Nickerson, David

An Overview of CellML 1.1, a Biological Model Description Language

Cuellar, A. A., Lloyd, C. M., Nielsen, P. F., Bullivant, D. P., Nickerson, D. P., & Hunter, P. J. (2003) · SIMULATION

Modeling and Simulation SystemsGene Regulatory Network Analysis

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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

The Physiome Model Repository 2

Yu, T., Lloyd, C. M., Nickerson, D. P., Cooling, M. T., Miller, A. K., Garny, A., Terkildsen, J. R., Lawson, J., Britten, R. D., Hunter, P. J., et al. (2011) · Bioinformatics

Scientific Computing and Data ManagementResearch Data Management Practices

Cited by 169

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

Harmonizing semantic annotations for computational models in biology

Neal, M. L., König, M., Nickerson, D., Mısırlı, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., et al. (2019) · Briefings in Bioinformatics

Biomedical Text Mining and OntologiesScientific Computing and Data Management

Cited by 74

Best Practices for Making Reproducible Biochemical Models

Porubsky, V. L., Goldberg, A. P., Rampadarath, A. K., Nickerson, D. P., Karr, J. R., & Sauro, H. M. (2020) · Cell Systems

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 45

Improving reproducibility in computational biology research

Papin, J. A., Mac Gabhann, F., Sauro, H. M., Nickerson, D., & Rampadarath, A. (2020) · PLOS Computational Biology

Scientific Computing and Data ManagementResearch Data Management Practices

Cited by 42

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

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

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

SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models

Shin, W., Hellerstein, J. L., Munarko, Y., Neal, M. L., Nickerson, D. P., Rampadarath, A. K., Sauro, H. M., & Gennari, J. H. (2021) · bioRxiv (Cold Spring Harbor Laboratory)

Biomedical Text Mining and OntologiesGene Regulatory Network Analysis

Cited by 2