Dr. Dagmar Waltemath

Current Projects

Simulation Experiment Management for Systems Biology (SEMS)

Standardization efforts and the exchange of protocols to generate data in the life sciences have become a necessity for large scale projects and multinational collaborations. Data in the life sciences are highly context dependent and if the processes by which the data were generated are not sufficiently well documented, it becomes difficult to reproduce these results and to share and integrate results across projects. The same arguments apply to the generation of scientific results that are based on mathematical models and computer simulations. Systems biology is a scientific approach characterized by an iterative cycle of data-driven modelling and model-driven experimentation. The present project is to provide support for this iterative cycle through techniques and tools that improve and ease the working with simulation setups.

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Research Interest

Reproducibility of simulation results.
"I am interested in standardisation efforts in Computational Biology, in particular for modeling and simulation."

With the growing number of efforts for the modeling of biological systems, standardisation became increasingly important to store, exchange, and reuse computational models. Languages like the Systems Biology Markup Language (SBML), CellML, NeuroML or alike enable the standardised encoding of simulation models in Systems Biology. With the demand to reuse models, a semantic layer was added on top of the model structure encoding; guidelines such as the Minimum Information Required in the Annotation of Models (MIRIAM), and the related MIRIAM URN scheme emerged.  Further approaches like the Systems Biology Graphical Notation (SBGN) now aim at standardising the representation of biological networks.

My main research interests are in the standardised encoding of annotations and of simulation experiment descriptions.

I am involved in the development of a new annotation scheme for SBML models that builds on RDF annotations and has a rich semantics for the encoding of meta-information on a computational model; for example, to provide information on the modelled species or mathematics.

Furthermore, I aim at making simulation experiments performed on a model both exchangeable and reusable. The Simulation Experiment Description Markup Language (SED-ML) is a first attempt to reach this goal. It is an XML format, developed as a community effort, involving international partners from different Systems Biology groups. SED-ML has been tested in a number of simulation tools (e.g. roadrunner, VCell) and software support exists (libSedml, SED-ML validator). SED-ML to date allows for the encoding of time course simulations. In my further research, I will expand the scope of SED-ML and promote it for different types of models.

For me, standardisation is a necessity if we want to move on in Systems Biology – researchers need to build on other people's findings and therefore reuse of existing work is essential. The best way to exchange knowledge then is to use standard formats.

Academic Background

2012 - present

Junior Research Group leader "SEMS", Dept. of Systems Biology and Bioinformatics
University of Rostock, Rostock/Germany

2012

postdoctoral research fellow, Dept. of Systems Biology and Bioinformatics
University of Rostock, Rostock/Germany

2011
postdoctoral research stay (DFG-funded) in the Computational Neuroscience group, Norwegian University of Life Science, Ã…s/Norway

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

2006
Diploma thesis via the DAAD-funded exchange program at Linköping University in the IDA Group  at Linköpings Universitet, Linköping/Sweden

Earlier publications can be found here

Publications

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

Improving the reuse of computational models through version control

Bioinformatics, 29: 742-728 (please contact us for further details about the manuscript)

access via Oxford Bioinformatics

Henkel R, Endler L, Le Novère N, Peters A, Waltemath D (2010)

Ranked Retrieval of Computational Biology Models

BMC Bioinformatics 11:423
open access

Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, et al. (2011)

Minimum Information About a Simulation Experiment (MIASE)

PLoS Computational Biology 7: 4

open access

Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, e al. (2011)

Controlled vocabularies and semantics in systems biology

Nature Molecular Systems Biology 7: 543
open access

Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, et al. (2011)

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

BMC Systems Biology 2011, 5:198
open access

Waltemath D, Henkel R, Winter F, Wolkenhauer O

Reproducibility of model-based results in systems biology

In Systems Biology: Integrative Biology and Simulation Tools, Volume 1.  Prokop A, Csukas B (eds) Springer.  in press

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

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

Proceedings of the 2012 INFORMATIK  conference, Jahrestagung der Gesellschaft für Informatik e.V. (GI) BRAUNSCHWEIG, 16.-21.09.2012 (please contact us for further details about the manuscript)

Dagmar Waltemath, Olaf Wolkenhauer, Nicolas Le Novère and Michel Dumontier

Possibilities for Integrating Model-related Data in Computational Biology

Proceedings of the 9th International Conference on Data Integration in the Life Sciences, CEUR WS (to appear)

Cooper J‚ Mirams G‚ Slaymaker M‚ Simpson A‚ Vik JO and Waltemath D

Virtual experiments for reusable models

Proceedings of the 2012 VPH Conference, London. (please contact us for further details about the manuscript)