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
Research interest
Management of Computational Models
In-silico simulation of biological systems has become a standard tool in the life sciences. Consequently, the number and complexity of computational models describing biological systems is increasing, which entails numerous organisational challenges.
I am developing tools and methods to improve the management of computational models, including:
- Versioning, Comparison, and Merging of models
- Data Integration and Tool Interoperability
- Dissemination of Reproducible Research Results
- Organisation and Representation of Knowledge
Mining, Analysing, and Presenting Complex Data
Data is supposed to be the oil of the 21st century. Collecting the data may be difficult, but integrating, processing, and understanding it is significantly harder.
I am ready to be challenged by convoluted data and enjoy for example:
- Mining, Converting, and Massaging Data
- Finding Patterns and Artifacts
- Visualising and Presenting Complex Structures
- Communicating facts, structures, and results to experts and the general public
Background
|
2020 - present |
Freelancing with CODE AHOI |
|
2018 - 2020 |
PostDoc at the SBI University of Rostock, Rostock/Germany |
|
2016 - 2020 |
Head of IT at the SBI (infrastructure, acquisition, maintenance, innovation etc) |
|
2012 -2018 |
PhD-Student at the SBI University of Rostock, Rostock/Germany |
|
2015 |
Research Internship University of Manchester, Manchester/UK |
| 2013 |
Science2020 intern University of Oxford, Oxford/UK |
| 2006 - 2012 |
Student of Bioinformatics |
Skills
- Research (Reading, Thinking, Developing, Publishing, Collaborating)
- Programming (C, Java, PHP, Python, Perl, Shell, Gnu R, etc)
- Administration (Docker, Web, Databases, Monitoring, Logic)
Memberships
| since years | Fellow of the Free Software Foundation Europr |
| since years | Member of the Chaos Computer Club |
Selected publications
Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models
GEMtractor: Extracting Views into Genome-scale Metabolic Models
Evolution of computational models in BioModels Database and the Physiome Model Repository
BMC Systems Biology 12:53 (2018)
SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies
Oxford Bioinformatics 33:8, pp. 1253–1254 (2017)
COMODI: An ontology to characterise differences in versions of computational models in biology
Open Access article in the Journal of Biomedical Semantics 7:46 (2016)
The Cardiac Electrophysiology Web Lab
Open Access article in the Biophysical Journal 110:2, pp 292-300 (2016)
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)
Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models
Harmonizing semantic annotations for computational models in biology
Brief Bioinform. (Epub ahead of print)
Toward community standards and software for whole-cell modeling
Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 2007-14 (2016)
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)
Improving the reuse of computational models through version control
Article in BIOINFORMATICS 29:6, pp. 742-7 (2014)
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices
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
Vertrauen oder Kontrolle? Meine Gesundheitsdaten und ich
Invited talk and panel discussion in the series "Vier Augen. Lebenswissenschaften in der Kontroverse" (2019)
Venue: Alfried Krupp Wissenschaftskolleg Greifswald
URL: https://www.wiko-greifswald.de/programm/vortraege/aktuelle-schwerpunkte/vier-augen/
Model Management in Systems Biology: Challenges – Approaches – Solutions
A talk in the FAIRDOM webinar series 2016
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, germany (2015)
Venue: Hamburg, Germany
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)
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)
Venue: Lisbon, Portugal
Improving Reproducibility and Reuse of Modelling Results in the Life Sciences
Research results are complex and include a variety of heterogeneous data. This entails major computational challenges to (i) to manage simulation studies, (ii) to ensure model exchangeability, stability and validity, and (iii) to foster communication between partners. I describe techniques to improve the reproducibility and reuse of modelling results. First, I introduce a method to characterise differences in computational models. Second, I present approaches to obtain shareable and reproducible research results. Altogether, my methods and tools foster exchange and reuse of modelling results.
Defense: 30 August 2018