Dr. Martin Scharm

Fighting for open knowledge, transparency, and free software. Working to improve reproducibility and reuse of research results. Paid to keep the SBI visible and online.

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.


2016 - present

Head of IT at the SBI (infrastructure, acquisition, maintenance, innovation etc)

2012 -2018

PhD-Student at the SBI Team at the University of Rostock,


Research Internship at the University of Manchester,



Science2020 intern at the University of Oxford,

2006 - 2012

Student of Bioinformatics
Martin Luther University Halle-Wittenberg



  • 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


Selected publications

GEMtractor: Extracting Views into Genome-scale Metabolic Models

Scharm M, Wolkenhauer O, Jalili M, Salehzadeh-Yazdi A

Under review at Bioinformatics (2019).

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)

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

Scharm M, Stanford NJ, Dobson PD et al.

Springer (2019), chapter in Yeast Systems Biology.
Methods in Molecular Biology.

Vertrauen oder Kontrolle? Meine Gesundheitsdaten und ich

Martin Scharm

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

Scharm M

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

Scharm M

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