Martin Scharm

Publication Activity (10 Years)

Years Active: 2013-2020
Publications (10 Years): 8

Top Topics

Computational Models

Version Control

Semantic Annotation

Top Venues

Publications

Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi
GEMtractor: extracting views into genome-scale metabolic models. Bioinform. 36 (10) (2020)
Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20 (2) (2019)
Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath
Evolution of computational models in BioModels Database and the Physiome Model Repository. BMC Syst. Biol. 12 (1) (2018)
Frank T. Bergmann, David P. Nickerson, Dagmar Waltemath, Martin Scharm
SED-ML web tools: generate, modify and export standard-compliant simulation studies. Bioinform. 33 (8) (2017)
Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer
COMODI: an ontology to characterise differences in versions of computational models in biology. J. Biomed. Semant. 7 (2016)
Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath
An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinform. 32 (4) (2016)
Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold F. Gómez, Jens Hahn, Tuure Hameri, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J. Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K. Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J. Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek M. Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber
Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans. Biomed. Eng. 63 (10) (2016)
Martin Scharm, Dagmar Waltemath
embryos. F1000Research 5 (2016)
Martin Scharm, Dagmar Waltemath
Extracting reproducible simulation studies from model repositories using the combinearchive toolkit. BTW Workshops (2015)
Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom Theile, Dagmar Waltemath
The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results. SWAT4LS (2014)
Frank T. Bergmann, Richard R. Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinform. 15 (2014)
Frank T. Bergmann, Richard Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère
COMBINE archive: One File To Share Them All. CoRR (2014)
Dagmar Waltemath, Ron Henkel, Robert Hälke, Martin Scharm, Olaf Wolkenhauer
Improving the reuse of computational models through version control. Bioinform. 29 (6) (2013)