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description Publicationkeyboard_double_arrow_right Preprint , Article 2021 FrancePublisher:Cold Spring Harbor Laboratory Authors: Aude Ratier; Sandrine Charles;Aude Ratier; Sandrine Charles;ABSTRACTRegulatory bodies requires evaluation of bioaccumulation of chemicals within organisms with the objective to better assess risks linked to the toxicity of active substances. To this end, toxicokinetic (TK) data are particularly useful to relate the chemical exposure concentration to the accumulation and depuration processes happening within organisms. The bioaccumulative property of substances is quantified by bioaccumulation metrics obtained by fitting TK models to data collected from bioaccumulation tests. The internal concentrations of the studied substances are measured within organisms at regular time points during both accumulation and depuration phases, and their time course is captured by TK models thus providing bioaccumulation metrics. Still today, raw TK data remain difficult to access, as most of the time provided within papers in plots only. To increase accessibility to TK data, we present in this paper a wide collection of raw data sets extracted from the scientific literature in support of TK modelling to be performed with the MOSAICbioacc web application (https://mosaic.univ-lyon1.fr/bioacc/).
Scientific Data arrow_drop_down INRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPreprint . 2021License: CC BY NC NDFull-Text: https://hal.science/hal-03362531/documentadd 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=10.1101/2021.04.15.439942&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Scientific Data arrow_drop_down INRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPreprint . 2021License: CC BY NC NDFull-Text: https://hal.science/hal-03362531/documentadd 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=10.1101/2021.04.15.439942&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint , Article 2020 FrancePublisher:Cold Spring Harbor Laboratory Funded by:ANR | H2O'LYON, ANR | APPROveANR| H2O'LYON ,ANR| APPROveAude Ratier; Christelle Lopes; Gauthier Multari; Vanessa Mazerolles; Patrice Carpentier; Sandrine Charles;pmid: 33982382
AbstractToday, only few ready‐to‐use and convenient decision‐making tools are available in ecotoxicology concerning accumulation and effects of chemical substances on organisms, accounting for exposure situations that are known to be complex (routes of exposure, metabolism, mixtures, etc.). This paper presents new perspectives on the generic calculation of bioaccumulation metrics via the innovative web tool MOSAICbioacc (http://mosaic.univ‐lyon1.fr/bioacc). MOSAICbioacc provides all kinds of bioaccumulation metrics associated with their uncertainty whatever the species‐compound combination. MOSAICbioacc expects accumulation‐depuration data as inputs, even with complex exposure and clearance patterns, to quickly perform their relevant analysis. MOSAICbioacc intends to facilitate the daily work of regulators, or any ecotoxicologist, who will freely benefit from a user‐friendly online interface that automatically fits toxicokinetic models without need for users to invest in the technical aspects to get bioaccumulation metrics estimates. MOSAICbioacc also provides all results in a fully transparent way to ensure reproducibility. Integr Environ Assess Manag 2022;18:10–18. © 2021 SETAC
https://www.biorxiv.... arrow_drop_down Integrated Environmental Assessment and ManagementArticle . 2021 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: CrossrefIntegrated Environmental Assessment and ManagementArticle . 2021Data sources: Europe PubMed Centraladd 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=10.1101/2020.07.07.185835&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 11 citations 11 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert https://www.biorxiv.... arrow_drop_down Integrated Environmental Assessment and ManagementArticle . 2021 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: CrossrefIntegrated Environmental Assessment and ManagementArticle . 2021Data sources: Europe PubMed Centraladd 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=10.1101/2020.07.07.185835&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 FranceVallenet, David; Calteau, Alexandra; Dubois, Mathieu; Amours, Paul; Bazin, Adelme; Beuvin, Mylène; BURLOT, Laura; Bussell, Xavier; Fouteau, Stéphanie; Gautreau, Guillaume; Lajus, Aurélie; Langlois, Jordan; Planel, Rémi; Roche, David; Rollin, Johan; Rouy, Zoe; Sabatet, Valentin; Médigue, Claudine;pmid: 31647104
pmc: PMC7145621
International audience; Abstract Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Here we present new improvements of the MicroScope user interface for genome selection, navigation and expert gene annotation. Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions. We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. To date, MicroScope contains data for >11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (>4500 personal accounts in September 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7145621Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-PasteurArticle . 2019add 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=PMC7145621&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 109 citations 109 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7145621Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-PasteurArticle . 2019add 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=PMC7145621&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 Denmark, Italy, Norway, Denmark, Netherlands, Denmark, Spain, France, Netherlands, Sweden, Netherlands EnglishPublisher:Springer Science and Business Media LLC Funded by:EC | OLISSIPO, EC | ELIXIR-EXCELERATE, WTEC| OLISSIPO ,EC| ELIXIR-EXCELERATE ,WTJon Ison; Hans Ienasescu; Piotr Jaroslaw Chmura; Emil Karol Rydza; Hervé Ménager; Matúš Kalaš; Veit Schwämmle; Björn Grüning; Niall Beard; Rodrigo Lopez; Séverine Duvaud; Heinz Stockinger; Bengt Persson; Radka Svobodová Vařeková; Tomáš Raček; Jiří Vondrášek; Hedi Peterson; Ahto Salumets; Inge Jonassen; Rob Hooft; Tommi Nyrönen; Alfonso Valencia; Salvador Capella; Josep Lluís Gelpí; Federico Zambelli; Babis Savakis; Brane Leskošek; Kristoffer Rapacki; Christophe Blanchet; Rafael C. Jimenez; Arlindo L. Oliveira; Gert Vriend; Olivier Collin; Jacques van Helden; Peter Løngreen; Søren Brunak;Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Contains fulltext : 208582.pdf (Publisher’s version ) (Open Access)
NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd 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=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 56visibility views 56 download downloads 103 Powered bymore_vert NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd 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=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 France EnglishPublisher:BioMed Central Funded by:ANR | IFB (ex Renabi-IFB), ANR | RESETANR| IFB (ex Renabi-IFB) ,ANR| RESETAuthors: Martin, Yannick; Page, Michel; Blanchet, Christophe; de Jong, Hidde;Martin, Yannick; Page, Michel; Blanchet, Christophe; de Jong, Hidde;pmc: PMC6558888
pmid: 31185910
Background Fluorescent reporter genes have become widely used for monitoring gene expression in living cells. When a microbial strain carrying a reporter gene is grown in a microplate reader, the fluorescence and the absorbance (optical density) of the culture can be automatically measured every few minutes in a highly parallelized way. The extraction of useful information from the resulting large amounts of data is not easy to achieve, because the fluorescence and absorbance measurements are only indirectly related to promoter activities and protein concentrations, requiring mathematical models of the expression of reporter genes for their interpretation. Although the principles of the analysis of reporter gene data are well-established today, there is a lack of general-purpose bioinformatics tools based on generic measurement models and sound inference procedures. This has motivated the development of WellInverter, a web application based on well-known methods for regularized linear inversion. Results We present a new version of WellInverter that considerably improves the performance and usability of the original application. In particular, we have put in place a parallel computing architecture with a load balancer to distribute analysis queries over several back-end servers, we have completely redesigned the graphical user interface to better support the different analysis steps, and we have developed a plug-in system for the parsing of data files produced by microplate readers from different manufacturers. We illustrate the functioning of WellInverter by analyzing data of the expression of a fluorescent reporter gene controlled by a phage promoter in growing Escherichia coli populations. We show that the expression pattern in different growth media, supporting different growth rates, corresponds to the pattern expected for a constitutive gene. Conclusions The new version of WellInverter is a robust, easy-to-use and scalable web application, which has been deployed on two publicly accessible web servers and which can also be installed locally. A demo version of the application with two sample datasets is available on-line. Electronic supplementary material The online version of this article (10.1186/s12859-019-2920-4) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6558888Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2019add 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=PMC6558888&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6558888Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2019add 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=PMC6558888&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 FrancePublisher:Oxford University Press (OUP) Authors: Ruiz Echartea, Maria Elisa; Chauvot de Beauchêne, Isaure; Ritchie, David;Ruiz Echartea, Maria Elisa; Chauvot de Beauchêne, Isaure; Ritchie, David;pmid: 31125060
Abstract Motivation Protein–protein docking algorithms aim to predict the 3D structure of a binary complex using the structures of the individual proteins. This typically involves searching and scoring in a 6D space. Many docking algorithms use FFT techniques to exhaustively cover the search space and to accelerate the scoring calculation. However, FFT docking results often depend on the initial protein orientations with respect to the Fourier sampling grid. Furthermore, Fourier-transforming a physics-base force field can involve a serious loss of precision. Results Here, we present EROS-DOCK, an algorithm to rigidly dock two proteins using a series of exhaustive 3D rotational searches in which non-clashing orientations are scored using the ATTRACT coarse-grained force field model. The rotational space is represented as a quaternion ‘π-ball’, which is systematically sub-divided in a ‘branch-and-bound’ manner, allowing efficient pruning of rotations that will give steric clashes. The algorithm was tested on 173 Docking Benchmark complexes, and results were compared with those of ATTRACT and ZDOCK. According to the CAPRI quality criteria, EROS-DOCK typically gives more acceptable or medium quality solutions than ATTRACT and ZDOCK. Availability and implementation The EROS-DOCK program is available for download at http://erosdock.loria.fr. Supplementary information Supplementary data are available at Bioinformatics online.
Bioinformatics arrow_drop_down BioinformaticsArticle . 2019 . Peer-reviewedLicense: OUP Standard Publication ReuseData sources: Crossrefadd 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=10.1093/bioinformatics/btz434&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routeshybrid 9 citations 9 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Bioinformatics arrow_drop_down BioinformaticsArticle . 2019 . Peer-reviewedLicense: OUP Standard Publication ReuseData sources: Crossrefadd 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=10.1093/bioinformatics/btz434&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 FrancePublisher:Oxford University Press (OUP) Funded by:ANR | Bip:BipANR| Bip:BipYasaman Karami; Julien Rey; Guillaume Postic; Samuel Murail; Pierre Tufféry; Sjoerd J. de Vries;AbstractLoop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6602439Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2019add 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=10.1093/nar/gkz403&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 31 citations 31 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6602439Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2019add 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=10.1093/nar/gkz403&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Part of book or chapter of book 2019 FrancePublisher:Springer New York Authors: Andrei, Oana; Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno;Andrei, Oana; Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno;International audience; This chapter presents Porgy—an interactive visual environment for rule-based modelling of biochemical systems. We model molecules and molecule interactions as port graphs and port graph rewrite rules, respectively. We use rewriting strategies to control which rules to apply, and where and when to apply them. Our main contributions to rule-based modelling of biochemical systems lie in the strategy language and the associated visual and interactive features offered by Porgy. These features facilitate an exploratory approach to test different ways of applying the rules while recording the model evolution, and tracking and plotting parameters. We illustrate Porgy’s features with a study of the role of a scaffold protein in RAF/MEK/ERK signalling.
Hal-Diderot arrow_drop_down Hal-DiderotPart of book or chapter of book . 2019https://doi.org/10.1007/978-1-...Part of book or chapter of book . 2019 . Peer-reviewedLicense: Springer TDMData sources: CrossrefINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPart of book or chapter of book . 2019Full-Text: https://hal.science/hal-01429890/documentadd 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=10.1007/978-1-4939-9102-0_3&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Hal-Diderot arrow_drop_down Hal-DiderotPart of book or chapter of book . 2019https://doi.org/10.1007/978-1-...Part of book or chapter of book . 2019 . Peer-reviewedLicense: Springer TDMData sources: CrossrefINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPart of book or chapter of book . 2019Full-Text: https://hal.science/hal-01429890/documentadd 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=10.1007/978-1-4939-9102-0_3&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2018 FranceAuthors: Zaharia, Alexandra; Labedan, Bernard; Froidevaux, Christine; Denise, Alain;Zaharia, Alexandra; Labedan, Bernard; Froidevaux, Christine; Denise, Alain;pmid: 30630411
pmc: PMC6327494
Background In systems biology, there is an acute need for integrative approaches in heterogeneous network mining in order to exploit the continuous flux of genomic data. Simultaneous analysis of the metabolic pathways and genomic context of a given species leads to the identification of patterns consisting in reaction chains catalyzed by products of neighboring genes. Similar such patterns across several species can reveal their mode of conservation throughout the tree of life. Results We present CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods), a novel method that identifies metabolic and genomic patterns consisting in maximal trails of reactions being catalyzed by products of neighboring genes. Patterns determined by CoMetGeNe in one species are subsequently employed in order to reflect their degree of conservation across multiple prokaryotic species. These interspecies comparisons help to improve genome annotation and can reveal putative alternative metabolic routes as well as unexpected gene ordering occurrences. Conclusions CoMetGeNe is an exploratory tool at both the genomic and the metabolic levels, leading to insights into the conservation of functionally related clusters of neighboring enzyme-coding genes. The open-source CoMetGeNe pipeline is freely available at https://cometgene.lri.fr. Electronic supplementary material The online version of this article (10.1186/s12859-018-2542-2) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6327494Data sources: PubMed CentralHyper Article en Ligne; Mémoires en Sciences de l'Information et de la Communication; HAL-CEAOther literature type . Article . 2019add 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=PMC6327494&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6327494Data sources: PubMed CentralHyper Article en Ligne; Mémoires en Sciences de l'Information et de la Communication; HAL-CEAOther literature type . Article . 2019add 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=PMC6327494&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2018 FrancePublisher:The Open Journal Authors: Bryan Brancotte; Christophe Blanchet; Hervé Ménager;Bryan Brancotte; Christophe Blanchet; Hervé Ménager;doi: 10.21105/joss.00698
International audience; The EDAM Browser is a client-side web-based visualization javascript widget for the navigation of the EDAM ontology (Ison et al. 2013). EDAM is a structured and controlled vocabulary describing bioinformatics and computational biology concepts. It is used to annotate resource descriptions (tools, web services) for discovery (Ison et al. 2015) and integration in platforms such as galaxy (Afgan et al. 2016). The EDAM Browser provides users a simple and performant interface to explore EDAM when annotating or searching for bioinformatics resources. User interface and functionalities The user interface (see Fig. 1) is divided in two main panels, a tree representation of the ontology on the left, and a properties card on the right. The tree on the left represents the different parts of the ontology (formats, data, operations and topics). By expanding or closing the nodes, users explore the hierarchy of the EDAM concepts. The selected concept is displayed in bold, and all the path(s) leading from the root to it are highlighted. The properties card panel on the right displays the main properties of the concept, such as its definition, comments, synonyms, and its non-hierarchical relations to other concepts (e.g. an operation has inputs, outputs, and belongs to a given topic). It also includes counts and links to entries in various databases that use this term, such as bio.tools, BioSphere (Brancotte et al. 2017), BioWeb and TeSS. The user may directly suggest a modification on a concept by clicking on the "edit" icons at the top-right corner of this panel ; creating a new concept is also possible thanks to the "add a child" button. Both lead the user to a form that directly formats suggestions as github issues ready to be submitted by the user (see Fig. 2). Additional components of the interface include a full-text search box to search for concepts on their names, synonyms or descriptions; a navigation toolbar to toggle the display of specific parts of the ontology only, or load locally modified versions of the ontology; and a history stack of the concepts that have been seen previously to the one currently selected, below the properties card panel.
Journal of Open Sour... arrow_drop_down add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess Routesgold 2 citations 2 popularity Average influence Average impulse Average Powered by BIP!more_vert Journal of Open Sour... arrow_drop_down add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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description Publicationkeyboard_double_arrow_right Preprint , Article 2021 FrancePublisher:Cold Spring Harbor Laboratory Authors: Aude Ratier; Sandrine Charles;Aude Ratier; Sandrine Charles;ABSTRACTRegulatory bodies requires evaluation of bioaccumulation of chemicals within organisms with the objective to better assess risks linked to the toxicity of active substances. To this end, toxicokinetic (TK) data are particularly useful to relate the chemical exposure concentration to the accumulation and depuration processes happening within organisms. The bioaccumulative property of substances is quantified by bioaccumulation metrics obtained by fitting TK models to data collected from bioaccumulation tests. The internal concentrations of the studied substances are measured within organisms at regular time points during both accumulation and depuration phases, and their time course is captured by TK models thus providing bioaccumulation metrics. Still today, raw TK data remain difficult to access, as most of the time provided within papers in plots only. To increase accessibility to TK data, we present in this paper a wide collection of raw data sets extracted from the scientific literature in support of TK modelling to be performed with the MOSAICbioacc web application (https://mosaic.univ-lyon1.fr/bioacc/).
Scientific Data arrow_drop_down INRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPreprint . 2021License: CC BY NC NDFull-Text: https://hal.science/hal-03362531/documentadd 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=10.1101/2021.04.15.439942&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesgold 8 citations 8 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Scientific Data arrow_drop_down INRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPreprint . 2021License: CC BY NC NDFull-Text: https://hal.science/hal-03362531/documentadd 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=10.1101/2021.04.15.439942&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Preprint , Article 2020 FrancePublisher:Cold Spring Harbor Laboratory Funded by:ANR | H2O'LYON, ANR | APPROveANR| H2O'LYON ,ANR| APPROveAude Ratier; Christelle Lopes; Gauthier Multari; Vanessa Mazerolles; Patrice Carpentier; Sandrine Charles;pmid: 33982382
AbstractToday, only few ready‐to‐use and convenient decision‐making tools are available in ecotoxicology concerning accumulation and effects of chemical substances on organisms, accounting for exposure situations that are known to be complex (routes of exposure, metabolism, mixtures, etc.). This paper presents new perspectives on the generic calculation of bioaccumulation metrics via the innovative web tool MOSAICbioacc (http://mosaic.univ‐lyon1.fr/bioacc). MOSAICbioacc provides all kinds of bioaccumulation metrics associated with their uncertainty whatever the species‐compound combination. MOSAICbioacc expects accumulation‐depuration data as inputs, even with complex exposure and clearance patterns, to quickly perform their relevant analysis. MOSAICbioacc intends to facilitate the daily work of regulators, or any ecotoxicologist, who will freely benefit from a user‐friendly online interface that automatically fits toxicokinetic models without need for users to invest in the technical aspects to get bioaccumulation metrics estimates. MOSAICbioacc also provides all results in a fully transparent way to ensure reproducibility. Integr Environ Assess Manag 2022;18:10–18. © 2021 SETAC
https://www.biorxiv.... arrow_drop_down Integrated Environmental Assessment and ManagementArticle . 2021 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: CrossrefIntegrated Environmental Assessment and ManagementArticle . 2021Data sources: Europe PubMed Centraladd 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=10.1101/2020.07.07.185835&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 11 citations 11 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert https://www.biorxiv.... arrow_drop_down Integrated Environmental Assessment and ManagementArticle . 2021 . Peer-reviewedLicense: Wiley Online Library User AgreementData sources: CrossrefIntegrated Environmental Assessment and ManagementArticle . 2021Data sources: Europe PubMed Centraladd 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=10.1101/2020.07.07.185835&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 FranceVallenet, David; Calteau, Alexandra; Dubois, Mathieu; Amours, Paul; Bazin, Adelme; Beuvin, Mylène; BURLOT, Laura; Bussell, Xavier; Fouteau, Stéphanie; Gautreau, Guillaume; Lajus, Aurélie; Langlois, Jordan; Planel, Rémi; Roche, David; Rollin, Johan; Rouy, Zoe; Sabatet, Valentin; Médigue, Claudine;pmid: 31647104
pmc: PMC7145621
International audience; Abstract Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Here we present new improvements of the MicroScope user interface for genome selection, navigation and expert gene annotation. Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions. We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. To date, MicroScope contains data for >11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (>4500 personal accounts in September 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7145621Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-PasteurArticle . 2019add 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=PMC7145621&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen 109 citations 109 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC7145621Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-PasteurArticle . 2019add 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=PMC7145621&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 Denmark, Italy, Norway, Denmark, Netherlands, Denmark, Spain, France, Netherlands, Sweden, Netherlands EnglishPublisher:Springer Science and Business Media LLC Funded by:EC | OLISSIPO, EC | ELIXIR-EXCELERATE, WTEC| OLISSIPO ,EC| ELIXIR-EXCELERATE ,WTJon Ison; Hans Ienasescu; Piotr Jaroslaw Chmura; Emil Karol Rydza; Hervé Ménager; Matúš Kalaš; Veit Schwämmle; Björn Grüning; Niall Beard; Rodrigo Lopez; Séverine Duvaud; Heinz Stockinger; Bengt Persson; Radka Svobodová Vařeková; Tomáš Raček; Jiří Vondrášek; Hedi Peterson; Ahto Salumets; Inge Jonassen; Rob Hooft; Tommi Nyrönen; Alfonso Valencia; Salvador Capella; Josep Lluís Gelpí; Federico Zambelli; Babis Savakis; Brane Leskošek; Kristoffer Rapacki; Christophe Blanchet; Rafael C. Jimenez; Arlindo L. Oliveira; Gert Vriend; Olivier Collin; Jacques van Helden; Peter Løngreen; Søren Brunak;Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Contains fulltext : 208582.pdf (Publisher’s version ) (Open Access)
NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd 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=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 56visibility views 56 download downloads 103 Powered bymore_vert NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd 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=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 France EnglishPublisher:BioMed Central Funded by:ANR | IFB (ex Renabi-IFB), ANR | RESETANR| IFB (ex Renabi-IFB) ,ANR| RESETAuthors: Martin, Yannick; Page, Michel; Blanchet, Christophe; de Jong, Hidde;Martin, Yannick; Page, Michel; Blanchet, Christophe; de Jong, Hidde;pmc: PMC6558888
pmid: 31185910
Background Fluorescent reporter genes have become widely used for monitoring gene expression in living cells. When a microbial strain carrying a reporter gene is grown in a microplate reader, the fluorescence and the absorbance (optical density) of the culture can be automatically measured every few minutes in a highly parallelized way. The extraction of useful information from the resulting large amounts of data is not easy to achieve, because the fluorescence and absorbance measurements are only indirectly related to promoter activities and protein concentrations, requiring mathematical models of the expression of reporter genes for their interpretation. Although the principles of the analysis of reporter gene data are well-established today, there is a lack of general-purpose bioinformatics tools based on generic measurement models and sound inference procedures. This has motivated the development of WellInverter, a web application based on well-known methods for regularized linear inversion. Results We present a new version of WellInverter that considerably improves the performance and usability of the original application. In particular, we have put in place a parallel computing architecture with a load balancer to distribute analysis queries over several back-end servers, we have completely redesigned the graphical user interface to better support the different analysis steps, and we have developed a plug-in system for the parsing of data files produced by microplate readers from different manufacturers. We illustrate the functioning of WellInverter by analyzing data of the expression of a fluorescent reporter gene controlled by a phage promoter in growing Escherichia coli populations. We show that the expression pattern in different growth media, supporting different growth rates, corresponds to the pattern expected for a constitutive gene. Conclusions The new version of WellInverter is a robust, easy-to-use and scalable web application, which has been deployed on two publicly accessible web servers and which can also be installed locally. A demo version of the application with two sample datasets is available on-line. Electronic supplementary material The online version of this article (10.1186/s12859-019-2920-4) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6558888Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2019add 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=PMC6558888&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6558888Data sources: PubMed CentralHAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotArticle . 2019add 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=PMC6558888&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 FrancePublisher:Oxford University Press (OUP) Authors: Ruiz Echartea, Maria Elisa; Chauvot de Beauchêne, Isaure; Ritchie, David;Ruiz Echartea, Maria Elisa; Chauvot de Beauchêne, Isaure; Ritchie, David;pmid: 31125060
Abstract Motivation Protein–protein docking algorithms aim to predict the 3D structure of a binary complex using the structures of the individual proteins. This typically involves searching and scoring in a 6D space. Many docking algorithms use FFT techniques to exhaustively cover the search space and to accelerate the scoring calculation. However, FFT docking results often depend on the initial protein orientations with respect to the Fourier sampling grid. Furthermore, Fourier-transforming a physics-base force field can involve a serious loss of precision. Results Here, we present EROS-DOCK, an algorithm to rigidly dock two proteins using a series of exhaustive 3D rotational searches in which non-clashing orientations are scored using the ATTRACT coarse-grained force field model. The rotational space is represented as a quaternion ‘π-ball’, which is systematically sub-divided in a ‘branch-and-bound’ manner, allowing efficient pruning of rotations that will give steric clashes. The algorithm was tested on 173 Docking Benchmark complexes, and results were compared with those of ATTRACT and ZDOCK. According to the CAPRI quality criteria, EROS-DOCK typically gives more acceptable or medium quality solutions than ATTRACT and ZDOCK. Availability and implementation The EROS-DOCK program is available for download at http://erosdock.loria.fr. Supplementary information Supplementary data are available at Bioinformatics online.
Bioinformatics arrow_drop_down BioinformaticsArticle . 2019 . Peer-reviewedLicense: OUP Standard Publication ReuseData sources: Crossrefadd 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=10.1093/bioinformatics/btz434&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routeshybrid 9 citations 9 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Bioinformatics arrow_drop_down BioinformaticsArticle . 2019 . Peer-reviewedLicense: OUP Standard Publication ReuseData sources: Crossrefadd 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=10.1093/bioinformatics/btz434&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 FrancePublisher:Oxford University Press (OUP) Funded by:ANR | Bip:BipANR| Bip:BipYasaman Karami; Julien Rey; Guillaume Postic; Samuel Murail; Pierre Tufféry; Sjoerd J. de Vries;AbstractLoop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6602439Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2019add 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=10.1093/nar/gkz403&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 31 citations 31 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6602439Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2019add 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=10.1093/nar/gkz403&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Part of book or chapter of book 2019 FrancePublisher:Springer New York Authors: Andrei, Oana; Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno;Andrei, Oana; Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno;International audience; This chapter presents Porgy—an interactive visual environment for rule-based modelling of biochemical systems. We model molecules and molecule interactions as port graphs and port graph rewrite rules, respectively. We use rewriting strategies to control which rules to apply, and where and when to apply them. Our main contributions to rule-based modelling of biochemical systems lie in the strategy language and the associated visual and interactive features offered by Porgy. These features facilitate an exploratory approach to test different ways of applying the rules while recording the model evolution, and tracking and plotting parameters. We illustrate Porgy’s features with a study of the role of a scaffold protein in RAF/MEK/ERK signalling.
Hal-Diderot arrow_drop_down Hal-DiderotPart of book or chapter of book . 2019https://doi.org/10.1007/978-1-...Part of book or chapter of book . 2019 . Peer-reviewedLicense: Springer TDMData sources: CrossrefINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPart of book or chapter of book . 2019Full-Text: https://hal.science/hal-01429890/documentadd 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=10.1007/978-1-4939-9102-0_3&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Hal-Diderot arrow_drop_down Hal-DiderotPart of book or chapter of book . 2019https://doi.org/10.1007/978-1-...Part of book or chapter of book . 2019 . Peer-reviewedLicense: Springer TDMData sources: CrossrefINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPart of book or chapter of book . 2019Full-Text: https://hal.science/hal-01429890/documentadd 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=10.1007/978-1-4939-9102-0_3&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2018 FranceAuthors: Zaharia, Alexandra; Labedan, Bernard; Froidevaux, Christine; Denise, Alain;Zaharia, Alexandra; Labedan, Bernard; Froidevaux, Christine; Denise, Alain;pmid: 30630411
pmc: PMC6327494
Background In systems biology, there is an acute need for integrative approaches in heterogeneous network mining in order to exploit the continuous flux of genomic data. Simultaneous analysis of the metabolic pathways and genomic context of a given species leads to the identification of patterns consisting in reaction chains catalyzed by products of neighboring genes. Similar such patterns across several species can reveal their mode of conservation throughout the tree of life. Results We present CoMetGeNe (COnserved METabolic and GEnomic NEighborhoods), a novel method that identifies metabolic and genomic patterns consisting in maximal trails of reactions being catalyzed by products of neighboring genes. Patterns determined by CoMetGeNe in one species are subsequently employed in order to reflect their degree of conservation across multiple prokaryotic species. These interspecies comparisons help to improve genome annotation and can reveal putative alternative metabolic routes as well as unexpected gene ordering occurrences. Conclusions CoMetGeNe is an exploratory tool at both the genomic and the metabolic levels, leading to insights into the conservation of functionally related clusters of neighboring enzyme-coding genes. The open-source CoMetGeNe pipeline is freely available at https://cometgene.lri.fr. Electronic supplementary material The online version of this article (10.1186/s12859-018-2542-2) contains supplementary material, which is available to authorized users.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6327494Data sources: PubMed CentralHyper Article en Ligne; Mémoires en Sciences de l'Information et de la Communication; HAL-CEAOther literature type . Article . 2019add 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=PMC6327494&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6327494Data sources: PubMed CentralHyper Article en Ligne; Mémoires en Sciences de l'Information et de la Communication; HAL-CEAOther literature type . Article . 2019add 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=PMC6327494&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2018 FrancePublisher:The Open Journal Authors: Bryan Brancotte; Christophe Blanchet; Hervé Ménager;Bryan Brancotte; Christophe Blanchet; Hervé Ménager;doi: 10.21105/joss.00698
International audience; The EDAM Browser is a client-side web-based visualization javascript widget for the navigation of the EDAM ontology (Ison et al. 2013). EDAM is a structured and controlled vocabulary describing bioinformatics and computational biology concepts. It is used to annotate resource descriptions (tools, web services) for discovery (Ison et al. 2015) and integration in platforms such as galaxy (Afgan et al. 2016). The EDAM Browser provides users a simple and performant interface to explore EDAM when annotating or searching for bioinformatics resources. User interface and functionalities The user interface (see Fig. 1) is divided in two main panels, a tree representation of the ontology on the left, and a properties card on the right. The tree on the left represents the different parts of the ontology (formats, data, operations and topics). By expanding or closing the nodes, users explore the hierarchy of the EDAM concepts. The selected concept is displayed in bold, and all the path(s) leading from the root to it are highlighted. The properties card panel on the right displays the main properties of the concept, such as its definition, comments, synonyms, and its non-hierarchical relations to other concepts (e.g. an operation has inputs, outputs, and belongs to a given topic). It also includes counts and links to entries in various databases that use this term, such as bio.tools, BioSphere (Brancotte et al. 2017), BioWeb and TeSS. The user may directly suggest a modification on a concept by clicking on the "edit" icons at the top-right corner of this panel ; creating a new concept is also possible thanks to the "add a child" button. Both lead the user to a form that directly formats suggestions as github issues ready to be submitted by the user (see Fig. 2). Additional components of the interface include a full-text search box to search for concepts on their names, synonyms or descriptions; a navigation toolbar to toggle the display of specific parts of the ontology only, or load locally modified versions of the ontology; and a history stack of the concepts that have been seen previously to the one currently selected, below the properties card panel.
Journal of Open Sour... arrow_drop_down add 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.
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For further information contact us at helpdesk@openaire.euAccess Routesgold 2 citations 2 popularity Average influence Average impulse Average Powered by BIP!more_vert Journal of Open Sour... arrow_drop_down add 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=10.21105/joss.00698&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu