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integration_instructions Research softwarekeyboard_double_arrow_right Software 2022 JavaPublisher:bio.tools Funded by:EC | EarlyCause, EC | EOSC-Life, WT +1 projectsEC| EarlyCause ,EC| EOSC-Life ,WT ,EC| BY-COVIDAuthors: Dispatcher, Job;Dispatcher, Job;EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::c2171559c58b4601490378769322cf6f&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::c2171559c58b4601490378769322cf6f&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2021 NetherlandsPublisher:4TU.ResearchData Funded by:EC | CriticalMaaSEC| CriticalMaaSAuthors: Kucharski, Rafal;Kucharski, Rafal;The dataset contains results of experiments for the study of our research https://arxiv.org/abs/2011.12770. Data is used to generate results with this reproducible notebook: https://github.com/RafalKucharskiPK/ExMAS/blob/master/ExMAS/spinoffs/corona/02_plots.ipynbFiles:- png with maps- .csv with epidemic modelling results (For any given day, the model outputs information about the number of travellers in each state (S-I-Q-R) and newly infected travellers, based on which we can reproduce epidemic spreading profiles.)Abstract of the study:Urban mobility needs alternative sustainable travel modes to keep our pandemic cities in motion. Ride-pooling, where a single vehicle is shared by more than one traveller, is not only appealing for mobility platforms and their travellers, but also for promoting the sustainability of urban mobility systems. Yet, the potential of ride-pooling rides to serve as a safe and effective alternative given the personal and public health risks considerations associated with the COVID-19 pandemic is hitherto unknown. To answer this, we combine epidemiological and behavioural shareability models to examine spreading among ride-pooling travellers, with an application for Amsterdam. Findings are at first sight devastating, with only few initially infected travellers needed to spread the virus to hundreds of ride-pooling users. Without intervention, ride-pooling system may substantially contribute to virus spreading. Notwithstanding, we identify an effective control measure allowing to halt the spreading before the outbreaks (at 50 instead of 800 infections) without sacrificing the efficiency achieved by pooling. Fixed matches among co-travellers disconnect the otherwise dense contact network, encapsulating the virus in small communities and preventing the outbreaks.
4TU.ResearchData; NA... arrow_drop_down NARCIS; 4TU.ResearchData | science.engineering.designDataset . 2021License: https://opensource.org/licenses/MIT4TU.ResearchDataDataset . 2021License: http://opensource.org/licenses/MITData sources: 4TU.ResearchDataadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.4121/14140616&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert 4TU.ResearchData; NA... arrow_drop_down NARCIS; 4TU.ResearchData | science.engineering.designDataset . 2021License: https://opensource.org/licenses/MIT4TU.ResearchDataDataset . 2021License: http://opensource.org/licenses/MITData sources: 4TU.ResearchDataadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.4121/14140616&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2021Publisher:bio.tools Funded by:EC | GeCoEC| GeCoAuthors: Ceri, Stefano;Ceri, Stefano;ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK, and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. The database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::f11cc3010f353a61a9fb0ca750d13128&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::f11cc3010f353a61a9fb0ca750d13128&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2021 GroovyPublisher:bio.tools Funded by:EC | BovRegEC| BovRegVarona, Sarai; Monzón, Sara; Patel, Harshil; Ewels, Philip A.; Garcia, Maxime U.; Espinosa-Carrasco, Jose;nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples. The pipeline supports short-read Illumina sequencing data from both shotgun (e.g. sequencing directly from clinical samples) and enrichment-based library preparation methods (e.g. amplicon-based: ARTIC SARS-CoV-2 enrichment protocol; or probe-capture-based).
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::59ba8278107dd8a74581009b1ff2a4f8&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::59ba8278107dd8a74581009b1ff2a4f8&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2017 JavaPublisher:bio.tools Funded by:WT, EC | EOSC-Life, EC | EarlyCause +2 projectsWT ,EC| EOSC-Life ,EC| EarlyCause ,NIH| The UniProt protein sequence and function knowledgebase ,EC| BY-COVIDAuthors: Dispatcher, Job;Dispatcher, Job;EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::d69774442f55239b41c29200871ade3f&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::d69774442f55239b41c29200871ade3f&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2016 SQLPublisher:bio.tools Funded by:EC | iNEXT, EC | West-Life, EC | ELIXIR-EXCELERATE +4 projectsEC| iNEXT ,EC| West-Life ,EC| ELIXIR-EXCELERATE ,EC| EOSC-Life ,EC| EGI-Engage ,EC| INSTRUCT-ULTRA ,EC| CORBELAuthors: Segura, Joan; Macias, Jose R.; Guerrero, Carolina Simon;Segura, Joan; Macias, Jose R.; Guerrero, Carolina Simon;Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::c19a3b09038f2ac4bddc78fcd6846eca&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::c19a3b09038f2ac4bddc78fcd6846eca&type=result"></script>'); --> </script>
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integration_instructions Research softwarekeyboard_double_arrow_right Software 2022 JavaPublisher:bio.tools Funded by:EC | EarlyCause, EC | EOSC-Life, WT +1 projectsEC| EarlyCause ,EC| EOSC-Life ,WT ,EC| BY-COVIDAuthors: Dispatcher, Job;Dispatcher, Job;EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::c2171559c58b4601490378769322cf6f&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::c2171559c58b4601490378769322cf6f&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2021 NetherlandsPublisher:4TU.ResearchData Funded by:EC | CriticalMaaSEC| CriticalMaaSAuthors: Kucharski, Rafal;Kucharski, Rafal;The dataset contains results of experiments for the study of our research https://arxiv.org/abs/2011.12770. Data is used to generate results with this reproducible notebook: https://github.com/RafalKucharskiPK/ExMAS/blob/master/ExMAS/spinoffs/corona/02_plots.ipynbFiles:- png with maps- .csv with epidemic modelling results (For any given day, the model outputs information about the number of travellers in each state (S-I-Q-R) and newly infected travellers, based on which we can reproduce epidemic spreading profiles.)Abstract of the study:Urban mobility needs alternative sustainable travel modes to keep our pandemic cities in motion. Ride-pooling, where a single vehicle is shared by more than one traveller, is not only appealing for mobility platforms and their travellers, but also for promoting the sustainability of urban mobility systems. Yet, the potential of ride-pooling rides to serve as a safe and effective alternative given the personal and public health risks considerations associated with the COVID-19 pandemic is hitherto unknown. To answer this, we combine epidemiological and behavioural shareability models to examine spreading among ride-pooling travellers, with an application for Amsterdam. Findings are at first sight devastating, with only few initially infected travellers needed to spread the virus to hundreds of ride-pooling users. Without intervention, ride-pooling system may substantially contribute to virus spreading. Notwithstanding, we identify an effective control measure allowing to halt the spreading before the outbreaks (at 50 instead of 800 infections) without sacrificing the efficiency achieved by pooling. Fixed matches among co-travellers disconnect the otherwise dense contact network, encapsulating the virus in small communities and preventing the outbreaks.
4TU.ResearchData; NA... arrow_drop_down NARCIS; 4TU.ResearchData | science.engineering.designDataset . 2021License: https://opensource.org/licenses/MIT4TU.ResearchDataDataset . 2021License: http://opensource.org/licenses/MITData sources: 4TU.ResearchDataadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.4121/14140616&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert 4TU.ResearchData; NA... arrow_drop_down NARCIS; 4TU.ResearchData | science.engineering.designDataset . 2021License: https://opensource.org/licenses/MIT4TU.ResearchDataDataset . 2021License: http://opensource.org/licenses/MITData sources: 4TU.ResearchDataadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.4121/14140616&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2021Publisher:bio.tools Funded by:EC | GeCoEC| GeCoAuthors: Ceri, Stefano;Ceri, Stefano;ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK, and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. The database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::f11cc3010f353a61a9fb0ca750d13128&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::f11cc3010f353a61a9fb0ca750d13128&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2021 GroovyPublisher:bio.tools Funded by:EC | BovRegEC| BovRegVarona, Sarai; Monzón, Sara; Patel, Harshil; Ewels, Philip A.; Garcia, Maxime U.; Espinosa-Carrasco, Jose;nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples. The pipeline supports short-read Illumina sequencing data from both shotgun (e.g. sequencing directly from clinical samples) and enrichment-based library preparation methods (e.g. amplicon-based: ARTIC SARS-CoV-2 enrichment protocol; or probe-capture-based).
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::59ba8278107dd8a74581009b1ff2a4f8&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::59ba8278107dd8a74581009b1ff2a4f8&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2017 JavaPublisher:bio.tools Funded by:WT, EC | EOSC-Life, EC | EarlyCause +2 projectsWT ,EC| EOSC-Life ,EC| EarlyCause ,NIH| The UniProt protein sequence and function knowledgebase ,EC| BY-COVIDAuthors: Dispatcher, Job;Dispatcher, Job;EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::d69774442f55239b41c29200871ade3f&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::d69774442f55239b41c29200871ade3f&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euintegration_instructions Research softwarekeyboard_double_arrow_right Software 2016 SQLPublisher:bio.tools Funded by:EC | iNEXT, EC | West-Life, EC | ELIXIR-EXCELERATE +4 projectsEC| iNEXT ,EC| West-Life ,EC| ELIXIR-EXCELERATE ,EC| EOSC-Life ,EC| EGI-Engage ,EC| INSTRUCT-ULTRA ,EC| CORBELAuthors: Segura, Joan; Macias, Jose R.; Guerrero, Carolina Simon;Segura, Joan; Macias, Jose R.; Guerrero, Carolina Simon;Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB structures and Uniprot sequences where the protein annotations stored in Uniprot, Immune Epitope DB, Phospho Site Plus, BioMuta and dSysMap can be explored interactively at sequence and structural level.
All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::c19a3b09038f2ac4bddc78fcd6846eca&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=__bioTools__::c19a3b09038f2ac4bddc78fcd6846eca&type=result"></script>'); --> </script>
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