BibTeX records: Martin Scharm

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@article{DBLP:journals/bioinformatics/ScharmWJS20,
  author    = {Martin Scharm and
               Olaf Wolkenhauer and
               Mahdi Jalili and
               Ali Salehzadeh{-}Yazdi},
  title     = {GEMtractor: extracting views into genome-scale metabolic models},
  journal   = {Bioinform.},
  volume    = {36},
  number    = {10},
  pages     = {3281--3282},
  year      = {2020},
  url       = {https://doi.org/10.1093/bioinformatics/btaa068},
  doi       = {10.1093/bioinformatics/btaa068},
  timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/bioinformatics/ScharmWJS20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/NealKNMKDACCCCA19,
  author    = {Maxwell Lewis Neal and
               Matthias K{\"{o}}nig and
               David P. Nickerson and
               Goksel Misirli and
               Reza Kalbasi and
               Andreas Dr{\"{a}}ger and
               Koray Atalag and
               Vijayalakshmi Chelliah and
               Michael T. Cooling and
               Daniel L. Cook and
               Sharon M. Crook and
               Miguel de Alba and
               Samuel H. Friedman and
               Alan Garny and
               John H. Gennari and
               Padraig Gleeson and
               Martin Golebiewski and
               Michael Hucka and
               Nick S. Juty and
               Chris J. Myers and
               Brett G. Olivier and
               Herbert M. Sauro and
               Martin Scharm and
               Jacky L. Snoep and
               Vasundra Tour{\'{e}} and
               Anil Wipat and
               Olaf Wolkenhauer and
               Dagmar Waltemath},
  title     = {Harmonizing semantic annotations for computational models in biology},
  journal   = {Briefings Bioinform.},
  volume    = {20},
  number    = {2},
  pages     = {540--550},
  year      = {2019},
  url       = {https://doi.org/10.1093/bib/bby087},
  doi       = {10.1093/bib/bby087},
  timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/bib/NealKNMKDACCCCA19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ScharmGTBSWW18,
  author    = {Martin Scharm and
               Tom Gebhardt and
               Vasundra Tour{\'{e}} and
               Andrea Bagnacani and
               Ali Salehzadeh{-}Yazdi and
               Olaf Wolkenhauer and
               Dagmar Waltemath},
  title     = {Evolution of computational models in BioModels Database and the Physiome
               Model Repository},
  journal   = {{BMC} Syst. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {53:1--53:10},
  year      = {2018},
  url       = {https://doi.org/10.1186/s12918-018-0553-2},
  doi       = {10.1186/s12918-018-0553-2},
  timestamp = {Tue, 05 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/bmcsb/ScharmGTBSWW18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BergmannNWS17,
  author    = {Frank T. Bergmann and
               David P. Nickerson and
               Dagmar Waltemath and
               Martin Scharm},
  title     = {{SED-ML} web tools: generate, modify and export standard-compliant
               simulation studies},
  journal   = {Bioinform.},
  volume    = {33},
  number    = {8},
  pages     = {1253--1254},
  year      = {2017},
  url       = {https://doi.org/10.1093/bioinformatics/btw812},
  doi       = {10.1093/bioinformatics/btw812},
  timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/bioinformatics/BergmannNWS17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ScharmWW16,
  author    = {Martin Scharm and
               Olaf Wolkenhauer and
               Dagmar Waltemath},
  title     = {An algorithm to detect and communicate the differences in computational
               models describing biological systems},
  journal   = {Bioinform.},
  volume    = {32},
  number    = {4},
  pages     = {563--570},
  year      = {2016},
  url       = {https://doi.org/10.1093/bioinformatics/btv484},
  doi       = {10.1093/bioinformatics/btv484},
  timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/bioinformatics/ScharmWW16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/ScharmWMW16,
  author    = {Martin Scharm and
               Dagmar Waltemath and
               Pedro Mendes and
               Olaf Wolkenhauer},
  title     = {{COMODI:} an ontology to characterise differences in versions of computational
               models in biology},
  journal   = {J. Biomed. Semant.},
  volume    = {7},
  pages     = {46},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13326-016-0080-2},
  doi       = {10.1186/s13326-016-0080-2},
  timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/biomedsem/ScharmWMW16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tbe/WaltemathKBCHKL16,
  author    = {Dagmar Waltemath and
               Jonathan R. Karr and
               Frank T. Bergmann and
               Vijayalakshmi Chelliah and
               Michael Hucka and
               Marcus Krantz and
               Wolfram Liebermeister and
               Pedro Mendes and
               Chris J. Myers and
               Pinar Pir and
               Begum Alaybeyoglu and
               Naveen K. Aranganathan and
               Kambiz Baghalian and
               Arne T. Bittig and
               Paulo E. Pinto Burke and
               Matteo Cantarelli and
               Yin Hoon Chew and
               Rafael S. Costa and
               Joseph Cursons and
               Tobias Czauderna and
               Arthur P. Goldberg and
               Harold F. G{\'{o}}mez and
               Jens Hahn and
               Tuure Hameri and
               Daniel F. Hernandez Gardiol and
               Denis Kazakiewicz and
               Ilya Kiselev and
               Vincent Knight{-}Schrijver and
               Christian Kn{\"{u}}pfer and
               Matthias K{\"{o}}nig and
               Daewon Lee and
               Audald Lloret{-}Villas and
               Nikita Mandrik and
               J. Kyle Medley and
               Bertrand Moreau and
               Hojjat Naderi{-}Meshkin and
               Sucheendra K. Palaniappan and
               Daniel Priego{-}Espinosa and
               Martin Scharm and
               Mahesh Sharma and
               Kieran Smallbone and
               Natalie J. Stanford and
               Je{-}Hoon Song and
               Tom Theile and
               Milenko Tokic and
               Namrata Tomar and
               Vasundra Tour{\'{e}} and
               Jannis Uhlendorf and
               Thawfeek M. Varusai and
               Leandro H. Watanabe and
               Florian Wendland and
               Markus Wolfien and
               James T. Yurkovich and
               Yan Zhu and
               Argyris Zardilis and
               Anna Zhukova and
               Falk Schreiber},
  title     = {Toward Community Standards and Software for Whole-Cell Modeling},
  journal   = {{IEEE} Trans. Biomed. Eng.},
  volume    = {63},
  number    = {10},
  pages     = {2007--2014},
  year      = {2016},
  url       = {https://doi.org/10.1109/TBME.2016.2560762},
  doi       = {10.1109/TBME.2016.2560762},
  timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/tbe/WaltemathKBCHKL16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/btw/ScharmW15,
  author    = {Martin Scharm and
               Dagmar Waltemath},
  editor    = {Norbert Ritter and
               Andreas Henrich and
               Wolfgang Lehner and
               Andreas Thor and
               Steffen Friedrich and
               Wolfram Wingerath},
  title     = {Extracting reproducible simulation studies from model repositories
               using the combinearchive toolkit},
  booktitle = {Datenbanksysteme f{\"{u}}r Business, Technologie und Web {(BTW}
               2015) - Workshopband, 2.-3. M{\"{a}}rz 2015, Hamburg, Germany},
  series    = {{LNI}},
  volume    = {{P-242}},
  pages     = {137--142},
  publisher = {{GI}},
  year      = {2015},
  url       = {https://dl.gi.de/20.500.12116/2376},
  timestamp = {Wed, 13 Jan 2021 11:09:37 +0100},
  biburl    = {https://dblp.org/rec/conf/btw/ScharmW15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BergmannAMCGGHLMNORSSSWYN14,
  author    = {Frank T. Bergmann and
               Richard R. Adams and
               Stuart L. Moodie and
               Jonathan Cooper and
               Mihai Glont and
               Martin Golebiewski and
               Michael Hucka and
               Camille Laibe and
               Andrew K. Miller and
               David P. Nickerson and
               Brett G. Olivier and
               Nicolas Rodriguez and
               Herbert M. Sauro and
               Martin Scharm and
               Stian Soiland{-}Reyes and
               Dagmar Waltemath and
               Florent Yvon and
               Nicolas Le Nov{\`{e}}re},
  title     = {{COMBINE} archive and {OMEX} format: one file to share all information
               to reproduce a modeling project},
  journal   = {{BMC} Bioinform.},
  volume    = {15},
  pages     = {369},
  year      = {2014},
  url       = {https://doi.org/10.1186/s12859-014-0369-z},
  doi       = {10.1186/s12859-014-0369-z},
  timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/bmcbi/BergmannAMCGGHLMNORSSSWYN14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swat4ls/ScharmWPWTW14,
  author    = {Martin Scharm and
               Florian Wendland and
               Martin Peters and
               Markus Wolfien and
               Tom Theile and
               Dagmar Waltemath},
  editor    = {Adrian Paschke and
               Albert Burger and
               Paolo Romano and
               M. Scott Marshall and
               Andrea Splendiani},
  title     = {The CombineArchiveWeb Application - {A} Web-based Tool to Handle Files
               Associated with Modelling Results},
  booktitle = {Proceedings of the 7th International Workshop on Semantic Web Applications
               and Tools for Life Sciences, Berlin, Germany, December 9-11, 2014},
  series    = {{CEUR} Workshop Proceedings},
  volume    = {1320},
  publisher = {CEUR-WS.org},
  year      = {2014},
  url       = {http://ceur-ws.org/Vol-1320/paper\_19.pdf},
  timestamp = {Wed, 12 Feb 2020 16:44:20 +0100},
  biburl    = {https://dblp.org/rec/conf/swat4ls/ScharmWPWTW14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BergmannAMCGGHLMNORSSSWYN14,
  author    = {Frank T. Bergmann and
               Richard Adams and
               Stuart L. Moodie and
               Jonathan Cooper and
               Mihai Glont and
               Martin Golebiewski and
               Michael Hucka and
               Camille Laibe and
               Andrew K. Miller and
               David P. Nickerson and
               Brett G. Olivier and
               Nicolas Rodriguez and
               Herbert M. Sauro and
               Martin Scharm and
               Stian Soiland{-}Reyes and
               Dagmar Waltemath and
               Florent Yvon and
               Nicolas Le Nov{\`{e}}re},
  title     = {{COMBINE} archive: One File To Share Them All},
  journal   = {CoRR},
  volume    = {abs/1407.4992},
  year      = {2014},
  url       = {http://arxiv.org/abs/1407.4992},
  archivePrefix = {arXiv},
  eprint    = {1407.4992},
  timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/corr/BergmannAMCGGHLMNORSSSWYN14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WaltemathHHSW13,
  author    = {Dagmar Waltemath and
               Ron Henkel and
               Robert H{\"{a}}lke and
               Martin Scharm and
               Olaf Wolkenhauer},
  title     = {Improving the reuse of computational models through version control},
  journal   = {Bioinform.},
  volume    = {29},
  number    = {6},
  pages     = {742--748},
  year      = {2013},
  url       = {https://doi.org/10.1093/bioinformatics/btt018},
  doi       = {10.1093/bioinformatics/btt018},
  timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/bioinformatics/WaltemathHHSW13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
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