CV: Martin Scharm

	Personal Information
Date of Birth	27. Oct. 1985
Nationality	Germany
Address	Warschauer Str. 22 18057 Rostock Germany
Work	Dept. of Systems Biology and Bioinformatics Ulmenstrasse 69 (building 3, 3rd floor) 18057 Rostock Germany
Web	Personal Blog Website at the Research Group Twitter GitHub LinkedIn LessComplex
Contact	see contact details
	Education
2005	John-Brinckmann-Gymnasium in Güstrow (Grammar School/High School), Abitur.
2006 - 2012	Martin-Luther-University in Halle-Wittenberg, Study of Bioinformatics. Grade: very good (1.0)
2012	Martin-Luther-University in Halle-Wittenberg, Diploma in Bioinformatics, Thesis: Bioinformatische Analyse von LC/MS-Daten zur Bestimmung von Biomarkern in Elastinproben. Grade: very good (1.0)
2011Sep - Oct	University of Reims Champagne-Ardenne, Internship.
2013Sep - Dec	University of Oxford, Science2020 Internship.
2015May - Jul	University of Manchester, Research stay.
2012 - 2018	University of Rostock, PhD candidate.
2012	University of Rostock, Dr.-Ing., Dissertation: Improving Reproducibility and Reuse of Modelling Results in the Life Sciences. Grade: magna cum laude
2018 - now	University of Rostock, Postdoctoral Researcher.
	Work Experience
2008 - 2012	Systems Administrator, Dept. of Computer Science, Martin-Luther-University in Halle-Wittenberg.
2011Sep - Oct	Intern in a research group, University of Reims Champagne-Ardenne.
2013Sep - Dec	Intern of the Science2020 project, University of Oxford.
2015May - July	Intern of the Information Management Group, School of Computer Science, University of Manchester.
2012 - now	Research Associate, Dept. of Systems Biology and Bioinformatics, University of Rostock.
2016 - now	Systems Engineer and Administrator, University of Rostock.
	Awards
2011	Scholarship of the Institut für angewandte Dermatopharmzie
2012	Scholarship of the Graduiertenförderung of Sachsen-Anhalt
2013	Award of the Georg-Cantor-Association
2015	HERMES research funding of the University of Rostock
2020	MTZ®-Award for Medical Systems Biology
	Misc & Skills
2011	Second place in Programming Contest of FreiesMagazin
2012October	Official motor boat licence (lake and sea)
2014 - 2015	Learnt sign language
2012 - now	Advanced Trainings on: Docker SSL/TLS and web security Statistics with R Networks and Operating Systems
2012 - now	Trainings and Courses to improve my soft skills: Scientific Academic Writing Networking for Scientists Slidewriting Writing: From frustration to passion Logic and Argumentation Producinig Videos for Teaching Didactic Design
2014	Third place in Programming Contest of FreiesMagazin
2014 - now	Speaker of the Graduate Academy at the University of Rostock
2015 - now	Appointed first aider at the Institute for Computer Science, University of Rostock
2017	Initiated and developed the DeinWal project to support the federal elections 2017. DeinWal.de reached millions of people.


	Publications
	Refereed Journals
2020January	Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi: GEMtractor: Extracting Views into Genome-scale Metabolic Models. Bioinformatics 36:10; [download — 10.1093/bioinformatics/btaa068]
2018April	Martin Scharm, Tom Gebhardt, Vasundra Touré, Andrea Bagnacani, Ali Salehzadeh-Yazdi, Olaf Wolkenhauer, Dagmar Waltemath: Evolution of computational models in BioModels Database and the Physiome Model Repository. BMC Systems Biology 12:53; [10.1186/s12918-018-0553-2]
2017January	Frank T. Bergmann, David Nickerson, Dagmar Waltemath, Martin Scharm: SED-ML web tools: generate, modify and export standard-compliant simulation studies. Bioinformatics 33:8, pp. 1253–1254; [10.1093/bioinformatics/btw812]
2016October	Dagmar Waltemath, Jonathan R. Karr, Frank T. Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Martin Scharm, et al.: Toward community standards and software for whole-cell modeling. IEEE Transactions on Biomedical Engineering 63:10, pp. 2007-14; [download — 10.1109/TBME.2016.2560762]
2016September	Martin Scharm, Dagmar Waltemath: A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos [version 1; referees: 1 approved, 2 approved with reservations]. F1000Research 5:2421; [10.12688/f1000research.9379.1]
2016July	Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer: COMODI: An ontology to characterise differences in versions of computational models in biology. Journal of Biomedical Semantics 2016 7:46; [download — 10.1186/s13326-016-0080-2]
2016January	Jonathan Cooper, Martin Scharm, Gary R. Mirams: The Cardiac Electrophysiology Web Lab. Biophysical Journal 110(2): 292-300; [download — 10.1016/j.bpj.2015.12.012]
2015October	Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinformatics 32 (4): 563-570; [download — 10.1093/bioinformatics/btv484]
2014December	Frank T. Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère: COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics 15:369; [download — 10.1186/s12859-014-0369-z]
2013January	Dagmar Waltemath, Ron Henkel, Robert Haelke, Martin Scharm, Olaf Wolkenhauer: Improving the reuse of computational models through version control. Bioinformatics 29(6), 742-748; [download — 10.1093/bioinformatics/btt018]
	Proceedings
2019October	Martin Scharm, Nataly J Stanford, Poul D Dobson, et al.: Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Springer; pp 285-314 Warning: Undefined array key "eventlink" in /site/index.php on line 222 Warning: Undefined array key "event" in /site/index.php on line 222 ; New York, NY; [download]
2015March	Martin Scharm, Dagmar Waltemath: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit. In GI-Edition Lecture Notes in Informatics (LNI); Workshop on Data Management for Life Sciences (DMforLS 2015) @ Datenbanksysteme für Business, Technologie und Web (BTW 2015); Hamburg, GER; [download]
2014December	Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom Theile, Dagmar Waltmath: The CombineArchiveWeb application — A web based tool to handle files associated with modelling results. In Proceedings of the SWAT4LS 2014; Semantic Web Applications and Tools for Life Sciences (SWAT4LS); Berlin, GER; [download]
2014July	Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Identifying, Interpreting, and Communicating Changes in XML-encoded Models of Biological Systems. In Proceedings of the 10th International Conference on Data Integration in the Life Sciences (DILS); Data Integration in the Life Sciences; Lisbon, PT; [download]
	Talks and Presentations
2019May	Martin Scharm: Vertrauen oder Kontrolle? Meine Gesundheitsdaten und ich. (Invited Talk) Warning: Undefined array key "eventlink" in /site/index.php on line 247 Vortragsreihe “Vier Augen. Lebenswissenschaften in der Kontroverse”; Alfried Krupp Kolleg Greifswald; Greifswald, GER
2016July	Martin Scharm, Dagmar Waltemath: Model Management in Systems Biology: Challenges – Approaches – Solutions . (Webinar) Warning: Undefined array key "location" in /site/index.php on line 247 FAIRDOM webinar series 2016; ; [download]
2016June	Markus Wolfien, Andrea Bagnacani, Tom Gebhardt, Martin Scharm: A Modeler's Tale. (Invited Talk) 10th International CellML Workshop; Auckland, New Zealand; Movie available from Figshare as 10.6084/m9.figshare.3423371.v1
2015November	Dagmar Waltemath, Martin Scharm: Tutor for COMBINE standards. (Tutor at a Workshop) COMBINE Tutorial; Singapore
2015October	Martin Scharm, Dagmar Waltemath: COMBINE Meta-data. (Break-Out-Session) COMBINE 2015; Salt Lake City, USA
2015September	Martin Scharm, Martin Peters: Tutor for COMBINE archives. (Tutor at a Workshop) Workshop on Citable Data and Reproducible Models; Warnemünde, GER
2015September	Martin Scharm, Dagmar Waltemath: Characterising differences in model versions. (Conference Talk) e:Bio Statusseminar; Essen, GER; [download]
2015July	Martin Scharm: Sharing Reproducible Research Results. (Invited Talk) Manchester University; Manchester, UK
2015May	Martin Scharm: Evolution of Computational Models in Systems Biology: what's the matter — what's there — what's next. (Invited Talk) School of Computer Science, Manchester University; Manchester, UK
2015April	Martin Scharm: M2CAT: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit. (Conference Talk) 9th international CellML Workshop; Waiheke Island, Auckland, NZ; [download]
2015April	Martin Scharm: M2CAT: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit. (Seminar Talk) SBI Research Seminar; Rostock, GER; [download]
2015April	Martin Scharm: HandsOn: git (or version control in general...). (Seminar Talk) Hochleistungslabor meeting; Rostock, GER; [download]
2015March	Martin Scharm, Dagmar Waltemath: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit. (Conference Talk) Workshop on Data Management for Life Sciences (DMforLS 2015) @ Datenbanksysteme für Business, Technologie und Web (BTW 2015); Hamburg, GER; [download]
2014December	Martin Scharm: The CombineArchiveWeb application — A web based tool to handle files associated with modelling results. (Demo) Semantic Web Applications and Tools for Life Sciences (SWAT4LS); Berlin, GER; [download]
2014October	Martin Scharm: The CombineArchive Toolkit - facilitating the transfer of research results. (Conference Talk) FAIRDOM Foundry Workshop; Heidelberg, GER; [download]
2014October	Martin Scharm: The CombineArchive Toolkit - facilitating the transfer of research results. (Seminar Talk) SBI Research Seminar; Rostock, GER; [download]
2014September	Dagmar Waltemath, Martin Scharm, Olaf Wolkenhauer: The COMBINE archive and the CombineArchive Toolkit. (Conference Talk) e:Bio Statusseminar; Berlin, GER; [download]
2014April	Martin Scharm: The CellML models' walk through the repository: a retrospective study. (Conference Talk) 8th international CellML Workshop; Waiheke Island, Auckland, NZ; [download]
2013November	Martin Scharm: Improving the Management of Computational Models. (Invited Talk) European Bioinformatics Institute (EBI); Cambridge, UK; [download]
2013September	Martin Scharm: BiVeS & BudHat: Difference Detection for Computational Models. (Conference Talk) COMBINE 2013; Paris, Fr; [download]
2013June	Martin Scharm: Model version control for computational biology. (Invited Talk) IPK (Leibniz Institute); Gatersleben, GER; [download]
2013May	Martin Scharm: BudHat: Version Control for Computational Models. (Conference Talk) HARMONY 2013; Farmington, CT, USA; [download]
2013March	Martin Scharm: BiVeS & BudHat: Version Control for Computational Models. (Conference Talk) 7th international CellML Workshop; Waiheke Island, Auckland, NZ; [download]
2013March	Martin Scharm: BudHat: Version Control for Computational Models. (Software Demo) International Symposium on Integrative Bioinformatics (IB); Gatersleben, GER
2012November	Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer: BiVeS & BudHat — Version Control for Computational Models. (Invited Talk) Sysmo-PALs meeting; Heidelberg, GER; [download]
2012September	Schmelzer CEH, Scharm M, Jung MC, Ruttkies CKH, Schräder C, Pankau R, Neubert RHH, Heinz A: Insights into the molecular alteration of elastic fibers. (Conference Talk) European ELASTIN meeting; Ghent, BEL
2011September	Schmelzer CEH, Scharm M, Jung MC, Heinz A, Ruttkies CKH, Pankau R, Wohlrab J, Neubert RHH: Molecular insights into the aging of elastic fibers. (Conference Talk) Jahrestagung der DPhG; Innsbruck, AUT
	Posters
2018September	Nina Fischer, Tom Gebhardt, Olga Krebs, Jan Hasenauer, Wolfgang Müller, Elba Raimundez, Martin Scharm, Olaf Wolkenhauer: INCOME — Improving collaborative research by model re-use, extension and integration. eMed Meeting 2018; Berlin
2015November	Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Diving into open Model Repositories: Investigating the Evolution of Computational Models. ICSB 2015; Singapore
2015October	Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: COMODI - because computational models differ. COMBINE 2015; Salt Lake City, US; [download]
2015March	Gary Mirams, Martin Scharm, Jonathan Cooper: A Web Lab for Cardiac Electrophysiology. Gordon Research Conference on Cardiac Arrhythmia Mechanisms; Lucca (Barga), IT; [download]
2015March	Martin Scharm, Vivek Garg, Srijana Kayastha, Martin Peters, Dagmar Waltemath: Improving the Management of Simulation Studies in Computational Biology. WholeCell Summer School; Rostock, GER; [download]
2015March	Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom Theile, Dagmar Waltmath: The CombineArchiveToolkit — facilitating the transfer of research results. WholeCell Summer School; Rostock, GER; [download]
2014December	Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: SEMS: Managing simulation models in systems biology. DAAD Science Tour 2014: Modelling the Future; Rostock, GER; [download]
2014December	Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Identifying, Interpreting, and Communicating Changes in XML-encoded Models of Biological Systems. DAAD Science Tour 2014: Modelling the Future; Rostock, GER; [download]
2014December	Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom Theile, Dagmar Waltmath: The CombineArchive Toolkit — facilitating the transfer of research results.. Semantic Web Applications and Tools for Life Sciences (SWAT4LS); Berlin, GER; [download]
2014December	Martin Scharm, Florian Wendland, Martin Peters, Markus Wolfien, Tom Theile, Dagmar Waltmath: The CombineArchiveToolkit — facilitating the transfer of research results. DAAD Science Tour 2014: Modelling the Future; Rostock, GER; [download]
2014September	Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Identifying, Interpreting, and Communicating Changes in XML-encoded Models of Biological Systems. e:Bio Statusseminar; Berlin, GER; [download]
2014July	Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Identifying, Interpreting, and Communicating Changes in XML-encoded Models of Biological Systems. 10th International Conference on Data Integration in the Life Sciences (DILS); Lisbon, PT; [download]
2014April	Martin Peters, Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Combining model management tools developed in SEMS. HARMONY 2014; Manchester, UK; [download]
2014April	Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: We did the statistics, your turn to analyze!. — An interactive Poster to be annotated by the visitors. HARMONY 2014; Manchester, UK; [download]
2014April	Ron Henkel, Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: The SEMS Project: Managing Simulation Models. HARMONY 2014; Manchester, UK; [download]
2013September	Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: Disentangling the Evolution of Computational Models. COMBINE 2013; Paris, Fr; [download]
2013May	Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: Disentangling the Evolution of Computational Models. HARMONY 2013; Farmington, CT, USA; [download]
2013May	Dagmar Waltemath, Ron Henkel, Rebekka Alm, Martin Scharm, Olaf Wolkenhauer: Managing Computational Models and Associated Simulation Descriptions in Standard Formats. HARMONY 2013; Farmington, CT, USA; [download]
2013March	Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: Disentangling the Evolution of Computational Models. International Symposium on Integrative Bioinformatics (IB); Gatersleben, GER; [download]
2013March	Dagmar Waltemath, Ron Henkel, Rebekka Alm, Martin Scharm, Olaf Wolkenhauer: Managing Computational Models and Associated Simulation Descriptions in Standard Formats. International Symposium on Integrative Bioinformatics (IB); Gatersleben, GER; [download]
2011November	Scharm M, Jung MC, Heinz A, Neubert RHH, Schmelzer CEH: IonHunter - Rapid Biomarker Discovery. Mass Spec Europe; Dublin, IRL
2011July	Jung MC, Scharm M, Heinz A, Pankau R, Wohlrab J, Sivan S, Merkher Y, Maroudas A, Neubert RHH, Schmelzer CEH: Molecular comparison of elastins from different human tissues. Gordon Research Conference Elastin & Elastic Fibers; Biddeford, ME, USA
	Teaching and Supervision
2016Autumn	Supervision of Bachelor Thesis at University of Rostock: I supervised a Bachelor's thesis on a Storage Solution for Models with Multiple Versions in Systems Biology: Concept and Prototype Implementation by Martin Peters. Thesis and code is available from GitHub.
2015Summer	Projektstudium at University of Rostock: The Projektstudium is offered by the Dept. of Business Informatics and spans 4 hours per week. The students work together on a whole project with a specific focus on project design (Gantt, Milestones, etc), communication with customers, project implementation on schedule and documentation.
2014 - now	Supervision of Pupils and Interns at University of Rostock: Present the business at our department for systems biology. Show the different aspects of research and academics. Among others we developed a self-driving car based on a neural network and did a lot with the Raspberry Pi...
2013 - now	Supervision of Student Assistants at University of Rostock: Among others: Development of web-based platforms and libraries, integration heterogeneous software solutions, development of an ontology.