7 za použití aplikačního frameworku Qt 4.8.0, která implementuje pokročilé RRT algoritmy s parametrizovatelným řešičem a speciálním dávkovým režimem. Tento mód slouží k testování efektivnosti nastavení řešiče pro dané úlohy a je založen na post-processingu a vizualizaci výstupu měřených úloh pomocí jazyka Python. Vypočtené cesty mohou být vylepšeny pomocí zkracovacích algoritmů a výsledná trajektorie odeslána do pohonů Maxon Compact Drive všesměrové mobilní platformy pomocí CANopen. Aplikace klade důraz na moderní grafické uživatelské rozhraní se spolehlivým a výkonným 2D grafickým engine., This master's thesis deals with path planning of omnidirectional mobile robot using the RRT algorithm (Rapidly-exploring Random Tree). Theoretical part describes basic algorithms of path planning and presents closer view on RRT and its potential. Practical part deals with designing and creation of essentially multiplatform C++ application in Windows 7 environment with Qt 4.8.0 application framework, which implements advanced RRT algorithms with user-programmable solver and special batch mode. This mode is used for testing the effectiveness of solver on given tasks and it is based on postprocessing and visualization of measurement tasks output by Python language. Computed paths can be enhanced by shortening algorithms and result trajectory sent to Maxon Compact Drives of omnidirectional platform via the CANopen. Application puts emphasis on modern GUI with reliable and powerful 2D graphics engine.

48. Genetické algoritmy – Multi-core CPU implementace

Author

Matoušek, Radomil, Kuba, Martin, Studnička, Vladimír, Matoušek, Radomil, Kuba, Martin, and Studnička, Vladimír

Abstract

Cílem diplomové práce je vytvořit co možná nejuniverzálnější knihovnu pro genetické algoritmy v jazyce C++, s určitým počtem implementovaných univerzálních operátorů a následně vytvořenou knihovnu otestovat na příkladech. Musí být implementována podpora více-jádrových procesorů pomocí OpenMP. Knihovna bude testována celkově na třech příkladech. První dva příklady jsou matematické funkce, které se používají právě k testování genetických algoritmů. Dalším testovacím příkladem je problém rozložení n-dam na šachovnici, aby se vzájemně neohrožovali. Nakonec se pokusíme pomocí navrhnutých algoritmů zjistit řešení puzzle s názvem Eternity II, za jehož vyřešení je vypsána odměna 2 milióny dolarů., his diploma thesis deals with creating the most universal library of genetic algorithms in C++, as much as possible, implemented with the certain number of universal operators, and then with testing created library on some examples. Library must support multi-core processors, implementation will be done over OpenMP. The library will be tested on three examples in all. The first two examples are mathematical functions, that are used just for genetic algorithms testing. Last problem for test is N-Queens problem. Finally we will use genetic algorithms to try find solution for Eternity II puzzle, there is declared a 2 million bounty for full solution.

49. Genetické programování - Java implementace

Author

Matoušek, Radomil, Kuba,, Martin, Tomaštík, Marek, Matoušek, Radomil, Kuba,, Martin, and Tomaštík, Marek

Abstract

Tato diplomová práce má za cíl vytvoření programové aplikace v jazyce Java, dále využitelné v oblasti automatického generování modelů, speciálně v úlohách tzv. symbolické regrese. Práce zahrnuje stručný popis genetického programování (GP) a vlastní implementací GP s důrazem na využití pokročilých operátorů (nedestruktivní operace, elitní přistup, zjednodušování výrazů). Pro zvolené datové množiny je technikou symbolické regrese generován matematický model. K ověření funkcionality je využito tzv. testovacích úloh. Pro vybrané parametry GP je hledáno optimální nastavení., This Master´s thesis implements computer program in Java, useful for automatic model generating, specially in symbolic regression problem. Thesis includes short description of genetic programming (GP) and own implementation with advanced GP operands (non-destructive operations, elitism, exptression reduction). Mathematical model is generating by symbolic regression, exacly for choosen data set. For functioning check are used test tasks. Optimal settings is found for choosen GP parameters.

50. Pokročilé plánování cesty robotu (RRT)

Author

Matoušek, Radomil, Kuba,, Martin, Matoušek, Radomil, and Kuba,, Martin

Abstract

Tato diplomová práce práce se zabývá plánováním cesty všesměrového mobilního robotu pomocí algoritmu RRT (Rapidly-exploring Random Tree – Rychle rostoucí náhodný strom). Teoretická část popisuje základní algoritmy plánování cesty a prezentuje bližší pohled na RRT a jeho potenciál. Praktická část práce řeší návrh a tvorbu v zásadě multiplatformní C++ aplikace v prostředí Windows 7 za použití aplikačního frameworku Qt 4.8.0, která implementuje pokročilé RRT algoritmy s parametrizovatelným řešičem a speciálním dávkovým režimem. Tento mód slouží k testování efektivnosti nastavení řešiče pro dané úlohy a je založen na post-processingu a vizualizaci výstupu měřených úloh pomocí jazyka Python. Vypočtené cesty mohou být vylepšeny pomocí zkracovacích algoritmů a výsledná trajektorie odeslána do pohonů Maxon Compact Drive všesměrové mobilní platformy pomocí CANopen. Aplikace klade důraz na moderní grafické uživatelské rozhraní se spolehlivým a výkonným 2D grafickým engine., This master's thesis deals with path planning of omnidirectional mobile robot using the RRT algorithm (Rapidly-exploring Random Tree). Theoretical part describes basic algorithms of path planning and presents closer view on RRT and its potential. Practical part deals with designing and creation of essentially multiplatform C++ application in Windows 7 environment with Qt 4.8.0 application framework, which implements advanced RRT algorithms with user-programmable solver and special batch mode. This mode is used for testing the effectiveness of solver on given tasks and it is based on postprocessing and visualization of measurement tasks output by Python language. Computed paths can be enhanced by shortening algorithms and result trajectory sent to Maxon Compact Drives of omnidirectional platform via the CANopen. Application puts emphasis on modern GUI with reliable and powerful 2D graphics engine.

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