SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
+49 381 498-7571
Version control in computational biology
"I am interested in the development of frameworks for improved reuse of models in computational biology."
The number of computational models describing biological systems is dramatically increasing. These models evolve over time and are subject to constant change and re-engineering. Due to the complexity of such models it is nearly impossible for the scientist to identify these modifications and to understand what has been done and what was the reason for that. In addition there are many models describing the same or similar systems, developed in the scope of different projects. What are the differences between these models? Do they just differ in their notation or are there any discrepancies or contradictions?
Our task is to develop tools to identify differences between computational models and to transfer these differences into an human readable format, to support the reuse of these models. On the one hand we are dedicated to develop a version control system for computational models that tracks the history and the evolution of a model over time. On the other hand we aim to identify and to analyze differences in models of similar systems. These works are crucial for the organization of large numbers of models and they improve the model reuse.
January 2016 - present
Head of IT at the SBI (infrastructure, acquisition, maintenance, innovation etc)
Aug 2012 - present
PhD-Student at the SBI Team at the University of Rostock,
|Sep 2013 - Dec 2013||
Science2020 intern at the University of Oxford,
|2006 - 2012||
Student of Bioinformatics
- Research (Reading, Thinking, Developing, Publishing, Collaborating)
- Programming (C, Java, PHP, Python, Perl, Shell, Gnu R, etc)
- Administration (Docker, Web, Databases, Monitoring, Logic)
|since years||Fellow of the Free Software Foundation Europr|
|since years||Member of the Chaos Computer Club|
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)
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)
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)
The Cardiac Electrophysiology Web Lab
Cooper J, Scharm M, and Mirams GR
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
Scharm M, Wolkenhauer O, and Waltemath D
Open Access article in BIOINFORMATICS 32:4, pp. 563-570 (2015)
Harmonizing semantic annotations for computational models in biology
Neal M, Dräger A, Wolkenhauer O et al.
Brief Bioinform. (Epub ahead of print)
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)
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)
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)
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
Scharm M and Waltemath D
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.
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)
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
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