Martin Scharm

According to our database, Martin Scharm authored at least 14 papers between 2013 and 2020.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2020

GEMtractor: extracting views into genome-scale metabolic models.

Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi

Bioinform., 2020

2019

Harmonizing semantic annotations for computational models in biology.

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

Briefings Bioinform., 2019

2018

Improving reproducibility and reuse of modelling results in the life sciences

Martin Scharm

PhD thesis, 2018

Evolution of computational models in BioModels Database and the Physiome Model Repository.

Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath

BMC Syst. Biol., 2018

2017

SED-ML web tools: generate, modify and export standard-compliant simulation studies.

Frank T. Bergmann, David P. Nickerson, Dagmar Waltemath, Martin Scharm

Bioinform., 2017

2016

Toward Community Standards and Software for Whole-Cell Modeling.

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

IEEE Trans. Biomed. Eng., 2016

A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in <i>Drosophila </i>embryos.

Martin Scharm, Dagmar Waltemath

F1000Research, 2016

COMODI: an ontology to characterise differences in versions of computational models in biology.

Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer

J. Biomed. Semant., 2016

An algorithm to detect and communicate the differences in computational models describing biological systems.

Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath

Bioinform., 2016

2015

Extracting reproducible simulation studies from model repositories using the combinearchive toolkit.

Martin Scharm, Dagmar Waltemath

Proceedings of the Datenbanksysteme für Business, Technologie und Web (BTW 2015), 2015

2014

COMBINE archive: One File To Share Them All.

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

CoRR, 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

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

BMC Bioinform., 2014

The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results.

Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom Theile, Dagmar Waltemath

Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2014

2013

Improving the reuse of computational models through version control.

Dagmar Waltemath, Ron Henkel, Robert Hälke, Martin Scharm, Olaf Wolkenhauer

Bioinform., 2013