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

Martin Scharm

Image: Martin Scharm

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

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.

Academic Background

Aug 2012 - present
PhD-Student at the SBI Team at the University of Rostock,
Rostock/Germany

Sep 2013 - Dec 2013
Science2020 intern at the University of Oxford,
Oxford/UK


2006 - 2012
Student of Bioinformatics
Martin Luther University Halle-Wittenberg

Publications

M Scharm
Model Management in Systems Biology: Challenges – Approaches – Solutions

A talk in the FAIRDOM webinar series 2016
recordings: fair-dom.org/knowledgehub/webinars-2/martin-scharm/
slides: slideshare.net/binfalse/model-management-in-systems-biology-challenges-approaches-solutions

M Scharm, D Waltemath, P Mendes and O Wolkenhauer
COMODI: an ontology to characterise differences in versions of computational models in biology

Open Access article in J of Biomedical Semantics 7:46 (2016)
DOI: 10.1186/s13326-016-0080-2
URL: http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0080-2

D Waltemath, JR Karr, FT Bergmann, V Chelliah et al.
Toward community standards and software for whole-cell modeling

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 2007-14 (2016)
DOI:
10.1109/TBME.2016.2560762
URL: http://ieeexplore.ieee.org/document/7489010/

Jonathan Cooper, Martin Scharm, Gary R. Mirams
The Cardiac Electrophysiology Web Lab

Open Access article at the Biophysical Journal.
DOI: 10.1016/j.bpj.2015.12.012
URL: http://www.cell.com/biophysj/references/S0006-3495%2815%2904753-0

M Scharm, O Wolkenhauer and D Waltemath
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)
DOI: 10.1093/bioinformatics/btv484
URL: http://bioinformatics.oxfordjournals.org/content/32/4/563

M Scharm and D Waltemath
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 (2015)
URL: http://www.btw-2015.de/res/proceedings/Workshops/DMS/Scharm-Extracting_reproducible_sim.pdf (PDF)

M Scharm, F Wendland, M Peters, M Wolfien, T Theile, D Waltemath
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)
URL: http://ceur-ws.org/Vol-1320/paper_19.pdf
PeerJ Preprint: https://peerj.com/preprints/639/

FT Bergmann, R Adams, ... M Scharm, ... D Waltemath et al.
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)
DOI: 10.1186/s12859-014-0369-z
URL: bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0369-z 

M Scharm, O Wolkenhauer, D Waltemath
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)
URL: http://dils2014.inesc-id.pt/data/uploads/paper_42.pdf

D Waltemath, R Henkel, R Hälke, M Scharm, O Wolkenhauer
Improving the reuse of computational models through version control

Article in BIOINFORMATICS 29:6, pp. 742-7 (2014)
DOI: 10.1093/bioinformatics/btt018
URL: bioinformatics.oxfordjournals.org/content/29/6/742

Contact Details

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

phone: +49 381 498-7574
fax: +49 381 498-7572
mail: martin.scharm(at)uni-rostock.de

Collaborators & Partners

Federal Ministry for Education and Research (BMBF)