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ORCIDBibTeX records: Matús Kalas
@article{DBLP:journals/f1000research/WaterhouseABBHHJKLPPPRBG23,
author = {Robert M. Waterhouse and
Anne{-}Fran{\c{c}}oise Adam{-}Blondon and
Bachir Balech and
Endre Barta and
Katharina F. Heil and
Graham M. Hughes and
Lars S. Jermiin and
Mat{\'{u}}s Kalas and
Jerry Lanfear and
Evangelos Pafilis and
Aristotelis C. Papageorgiou and
Fotis E. Psomopoulos and
Niels Raes and
Josephine Burgin and
Toni Gabald{\'{o}}n},
title = {The {ELIXIR} Biodiversity Community: Understanding short- and long-term
changes in biodiversity},
journal = {F1000Research},
volume = {12},
pages = {499},
year = {2023},
url = {https://doi.org/10.12688/f1000research.133724.1},
doi = {10.12688/F1000RESEARCH.133724.1},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/f1000research/WaterhouseABBHHJKLPPPRBG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dint/Serrano-SolanoF22,
author = {Beatriz Serrano{-}Solano and
Anne Fouilloux and
Ignacio Eguinoa and
Mat{\'{u}}s Kalas and
Bj{\"{o}}rn A. Gr{\"{u}}ning and
Frederik Coppens},
title = {Galaxy: {A} Decade of Realising {CWFR} Concepts},
journal = {Data Intell.},
volume = {4},
number = {2},
pages = {358--371},
year = {2022},
url = {https://doi.org/10.1162/dint\_a\_00136},
doi = {10.1162/DINT\_A\_00136},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dint/Serrano-SolanoF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ShaikhSVMWAAAAB22,
author = {Bilal Shaikh and
Lucian P. Smith and
Dan Vasilescu and
Gnaneswara Marupilla and
Michael Wilson and
Eran Agmon and
Henry Agnew and
Steven S. Andrews and
Azraf Anwar and
Moritz E. Beber and
Frank T. Bergmann and
David Brooks and
Lutz Brusch and
Laurence Calzone and
Kiri Choi and
Joshua Cooper and
John Detloff and
Brian Drawert and
Michel Dumontier and
G. Bard Ermentrout and
James R. Faeder and
Andrew P. Freiburger and
Fabian Fr{\"{o}}hlich and
Akira Funahashi and
Alan Garny and
John H. Gennari and
Padraig Gleeson and
Anne Goelzer and
Zachary B. Haiman and
Jan Hasenauer and
Joseph L. Hellerstein and
Henning Hermjakob and
Stefan Hoops and
Jon C. Ison and
Diego Jahn and
Henry V. Jakubowski and
Ryann Jordan and
Mat{\'{u}}s Kalas and
Matthias K{\"{o}}nig and
Wolfram Liebermeister and
Rahuman S. Malik{-}Sheriff and
Synchon Mandal and
Robert A. McDougal and
J. Kyle Medley and
Pedro Mendes and
Robert M{\"{u}}ller and
Chris J. Myers and
Aur{\'{e}}lien Naldi and
Tung V. N. Nguyen and
David P. Nickerson and
Brett G. Olivier and
Drashti Patoliya and
Lo{\"{\i}}c Paulev{\'{e}} and
Linda R. Petzold and
Ankita Priya and
Anand K. Rampadarath and
Johann M. Rohwer and
Ali S. Saglam and
Dilawar Singh and
Ankur Sinha and
Jacky L. Snoep and
Hugh Sorby and
Ryan K. Spangler and
J{\"{o}}rn Starru{\ss} and
Payton J. Thomas and
David D. van Niekerk and
Daniel Weindl and
Fengkai Zhang and
Anna Zhukova and
Arthur P. Goldberg and
James C. Schaff and
Michael L. Blinov and
Herbert M. Sauro and
Ion I. Moraru and
Jonathan R. Karr},
title = {BioSimulators: a central registry of simulation engines and services
for recommending specific tools},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {108--114},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac331},
doi = {10.1093/NAR/GKAC331},
timestamp = {Tue, 24 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ShaikhSVMWAAAAB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-06732,
author = {Bilal Shaikh and
Lucian P. Smith and
Dan Vasilescu and
Gnaneswara Marupilla and
Michael Wilson and
Eran Agmon and
Henry Agnew and
Steven S. Andrews and
Azraf Anwar and
Moritz E. Beber and
Frank T. Bergmann and
David Brooks and
Lutz Brusch and
Laurence Calzone and
Kiri Choi and
Joshua Cooper and
John Detloff and
Brian Drawert and
Michel Dumontier and
G. Bard Ermentrout and
James R. Faeder and
Andrew P. Freiburger and
Fabian Fr{\"{o}}hlich and
Akira Funahashi and
Alan Garny and
John H. Gennari and
Padraig Gleeson and
Anne Goelzer and
Zachary B. Haiman and
Joseph L. Hellerstein and
Stefan Hoops and
Jon C. Ison and
Diego Jahn and
Henry V. Jakubowski and
Ryann Jordan and
Mat{\'{u}}s Kalas and
Matthias K{\"{o}}nig and
Wolfram Liebermeister and
Synchon Mandal and
Robert A. McDougal and
J. Kyle Medley and
Pedro Mendes and
Robert M{\"{u}}ller and
Chris J. Myers and
Aur{\'{e}}lien Naldi and
Tung V. N. Nguyen and
David P. Nickerson and
Brett G. Olivier and
Drashti Patoliya and
Lo{\"{\i}}c Paulev{\'{e}} and
Linda R. Petzold and
Ankita Priya and
Anand K. Rampadarath and
Johann M. Rohwer and
Ali S. Saglam and
Dilawar Singh and
Ankur Sinha and
Jacky L. Snoep and
Hugh Sorby and
Ryan K. Spangler and
J{\"{o}}rn Starru{\ss} and
Payton J. Thomas and
David D. van Niekerk and
Daniel Weindl and
Fengkai Zhang and
Anna Zhukova and
Arthur P. Goldberg and
Michael L. Blinov and
Herbert M. Sauro and
Ion I. Moraru and
Jonathan R. Karr},
title = {BioSimulators: a central registry of simulation engines and services
for recommending specific tools},
journal = {CoRR},
volume = {abs/2203.06732},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2203.06732},
doi = {10.48550/ARXIV.2203.06732},
eprinttype = {arXiv},
eprint = {2203.06732},
timestamp = {Tue, 24 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2203-06732.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/PaulGilloteauxTHGMMBKKZMC21,
author = {Perrine Paul{-}Gilloteaux and
S{\'{e}}bastien Tosi and
Jean{-}Karim H{\'{e}}rich{\'{e}} and
Alban Gaignard and
Herv{\'{e}} M{\'{e}}nager and
Rapha{\"{e}}l Mar{\'{e}}e and
Volker B{\"{a}}cker and
Anna H. Klemm and
Mat{\'{u}}s Kalas and
Chong Zhang and
Kota Miura and
Julien Colombelli},
title = {Bioimage analysis workflows: community resources to navigate through
a complex ecosystem},
journal = {F1000Research},
volume = {10},
pages = {320},
year = {2021},
url = {https://doi.org/10.12688/f1000research.52569.1},
doi = {10.12688/F1000RESEARCH.52569.1},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/PaulGilloteauxTHGMMBKKZMC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/LamprechtPISMABACCCGGGGIJ21,
author = {Anna{-}Lena Lamprecht and
Magnus Palmblad and
Jon C. Ison and
Veit Schw{\"{a}}mmle and
Mohammad Sadnan Al Manir and
Ilkay Altintas and
Christopher J. O. Baker and
Ammar Ben Hadj Amor and
Salvador Capella{-}Guti{\'{e}}rrez and
Paulos Charonyktakis and
Michael R. Crusoe and
Yolanda Gil and
Carole A. Goble and
Timothy J. Griffin and
Paul Groth and
Hans Ienasescu and
Pratik D. Jagtap and
Mat{\'{u}}s Kalas and
Vedran Kasalica and
Alireza Khanteymoori and
Tobias Kuhn and
Hailiang Mei and
Herv{\'{e}} M{\'{e}}nager and
Steffen M{\"{o}}ller and
Robin A. Richardson and
Vincent Robert and
Stian Soiland{-}Reyes and
Robert Stevens and
Szaniszlo Szoke and
Suzan Verberne and
Aswin Verhoeven and
Katherine Wolstencroft},
title = {Perspectives on automated composition of workflows in the life sciences},
journal = {F1000Research},
volume = {10},
pages = {897},
year = {2021},
url = {https://doi.org/10.12688/f1000research.54159.1},
doi = {10.12688/F1000RESEARCH.54159.1},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/f1000research/LamprechtPISMABACCCGGGGIJ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/IsonMBJSRLPKCHS20,
author = {Jon C. Ison and
Herv{\'{e}} M{\'{e}}nager and
Bryan Brancotte and
Erik Jaaniso and
Ahto Salumets and
Tom{\'{a}}s Racek and
Anna{-}Lena Lamprecht and
Magnus Palmblad and
Mat{\'{u}}s Kalas and
Piotr Chmura and
John M. Hancock and
Veit Schw{\"{a}}mmle and
Hans{-}Ioan Ienasescu},
title = {Community curation of bioinformatics software and data resources},
journal = {Briefings Bioinform.},
volume = {21},
number = {5},
pages = {1697--1705},
year = {2020},
url = {https://doi.org/10.1093/bib/bbz075},
doi = {10.1093/BIB/BBZ075},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/IsonMBJSRLPKCHS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/TekleGKBRLZAMKRHSFAVHWDNP18,
author = {Kidane M. Tekle and
Sveinung Gundersen and
Kjetil Klepper and
Lars Ailo Bongo and
Inge Alexander Raknes and
Xiaxi Li and
Wei Zhang and
Christian Andreetta and
Teshome Dagne Mulugeta and
Mat{\'{u}}s Kalas and
Morten B. Rye and
Erik Hjerde and
Jeevan Karloss Antony Samy and
Ghislain Fornous and
Abdulrahman Azab and
Dag Inge V{\aa}ge and
Eivind Hovig and
Nils Peder Willassen and
Finn Drabl{\o}s and
St{\aa}le Nyg{\aa}rd and
Kjell Petersen and
Inge Jonassen},
title = {Norwegian e-Infrastructure for Life Sciences (NeLS)},
journal = {F1000Research},
volume = {7},
pages = {968},
year = {2018},
url = {https://doi.org/10.12688/f1000research.15119.1},
doi = {10.12688/F1000RESEARCH.15119.1},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/TekleGKBRLZAMKRHSFAVHWDNP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dase/MollerPWRCPSKBK17,
author = {Steffen M{\"{o}}ller and
Stuart W. Prescott and
Lars Wirzenius and
Petter Reinholdtsen and
Brad Chapman and
Pjotr Prins and
Stian Soiland{-}Reyes and
Fabian Kl{\"{o}}tzl and
Andrea Bagnacani and
Mat{\'{u}}s Kalas and
Andreas Tille and
Michael R. Crusoe},
title = {Robust Cross-Platform Workflows: How Technical and Scientific Communities
Collaborate to Develop, Test and Share Best Practices for Data Analysis},
journal = {Data Sci. Eng.},
volume = {2},
number = {3},
pages = {232--244},
year = {2017},
url = {https://doi.org/10.1007/s41019-017-0050-4},
doi = {10.1007/S41019-017-0050-4},
timestamp = {Tue, 01 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dase/MollerPWRCPSKBK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/IsonRMKRCABBBBB16,
author = {Jon C. Ison and
Kristoffer Rapacki and
Herv{\'{e}} M{\'{e}}nager and
Mat{\'{u}}s Kalas and
Emil Rydza and
Piotr Chmura and
Christian Anthon and
Niall Beard and
Karel Berka and
Dan M. Bolser and
Tim Booth and
Anthony Bretaudeau and
Jan Brezovsky and
Rita Casadio and
Gianni Cesareni and
Frederik Coppens and
Michael Cornell and
Gianmauro Cuccuru and
Kristian Davidsen and
Gianluca Della Vedova and
Tunca Dogan and
Olivia Doppelt{-}Azeroual and
Laura Emery and
Elisabeth Gasteiger and
Thomas Gatter and
Tatyana Goldberg and
Marie Grosjean and
Bj{\"{o}}rn A. Gr{\"{u}}ning and
Manuela Helmer{-}Citterich and
Hans Ienasescu and
Vassilios Ioannidis and
Martin Closter Jespersen and
Rafael C. Jim{\'{e}}nez and
Nick S. Juty and
Peter Juvan and
Maximilian Koch and
Camille Laibe and
Jing{-}Woei Li and
Luana Licata and
Fabien Mareuil and
Ivan Micetic and
Rune M{\o}llegaard Friborg and
S{\'{e}}bastien Moretti and
Chris Morris and
Steffen M{\"{o}}ller and
Aleksandra Nenadic and
Hedi Peterson and
Giuseppe Profiti and
Peter M. Rice and
Paolo Romano and
Paola Roncaglia and
Rabie Saidi and
Andrea Schafferhans and
Veit Schw{\"{a}}mmle and
Callum Smith and
Maria Maddalena Sperotto and
Heinz Stockinger and
Radka Svobodov{\'{a}} Varekov{\'{a}} and
Silvio C. E. Tosatto and
Victor de la Torre and
Paolo Uva and
Allegra Via and
Guy Yachdav and
Federico Zambelli and
Gert Vriend and
Burkhard Rost and
Helen E. Parkinson and
Peter L{\o}ngreen and
S{\o}ren Brunak},
title = {Tools and data services registry: a community effort to document bioinformatics
resources},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {38--47},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1116},
doi = {10.1093/NAR/GKV1116},
timestamp = {Thu, 25 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/IsonRMKRCABBBBB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sttt/MenagerKRI16,
author = {Herv{\'{e}} M{\'{e}}nager and
Mat{\'{u}}s Kalas and
Kristoffer Rapacki and
Jon C. Ison},
title = {Using registries to integrate bioinformatics tools and services into
workbench environments},
journal = {Int. J. Softw. Tools Technol. Transf.},
volume = {18},
number = {6},
pages = {581--586},
year = {2016},
url = {https://doi.org/10.1007/s10009-015-0392-z},
doi = {10.1007/S10009-015-0392-Z},
timestamp = {Thu, 02 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/sttt/MenagerKRI16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KajanHKMR14,
author = {L{\'{a}}szl{\'{o}} Kaj{\'{a}}n and
Thomas A. Hopf and
Mat{\'{u}} Kala and
Debora S. Marks and
Burkhard Rost},
title = {FreeContact: fast and free software for protein contact prediction
from residue co-evolution},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {85},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-85},
doi = {10.1186/1471-2105-15-85},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KajanHKMR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MollerABBBCCGHHKKKPPQSSSSSSSTTGKC14,
author = {Steffen M{\"{o}}ller and
Enis Afgan and
Michael Banck and
Raoul Jean Pierre Bonnal and
Timothy Booth and
John Chilton and
Peter J. A. Cock and
Markus Gumbel and
Nomi L. Harris and
Richard C. G. Holland and
Mat{\'{u}}s Kalas and
L{\'{a}}szl{\'{o}} Kaj{\'{a}}n and
Eri Kibukawa and
David R. Powell and
Pjotr Prins and
Jacqueline Quinn and
Olivier Sallou and
Francesco Strozzi and
Torsten Seemann and
Clare Sloggett and
Stian Soiland{-}Reyes and
William Spooner and
Sascha Steinbiss and
Andreas Tille and
Anthony J. Travis and
Roman Guimera and
Toshiaki Katayama and
Brad A. Chapman},
title = {Community-driven development for computational biology at Sprints,
Hackathons and Codefests},
journal = {{BMC} Bioinform.},
volume = {15},
number = {{S-14}},
pages = {S7},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-S14-S7},
doi = {10.1186/1471-2105-15-S14-S7},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MollerABBBCCGHHKKKPPQSSSSSSSTTGKC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IsonKJBUMMLPR13,
author = {Jon C. Ison and
Mat{\'{u}}s Kalas and
Inge Jonassen and
Dan M. Bolser and
Mahmut Uludag and
Hamish McWilliam and
James Malone and
Rodrigo Lopez and
Steve Pettifer and
Peter M. Rice},
title = {{EDAM:} an ontology of bioinformatics operations, types of data and
identifiers, topics and formats},
journal = {Bioinform.},
volume = {29},
number = {10},
pages = {1325--1332},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt113},
doi = {10.1093/BIOINFORMATICS/BTT113},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/IsonKJBUMMLPR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SandveGJGGHHLNNPRTCDFKLRFH13,
author = {Geir Kjetil Sandve and
Sveinung Gundersen and
Morten Johansen and
Ingrid Kristine Glad and
Krishanthi Gunathasan and
Lars Holden and
Marit Holden and
Knut Liest{\o}l and
St{\aa}le Nyg{\aa}rd and
Vegard Nygaard and
Jonas Paulsen and
Halfdan Rydbeck and
Kai Trengereid and
Trevor Clancy and
Finn Drabl{\o}s and
Egil Ferkingstad and
Mat{\'{u}}s Kalas and
Tonje Lien and
Morten Rye and
Arnoldo Frigessi and
Eivind Hovig},
title = {The Genomic HyperBrowser: an analysis web server for genome-scale
data},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Webserver-Issue},
pages = {133--141},
year = {2013},
url = {https://doi.org/10.1093/nar/gkt342},
doi = {10.1093/NAR/GKT342},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SandveGJGGHHLNNPRTCDFKLRFH13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GundersenKAFHS11,
author = {Sveinung Gundersen and
Mat{\'{u}}s Kalas and
Osman Abul and
Arnoldo Frigessi and
Eivind Hovig and
Geir Kjetil Sandve},
title = {Identifying elemental genomic track types and representing them uniformly},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {494},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-494},
doi = {10.1186/1471-2105-12-494},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GundersenKAFHS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KalasPJBTVPBIBRJ10,
author = {Mat{\'{u}}s Kalas and
P{\aa}l Puntervoll and
Alexandre Joseph and
Edita Bartaseviciute and
Armin T{\"{o}}pfer and
Prabakar Venkataraman and
Steve Pettifer and
Jan Christian Bryne and
Jon C. Ison and
Christophe Blanchet and
Kristoffer Rapacki and
Inge Jonassen},
title = {BioXSD: the common data-exchange format for everyday bioinformatics
web services},
journal = {Bioinform.},
volume = {26},
number = {18},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq391},
doi = {10.1093/BIOINFORMATICS/BTQ391},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KalasPJBTVPBIBRJ10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PettiferIKTMJLFRIPBURBRHSSCBSBACV10,
author = {Steve Pettifer and
Jon C. Ison and
Mat{\'{u}}s Kalas and
Dave Thorne and
Philip McDermott and
Inge Jonassen and
Ali Liaquat and
Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and
Jose Manuel Rodriguez and
David G. Pisano and
Christophe Blanchet and
Mahmut Uludag and
Peter M. Rice and
Edita Bartaseviciute and
Kristoffer Rapacki and
Maarten L. Hekkelman and
Olivier Sand and
Heinz Stockinger and
Andrew B. Clegg and
Erik Bongcam{-}Rudloff and
Jean Salzemann and
Vincent Breton and
Teresa K. Attwood and
Graham Cameron and
Gert Vriend},
title = {The {EMBRACE} web service collection},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Web-Server-Issue},
pages = {683--688},
year = {2010},
url = {https://doi.org/10.1093/nar/gkq297},
doi = {10.1093/NAR/GKQ297},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PettiferIKTMJLFRIPBURBRHSSCBSBACV10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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