LOgo SBI Uni Rostock

SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
Germany
  +49 381 498-7571
  olaf.wolkenhauer@uni-rostock.de

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

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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

A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools

Freiesleben S, Unverricht-Yeboah M, Gütebier L, Waltemath D, Kriehuber R, Wolkenhauer O

accepted for publication in Frontiers in Systems Biology

Harmonizing semantic annotations for computational models in biology

Neal M, Dräger A, Wolkenhauer O et al.

Brief Bioinform. (Epub ahead of print)

DOI: 10.1093/bib/bby087

Pubmed: https://www.ncbi.nlm.nih.gov/pubmed/30462164?dopt=Abstract

URL: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bby087/5164345

Identifying Frequent Patterns in Biochemical Reaction Networks - a Workflow

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

Database, Volume 2018

DOI: https://doi.org/10.1093/database/bay051

URL: https://academic.oup.com/database/article/doi/10.1093/database/bay051/5048438

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)

DOI: https://doi.org/10.1186/s12918-018-0553-2

URL: https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-018-0553-2

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

DOI: https://doi.org/10.1371/journal.pcbi.1005740

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)

DOI: https://doi.org/10.1093/bioinformatics/btw812

URL: https://academic.oup.com/bioinformatics/article/33/8/1253/2881437

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

DOI: https://doi.org/10.1093/bib/bbw090

URL: http://bib.oxfordjournals.org/content/early/2016/10/11/bib.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)

DOI: https://doi.org/10.2390/biecoll-jib-2016-289

URL: http://journal.imbio.de/article.php?aid=289

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

DOI: https://dx.doi.org/10.1186/s12859-016-1394-x

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)

DOI: https://dx.doi.org/10.1186/s13326-016-0080-2

URL: http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0080-2

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)

DOI: http://dx.doi.org/10.1109/TBME.2016.2560762

URL: http://ieeexplore.ieee.org/document/7489010/

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)

DOI: http://dx.doi.org/10.1109/TBME.2016.2555481

URL: http://ieeexplore.ieee.org/document/7484267/

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)

DOI: http://dx.doi.org/10.1093/bioinformatics/btv484

URL: http://bioinformatics.oxfordjournals.org/content/32/4/563

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)

DOI: http://dx.doi.org/10.2390/biecoll-jib-2015-271

URL: http://journal.imbio.de/article.php?aid=271

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)

DOI: http://dx.doi.org/10.2390/biecoll-jib-2015-262

URL: http://journal.imbio.de/article.php?aid=262

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)

DOI: https://dx.doi.org/10.2390/biecoll-jib-2015-258

URL: https://www.ncbi.nlm.nih.gov/pubmed/26528556

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)

DOI: http://dx.doi.org/10.1093/database/bau130

URL: http://database.oxfordjournals.org/content/2015/bau130.full

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)

DOI: http://dx.doi.org/10.1186/s13326-015-0014-4

URL: http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-015-0014-4

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)

DOI: http://dx.doi.org/10.3389/fbioe.2015.00019

URL: http://journal.frontiersin.org/article/10.3389/fbioe.2015.00019/

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)

DOI: http://dx.doi.org/10.1016/j.pbiomolbio.2014.10.001

URL: http://www.sciencedirect.com/science/article/pii/S0079610714001825

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)

DOI: http://dx.doi.org/10.1007/978-3-319-08590-6_8

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)

DOI: http://dx.doi.org/10.1186/s12859-014-0369-z

URL: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0369-z

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)

DOI: http://dx.doi.org/10.4056/sigs.5279417

URL: http://standardsingenomics.biomedcentral.com/articles/10.4056/sigs.5279417

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)

DOI: http://dx.doi.org/10.1093/bioinformatics/btt018

URL: bioinformatics.oxfordjournals.org/content/29/6/742

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)

DOI: http://dx.doi.org/10.1186/1752-0509-5-198

URL: http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198

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)

DOI: http://dx.doi.org/10.1038/msb.2011.77

URL: http://msb.embopress.org/content/7/1/543

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)

DOI: http://dx.doi.org/10.1371/journal.pcbi.1001122

URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001122

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)

DOI: https://doi.org/10.1186/1471-2105-11-423

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

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

Scharm M, Stanford NJ, Dobson PD et al.

Springer (2019), chapter in Yeast Systems Biology.
Methods in Molecular Biology.

ISBN 10 (online): 978-1-4939-9736-7

DOI: https://doi.org/10.1007/978-1-4939-9736-7_17

URL: https://link.springer.com/protocol/10.1007%2F978-1-4939-9736-7_17

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)

DOI: http://dx.doi.org/10.1007/978-94-007-6803-1_10

URL: http://link.springer.com/chapter/10.1007/978-94-007-6803-1_10

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

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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

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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)

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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

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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).

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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)

DOI: http://dx.doi.org/10.1007/978-3-642-41281-3_3

URL: http://link.springer.com/chapter/10.1007/978-3-642-41281-3_3

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