Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Dr. Dagmar Waltemath

Image: Dr. Dagmar Waltemath

Current Projects

Simulation Experiment Management for Systems Biology (SEMS)
Systems biology is a scientific approach characterised 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, using standard formats and ensuring result reproducibility.
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de.NBI:SYSBIO
Data Management node in the German Network for Bioinformatics Infrastructure
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SBGN-ED
An extended editor for the Systems Biology Graphical Notation.
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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

  1. 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).
  2. 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);
  3. the education of researchers in using standards and reusing model-based results (e.g., through de.NBI or the COMBINE network)

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


2006

Diploma thesis via the DAAD-funded exchange program at Link

Publications

Waltemath D and Wolkenhauer O
How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine

accepted for publication in IEEE Transactions on Biomedical Engineering (2016).

Martin Scharm, Olaf Wolkenhauer, and Dagmar Waltemath
An algorithm to detect and communicate the differences in computational models describing biological systems

Open Access article at Oxford Journals BIOINFORMATICS.
DOI: 10.1093/bioinformatics/btv484
URL: http://bioinformatics.oxfordjournals.org/content/early/2015/10/20/bioinformatics.btv484.abstract

Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Nicolas Le Novere, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S (2015)
Specifications of Standards in Systems and Synthetic Biology

Journal of Integrative Bioinformatics 12:2(258)
open access

Frank Bergmann FT, Cooper J, Le Novèr N, Nickerson D, Waltemath D (2015)
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2

Journal of Integrative Bioinformatics 12:2
open access

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novere N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ (2015)
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Journal of Integrative Bioinformatics 12:2
open access

Hucka M, Nickerson DP, Bader G, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N (2015)
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

Front. Bioeng. Biotechnol. 3:19.
access via Frontiers web page 

Scharm M and Waltemath D (2015)
Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit

Workshop on Data management in Life Sciences, BTW 2015, Hamburg, March 2015
 PDF version available at conference homepage

Henkel R, Wolkenhauer O, Waltemath D
Combining computational models, semantic annotations and simulation experiments in a graph database

Oxford DATABASE 2015 bau130 

open access

Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson AP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N (2014)
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

BMC Bioinformatics 15:369  doi:10.1186/s12859-014-0369-z

open access

Cooper J, Vik JO, Waltemath D (2014)
A call for virtual experiments: Accelerating the scientific process

Progress in Biophysics and Molecular Biology
 access via ScienceDirect (or contact us for further details)

Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C et al. (2014)
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Standards in Genomic Sciences, 9:3

access via SIGS web page (or contact us for further details about the manuscript)

Alm R, Waltemath D, Wolkenhauer O, Henkel R (2014)
Annotation-Based Feature Extraction from Sets of SBML Models

Proceedings of the 10th International Conference on Data Integration in the Life Sciences, Lisbon, Portugal, July 2014

access via Springer (or contact us for further details)

Scharm M, Wendland F, Peters M, Wolfien M, Theile T, Waltemath D (2014)
The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results.

Proceedings of the 2014 Workshop on Semantic Web Applications and Tools for life sciences. Demo paper.
open access (PDF)

Scharm M, Wolkenhauer O, Waltemath D (2014)
Identifying, interpreting, and communicating changes in XML-encoded models of biological systems

Proceedings of the 10th International Conference on Data Integration in the Life Sciences, Poster and Demo Papers, H. Galhardas and E. Rahm (eds.), Lisbon, Portugal, July 2014.
 PDF via DILS webpage

Lange M, Henkel R, Müller W, Waltemath D, Weise S (2014)
Information Retrieval in Life Sciences: A Programmatic Survey

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

access via Springer Link (or contact us for further details about the manuscript)

Waltemath D, Henkel R, Hälke R, Scharm M, Wolkenhauer O (2014)
Improving the reuse of computational models through version control

Bioinformatics, 29: 742-72.

access via Oxford Bioinformatics (or contact us for further details about the manuscript)

Waltemath D, Henkel R, Winter F, Wolkenhauer O (2013)
Reproducibility of model-based results in systems biology

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

access via Springer Link (or contact us for further details about the manuscript)

Waltemath D, Wolkenhauer O, Le Novère N, Dumontier M (2013)
Possibilities for Integrating Model-related Data in Computational Biology

Proceedings of the 9th International Conference on Data Integration in the Life Sciences, CEUR WS. 2013 
PDF Open Access

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)

Cooper J, Mirams G, Slaymaker M, Simpson A, Vik JO, Waltemath D (2013)
Virtual experiments for reusable models

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

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

Henkel R, Endler L, Le Novère N, Peters A, Waltemath D (2010)
Ranked Retrieval of Computational Biology Models

BMC Bioinformatics 11:423
open access

Contact Details

Dept. of Systems Biology and Bioinformatics,
Ulmenstrasse 69 (building 3, 3rd floor)
18057 Rostock, Germany
Room 411

phone: +49 381 498-7575
fax: +49 381 498-7572
mail: dagmar.waltemath(at)uni-rostock.de

Collaborators & Partners

Computational Systems Neurobiology Group
European Bioinformatics Institute (EBI), UK
Federal Ministry for Education and Research (BMBF)
HITS gGmbH
Heidelberg Institute for Theoretical Studies
Prof. Falk Schreiber
Faculty of Information Technology,
Monash University,
Australia
Volkswagen Stiftung