Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Rebekka Alm

Image: Rebekka Alm

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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Research Interest

Using graph databases for storing simulation data
 "I am interested in providing a graph database that contains SED-ML encoded data."


The Simulation Experiment Description Markup Language (SED-ML) is a first attempt to reach the goal of exchangeability and reusability of simulation experiences. It is an XML format, developed as a community effort, involving international partners from different Systems Biology groups.
Since XML has a graph-like structure it is advantageous to use graph databases as storage model. Model data and simulation data is linked and Information Retrieval techniques are used toprovide a userfriendly search option. It's my task to construct a graph database suitable for  representing SED-ML data.
It is interesting to work with this very different database type. Graph databases are very different from relational and object databases that are usually teached to students. It's fun to shape the database schema and watch it grow.

Academic Background

2012 - present
Master Degree in Business Informatics
University of Rostock, Rostock/Germany

2008 - 2012
Bachelor Degree in Business Informatics
University of Rostock, Rostock/Germany

Contact Details

Systems Biology and Bioinformatics
Ulmenstrasse 69 (building 3, 3rd floor)
18057 Rostock, Germany
Room 413a

+49 381 498-7577
+49 381 498-7572
rebekka.alm@uni-rostock.de

Collaborators & Partners

University of Rostock
Rostock/Germany
Deutsche Forschungsgemeinschaft (DFG)