Dr. Martin Scharm

Fighting for open knowledge, transparency, and free software. Working to improve reproducibility and reuse of research results. Looking for challenging data and complex systems.

Research interest

Management of Computational Models

In-silico simulation of biological systems has become a standard tool in the life sciences. Consequently, the number and complexity of computational models describing biological systems is increasing, which entails numerous organisational challenges.
I am developing tools and methods to improve the management of computational models, including:

  • Versioning, Comparison, and Merging of models
  • Data Integration and Tool Interoperability
  • Dissemination of Reproducible Research Results
  • Organisation and Representation of Knowledge

Mining, Analysing, and Presenting Complex Data

Data is supposed to be the oil of the 21st century. Collecting the data may be difficult, but integrating, processing, and understanding it is significantly harder.
I am ready to be challenged by convoluted data and enjoy for example:

  • Mining, Converting, and Massaging Data
  • Finding Patterns and Artifacts
  • Visualising and Presenting Complex Structures
  • Communicating facts, structures, and results to experts and the general public



2020 - present

Freelancing with CODE AHOI

2018 - 2020

PostDoc at the SBI

University of Rostock, Rostock/Germany

2016 - 2020

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

2012 -2018

PhD-Student at the SBI

University of Rostock, Rostock/Germany


Research Internship

University of Manchester, Manchester/UK


Science2020 intern

University of Oxford, Oxford/UK

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

Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models

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

GEMtractor: Extracting Views into Genome-scale Metabolic Models

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

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