Dr. Dagmar Waltemath

I develop tailor-made solutions for the management and standardisation of data arising from modeling projects to improve the reproducibility of simulation studies in biology.

Research interest

Reproducibility of model-based results.

"I develop tailor-made solutions for the management and standardisation of data arising from modeling projects to improve the reproducibility of simulation studies in biology."

Reproducibility of results is fundamental to all sciences. In computational biology, standard formats like Systems Biology Markup Language (SBML), CellML, or NeuroML enable the exchange of simulation models, and foster interoperability between software tools.

My main research interest is in developing methods and tools that (1) improve the reuse of computational models in biology, (2) ensure reproducibility of model-based results and (3) that lead to easier access to and understanding of scientific findings. More specifically, my work focuses on

  • the further development of standard formats (semantically enriched models in SBML and CellML formats, simulation descriptions in SED-ML, and other meta-data in XML and RDF flavors).
  • the application and adaptation of methods from the research area of database and information systems on models (integrated model storage in MASYMOS, ranked model retrieval with MORRE, model version control with BiVeS);
  • the education of researchers in using standards and reusing model-based results (e.g., through de.NBI or the COMBINE network)

Projects

Research Projects

de.NBI:SYSBIO

Data Management node in the German Network for Bioinformatics Infrastructure

More

Academic background

2012 - present Junior Research Group leader, SEMS.
2012 Postdoctoral research fellow, Dept. of Adaptive and regenerative software systems (ARS). University of Rostock, Rostock/Germany

 

2011

Postdoctoral researcher, Computational Neuroscience, Norwegian University of Life Science, Aas/Norway (DFG-funded)

2006 - 2011

PhD candidate in the DFG-funded research training school dIEM oSiRiS, University of Rostock, Rostock/Germany (Title of dissertation: Annotation-based storage and retrieval of models and simulation descriptions in computational biology)

2007

Marie Curie Internship in the Compneur Group at the European Bioinformatics Institute, Cambridge/UK

1999-2006

Diploma thesis degree, University of Rostock, Rostock/Germany

 

Selected publications

Harmonizing semantic annotations for computational models in biology

Neal M, Dräger A, Wolkenhauer O et al.

Brief Bioinform. (Epub ahead of print)

Identifying Frequent Patterns in Biochemical Reaction Networks - a Workflow

Lambusch F, Waltemath D, Wolkenhauer O, Sandkuhl K, Rosenke C, Henkel R

Database, Volume 2018

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

Scharm M, Gebhardt T, Touré V, Bagnacani A, Salehzadeh-Yazdi A, Wolkenhauer O, Waltemath D

BMC Systems Biology 12:53 (2018)

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation

Touré V, Le Novère N, Waltemath D, Wolkenhauer O

Plos Computational Biology

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

Bergmann FT, Nickerson D, Waltemath D, Scharm M

Oxford Bioinformatics 33:8, pp. 1253–1254 (2017)

Notions of similarity for computational biology models

D Waltemath, R Henkel, R Hoehndorf, T Kacprowski, C Knuepfer, W Liebermeister

Open Access article in Briefings in Bioinformatics (2016) bbw090

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

F Schreiber, GD Bader, P Gleeson, M Golebiewski, M Hucka, N Le Novere, C Myers, D Nickerson, B Sommer, D Waltemath

Open Access article in J Integrative Bioinformatics 2016 13(3)

STON: exploring biological pathways using the SBGN standard and graph databases

Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C

Open Access article in BMC Bioinformatics 2016, 17:494

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

Scharm M, Waltemath D, Mendes P, and Wolkenhauer O

Open Access article in the Journal of Biomedical Semantics 7:46 (2016)

Toward community standards and software for whole-cell modeling

Waltemath D, Karr JT, Bergmann FT, Chelliah V ... Scharm M et al.

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 2007-14 (2016)

How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine

D Waltemath and O Wolkenhauer

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 1999-2006 (2016)

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

Scharm M, Wolkenhauer O, and Waltemath D

Open Access article in BIOINFORMATICS 32:4, pp. 563-570 (2015)

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

M Hucka, FT Bergmann, A Dräger, ... D Waltemath, DJ Wilkinson

Open Access article in J Integrative Bioinformatics 12:2 (2015)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2

FT Bergmann, J Cooper, N Le Novere, D Nickerson, D Waltemath

Open Access article in J Integrative Bioinformatics 12:2 (2015)

Specifications of Standards in Systems and Synthetic Biology

F Schreiber, GD Bader, M Golebiewski, ... D Waltemath, S Weise

Open Access article in J Integrative Bioinformatics 12:2, p. 258 (2015)

Combining computational models, semantic annotations and simulation experiments in a graph database

R Henkel, O Wolkenhauer, D Waltemath

Open Access article in DATABASE bau130 (2015)

Annotation-Based Feature Extraction from Sets of SBML Models

R Alm, D Waltemath, M Wolfien, O Wolkenhauer et al.

Open Access article in J Biomedical Semantics 6:20 (2015)

Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

M Hucka, DP Nickerson, G Bader, ... D Waltemath, N Le Novère

Article in Front. Bioeng. Biotechnol. 3:19 (2015)

A call for virtual experiments: Accelerating the scientific process

J Cooper, JO Vik, D Waltemath

Article in Progress in Biophysics and Molecular Biology 117:1, pp. 99-106 (2014)

Annotation-Based Feature Extraction from Sets of SBML Models

R Alm, D Waltemath, O Wolkenhauer, R Henkel

Article in Lecture notes in computer science 8574, pp 81-95 (2014)

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

Bergmann FT, Adams R, ... Scharm M, ... Waltemath D et al.

Open Access article in BMC Bioinformatics 15:369 (2014)

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

D Waltemath, FT Bergmann, C Chaouiya et al.

Open Access article in Standards in Genomic Sciences 9:3 (2014)

Possibilities for Integrating Model-related Data in Computational Biology

D Waltemath, O Wolkenhauer, N Le Novère, M Dumontier

Proceedings of the 9th International Conference on Data Integration in the Life Sciences (2013)

Downloads & more:

Improving the reuse of computational models through version control

Waltemath D, Henkel R, Hälke R, Scharm M, and Wolkenhauer O

Article in BIOINFORMATICS 29:6, pp. 742-7 (2014)

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

D Waltemath, R Adams, FT Bergmann, M Hucka et al.

Open Access article in BMC Systems Biology 2011, 5:198 (2011)

Controlled vocabularies and semantics in systems biology

M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova et al.

Open Access article in Nat Molecular Systems Biology 7:543 (2011)

Minimum Information About a Simulation Experiment (MIASE)

D Waltemath, R Adams, DA Beard et al.

Open Access article in PLoS Computational Biology 7: 4 (2011)

Ranked Retrieval of Computational Biology Models

R Henkel, L Endler, N Le Novère, A Peters, D Waltemath

Open Access article in BMC Bioinformatics 11:423 (2010)

Reproducibility of model-based results in systems biology

D Waltemath, R Henkel, F Winter, O Wolkenhauer

In: Systems Biology: Integrative Biology and Simulation Tools 1, pp 301-320. Prokop A, Csukas B (eds) Springer (2013)

Challenges and opportunities for system biology standards and tools in medical research

M König, A Oellrich, D Waltemath, ... O Wolkenhauer

Open Access article in Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, F Loebe, M Boeker, H Herre, L Jansen, D Schober (eds.), Halle, Germany, 2016

Venue: Halle, Germany

Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit

Scharm M and Waltemath D

Article in Proceedings of the Workshop on Data management in Life Sciences, BTW, Hamburg, germany (2015)

Venue: Hamburg, Germany

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

Scharm M, Wendland F, Peters M, Wolfien M, Theile T, and Waltemath D

Open Access demo paper in Proceedings of the 2014 Workshop on Semantic Web Applications and Tools for life sciences (2014)

Identifying, interpreting, and communicating changes in XML-encoded models of biological systems

Scharm M, Wolkenhauer O, and Waltemath D

Demo paper in Proceedings of the 10th International Conference on Data Integration in the Life Sciences, Lisbon, Portugal (2014)

Venue: Lisbon, Portugal

Considerations of graph-based concepts to manage computational biology models and associated simulations

R Henkel, N Le Novère, O Wolkenhauer, D Waltemath

Article in Proceedings of the 2012 INFORMATIK conference, Jahrestagung der GI e.V., Braunschweig (2012).

Virtual experiments for reusable models

Cooper J, Mirams G, Slaymaker M, Simpson A, Vik JO, Waltemath D (2013)

Proceedings of the 2012 VPH Conference, London, UK.
Access to PDF version through Researchgate (or contact us for further details about the manuscript)

Venue: London, UK

Information Retrieval in Life Sciences: A Programmatic Survey

M Lange, R Henkel, W Müller, D Waltemath, S Weise

In: Approaches in Integrative Bioinformatics, pp 73-109. Ming C, Hofestädt R (eds), Springer.(2014)