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+
Promotion of the SBGN standard and extentions to SBGN-ED.
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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

M König, A Oellrich, D Waltemath, ... O Wolkenhauer
Challenges and opportunities for system biology standards and tools in medical research

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)
URL: http://ceur-ws.org/Vol-1692/paperC.pdf (PDF)

D Waltemath, JR Karr, FT Bergmann, V Chelliah et al.
Toward community standards and software for whole-cell modeling

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 2007-14 (2016)
DOI:
10.1109/TBME.2016.2560762
URL: http://ieeexplore.ieee.org/document/7489010/

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

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 1999-2006 (2016)
DOI: 10.1109/TBME.2016.2555481
URL: http://ieeexplore.ieee.org/document/7484267/
http://dx.doi.org/10.1109/TBME.2016.2555481

M Scharm, D Waltemath, P Mendes and O Wolkenhauer
COMODI: an ontology to characterise differences in versions of computational models in biology

Open Access article in J of Biomedical Semantics 7:46 (2016)
DOI: 10.1186/s13326-016-0080-2
URL: http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0080-2

M Scharm, O Wolkenhauer and D Waltemath
An algorithm to detect and communicate the differences in computational models describing biological systems

Open Access article in BIOINFORMATICS 32:4, pp. 563-570 (2015)
DOI: 10.1093/bioinformatics/btv484
URL: http://bioinformatics.oxfordjournals.org/content/32/4/563

F Schreiber, GD Bader, M Golebiewski, ... D Waltemath, S Weise
Specifications of Standards in Systems and Synthetic Biology

Open Access article in J Integrative Bioinformatics 12:2, p. 258 (2015)
DOI: 10.2390/biecoll-jib-2015-258
URL: https://www.ncbi.nlm.nih.gov/pubmed/26528556

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

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

DOI: 10.2390/biecoll-jib-2015-262
URL: http://journal.imbio.de/article.php?aid=262

M Hucka, FT Bergmann, A Dräger, ... D Waltemath, DJ Wilkinson
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

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

DOI: 10.2390/biecoll-jib-2015-271
URL: http://journal.imbio.de/article.php?aid=271

M Hucka, DP Nickerson, G Bader, ... D Waltemath, N Le Novère
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

Article in Front. Bioeng. Biotechnol. 3:19 (2015)
DOI: 10.3389/fbioe.2015.00019
URL: http://journal.frontiersin.org/article/10.3389/fbioe.2015.00019/

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

Article in Proceedings of the Workshop on Data management in Life Sciences, BTW, Hamburg (2015)
URL: http://www.btw-2015.de/res/proceedings/Workshops/DMS/Scharm-Extracting_reproducible_sim.pdf (PDF)

R Alm, D Waltemath, M Wolfien, O Wolkenhauer et al.
Annotation-Based Feature Extraction from Sets of SBML Models

Open Access article in J Biomedical Semantics 6:20 (2015)
DOI: 10.1186/s13326-015-0014-4
URL: http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-015-0014-4

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

Open Access article in DATABASE bau130 (2015)
DOI: dx.doi.org/10.1093/database/bau130
URL: http://database.oxfordjournals.org/content/2015/bau130.full

FT Bergmann, R Adams, ... M Scharm, ... D Waltemath et al.
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Open Access article in BMC Bioinformatics 15:369 (2014)
DOI: 10.1186/s12859-014-0369-z
URL: bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0369-z 

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

Article in Progress in Biophysics and Molecular Biology 117:1, pp. 99-106 (2014)
DOI: 10.1016/j.pbiomolbio.2014.10.001
URL: http://www.sciencedirect.com/science/article/pii/S0079610714001825 

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

Open Access article in Standards in Genomic Sciences 9:3 (2014)
DOI: 10.4056/sigs.5279417
URL: http://standardsingenomics.biomedcentral.com/articles/10.4056/sigs.5279417

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

Article in Lecture notes in computer science 8574, pp 81-95 (2014)
DOI: 10.1007/978-3-319-08590-6_8

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

Open Access demo paper in Proceedings of the 2014 Workshop on Semantic Web Applications and Tools for life sciences (2014)
URL: http://ceur-ws.org/Vol-1320/paper_19.pdf
PeerJ Preprint: https://peerj.com/preprints/639/

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

Demo paper in Proceedings of the 10th International Conference on Data Integration in the Life Sciences, Lisbon, Portugal (2014)
URL: http://dils2014.inesc-id.pt/data/uploads/paper_42.pdf

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

In: Approaches in Integrative Bioinformatics,  pp 73-109. Ming C, Hofestädt R (eds), Springer.(2014)
DOI: 10.1007/978-3-642-41281-3_3
URL: http://link.springer.com/chapter/10.1007/978-3-642-41281-3_3

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

Article in BIOINFORMATICS 29:6, pp. 742-7 (2014)
DOI: 10.1093/bioinformatics/btt018
URL: bioinformatics.oxfordjournals.org/content/29/6/742

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

In: Systems Biology: Integrative Biology and Simulation Tools 1, pp 301-320. Prokop A, Csukas B (eds) Springer (2013)
DOI: 10.1007/978-94-007-6803-1_10
URL: http://link.springer.com/chapter/10.1007/978-94-007-6803-1_10

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

Proceedings of the 9th International Conference on Data Integration in the Life Sciences (2013)
URL: http://www2.unb.ca/csas/data/ws/dils2013/papers/DILS-SYS-EC-paper8.pdf (workshop proceedings)

R Henkel, N Le Novère, O Wolkenhauer, D Waltemath
Considerations of graph-based concepts to manage computational biology models and associated simulations

Article in Proceedings of the 2012 INFORMATIK  conference, Jahrestagung der GI e.V., Braunschweig (2012).
URL: http://cs.emis.de/LNI/Proceedings/Proceedings208/1545.pdf

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)

D Waltemath, R Adams, DA Beard et al.
Minimum Information About a Simulation Experiment (MIASE)

Open Access article in PLoS Computational Biology 7: 4 (2011)
DOI: 10.1371/journal.pcbi.1001122
URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001122 

M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova et al.
Controlled vocabularies and semantics in systems biology

Open Access article in Nat Molecular Systems Biology 7:543 (2011)
DOI: 10.1038/msb.2011.77
URL: http://msb.embopress.org/content/7/1/543

D Waltemath, R Adams, FT Bergmann, M Hucka et al.
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Open Access article in BMC Systems Biology 2011, 5:198 (2011)
DOI: 10.1186/1752-0509-5-198
URL: http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198 

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

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

DOI: 10.1186/1471-2105-11-423
URL: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-423

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