Waltemath, Dagmar

Controlled vocabularies and semantics in systems biology

Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., et al. (2011) · Molecular Systems Biology

Biomedical Text Mining and OntologiesGene Regulatory Network Analysis

Cited by 316

The Systems Biology Markup Language (SBML): language specification for level 3 version 2 core release 2

Hucka, M., Bergmann, F. T., Chaouiya, C., Dräger, A., Hoops, S., Keating, S. M., König, M., Novère, N. L., Myers, C. J., Olivier, B. G., et al. (2019) · Journal of Integrative Bioinformatics

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 258

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

Bergmann, F. T., Adams, R., Moodie, S., Cooper, J., Glont, M., Golebiewski, M., Hucka, M., Laibe, C., Miller, A. K., Nickerson, D. P., et al. (2014) · BMC Bioinformatics

Scientific Computing and Data ManagementResearch Data Management Practices

Cited by 173

Minimum Information About a Simulation Experiment (MIASE)

Waltemath, D., Adams, R., Beard, D. A., Bergmann, F. T., Bhalla, U. S., Britten, R., Chelliah, V., Cooling, M. T., Cooper, J., Crampin, E. J., et al. (2011) · PLoS Computational Biology

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 168

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

Waltemath, D., & Wolkenhauer, O. (2016) · IEEE Transactions on Biomedical Engineering

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 49

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Le Novère, N., Olivier, B. G., Sahle, S., Smith, L., & Waltemath, D. (2018) · Journal of Integrative Bioinformatics

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 37

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

Scharm, M., Wolkenhauer, O., & Waltemath, D. (2016) · Bioinformatics

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 24

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

Smith, L. P., Bergmann, F. T., Garny, A., Helikar, T., Karr, J., Nickerson, D., Sauro, H., Waltemath, D., & König, M. (2021) · Journal of Integrative Bioinformatics

Scientific Computing and Data ManagementResearch Data Management Practices

Cited by 17

Specifications of standards in systems and synthetic biology: status and developments in 2020

Schreiber, F., Sommer, B., Czauderna, T., Golebiewski, M., Gorochowski, T. E., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., et al. (2020) · Journal of Integrative Bioinformatics

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 17

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., et al. (2015) · Journal of Integrative Bioinformatics

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 16

OMEX metadata specification (version 1.2)

Gennari, J. H., König, M., Misirli, G., Neal, M. L., Nickerson, D. P., & Waltemath, D. (2021) · Journal of Integrative Bioinformatics

Scientific Computing and Data ManagementResearch Data Management Practices

Cited by 11