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.
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
Martin Luther University Halle-Wittenberg
A talk in the FAIRDOM webinar series 2016
Open Access article in J of Biomedical Semantics 7:46 (2016)
Open Access article at the Biophysical Journal.
Open Access article in BIOINFORMATICS 32:4, pp. 563-570 (2015)
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)
Open Access demo paper in Proceedings of the 2014 Workshop on Semantic Web Applications and Tools for life sciences (2014)
PeerJ Preprint: https://peerj.com/preprints/639/
Open Access article in BMC Bioinformatics 15:369 (2014)
Demo paper in Proceedings of the 10th International Conference on Data Integration in the Life Sciences, Lisbon, Portugal (2014)
Article in BIOINFORMATICS 29:6, pp. 742-7 (2014)
Dept. of Systems Biology and Bioinformatics,
Ulmenstrasse 69 (building 3, 3rd floor)
18057 Rostock, Germany
phone: +49 381 498-7574
fax: +49 381 498-7572