martin scharm
Personal Information
Date of Birth27. Oct. 1985
NationalityGermany
AddressWarschauer Str. 22
18057 Rostock
Germany
WorkDept. 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
Contactsee contact details
Education
2005John-Brinckmann-Gymnasium in Güstrow (Grammar School/High School), Abitur.
2006 - 2012Martin-Luther-University in Halle-Wittenberg, Study of Bioinformatics. Grade: very good (1.0)
2012Martin-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 - OctUniversity of Reims Champagne-Ardenne, Internship.
2013Sep - DecUniversity of Oxford, Science2020 Internship.
2015May - JulUniversity of Manchester, Research stay.
2012 - nowUniversity of Rostock, PhD candidate.
Work Experience
2008 - 2012Systems Administrator, Dept. of Computer Science, Martin-Luther-University in Halle-Wittenberg.
2011Sep - OctIntern in a research group, University of Reims Champagne-Ardenne.
2013Sep - DecIntern of the Science2020 project, University of Oxford.
2015May - JulyIntern of the Information Management Group, School of Computer Science, University of Manchester.
2012 - nowResearch Associate, Dept. of Systems Biology and Bioinformatics, University of Rostock.
2016 - nowSystems Engineer and Administrator, University of Rostock.
Awards
2011Scholarship of the Institut für angewandte Dermatopharmzie
2012Scholarship of the Graduiertenförderung of Sachsen-Anhalt
2013Award of the Georg-Cantor-Association
2015HERMES research funding of the University of Rostock
Misc & Skills
2011Second place in Programming Contest of FreiesMagazin
2012OctoberOfficial motor boat licence (lake and sea)
2014 - 2015Learnt sign language
2012 - nowAdvanced Trainings on:
  • Docker
  • SSL/TLS and web security
  • Statistics with R
  • Networks and Operating Systems
2012 - nowTrainings 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
2014Third place in Programming Contest of FreiesMagazin
2014 - nowSpeaker of the Graduate Academy at the University of Rostock
2015 - nowAppointed first aider at the Institute for Computer Science, University of Rostock
Publications
Refereed Journals
2017JanuaryFrank T. Bergmann, David Nickerson, Dagmar Waltemath, Martin Scharm: SED-ML web tools: generate, modify and export standard-compliant simulation studies. Bioinformatics ; [10.1093/bioinformatics/btw812]
2016OctoberDagmar 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; [download10.1109/TBME.2016.2560762]
2016JulyMartin 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; [download10.1186/s13326-016-0080-2]
2016JanuaryJonathan Cooper, Martin Scharm, Gary R. Mirams: The Cardiac Electrophysiology Web Lab. Biophysical Journal 110(2): 292-300; [download10.1016/j.bpj.2015.12.012]
2015OctoberMartin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinformatics 32 (4): 563-570; [download10.1093/bioinformatics/btv484]
2014DecemberFrank 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; [download10.1186/s12859-014-0369-z]
2013JanuaryDagmar Waltemath, Ron Henkel, Robert Haelke, Martin Scharm, Olaf Wolkenhauer: Improving the reuse of computational models through version control. Bioinformatics 29(6), 742-748; [download10.1093/bioinformatics/btt018]
Proceedings
2015MarchMartin 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]
2014DecemberMartin 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]
2014JulyMartin 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
2016JulyMartin Scharm, Dagmar Waltemath: Model Management in Systems Biology: Challenges – Approaches – Solutions . (Webinar) FAIRDOM webinar series 2016; ; [download]
2016JuneMarkus 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
2015NovemberDagmar Waltemath, Martin Scharm: Tutor for COMBINE standards. (Tutor at a Workshop) COMBINE Tutorial; Singapore
2015OctoberMartin Scharm, Dagmar Waltemath: COMBINE Meta-data. (Break-Out-Session) COMBINE 2015; Salt Lake City, USA
2015SeptemberMartin Scharm, Dagmar Waltemath: Characterising differences in model versions. (Conference Talk) e:Bio Statusseminar; Essen, GER; [download]
2015SeptemberMartin Scharm, Martin Peters: Tutor for COMBINE archives. (Tutor at a Workshop) Workshop on Citable Data and Reproducible Models; Warnemünde, GER
2015JulyMartin Scharm: Sharing Reproducible Research Results. (Invited Talk) Manchester University; Manchester, UK
2015MayMartin 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
2015AprilMartin Scharm: M2CAT: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit. (Conference Talk) 9th international CellML Workshop; Waiheke Island, Auckland, NZ; [download]
2015AprilMartin Scharm: M2CAT: Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit. (Seminar Talk) SBI Research Seminar; Rostock, GER; [download]
2015AprilMartin Scharm: HandsOn: git (or version control in general...). (Seminar Talk) Hochleistungslabor meeting; Rostock, GER; [download]
2015MarchMartin 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]
2014DecemberMartin 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]
2014OctoberMartin Scharm: The CombineArchive Toolkit - facilitating the transfer of research results. (Conference Talk) FAIRDOM Foundry Workshop; Heidelberg, GER; [download]
2014OctoberMartin Scharm: The CombineArchive Toolkit - facilitating the transfer of research results. (Seminar Talk) SBI Research Seminar; Rostock, GER; [download]
2014SeptemberDagmar Waltemath, Martin Scharm, Olaf Wolkenhauer: The COMBINE archive and the CombineArchive Toolkit. (Conference Talk) e:Bio Statusseminar; Berlin, GER; [download]
2014AprilMartin Scharm: The CellML models' walk through the repository: a retrospective study. (Conference Talk) 8th international CellML Workshop; Waiheke Island, Auckland, NZ; [download]
2013NovemberMartin Scharm: Improving the Management of Computational Models. (Invited Talk) European Bioinformatics Institute (EBI); Cambridge, UK; [download]
2013SeptemberMartin Scharm: BiVeS & BudHat: Difference Detection for Computational Models. (Conference Talk) COMBINE 2013; Paris, Fr; [download]
2013JuneMartin Scharm: Model version control for computational biology. (Invited Talk) IPK (Leibniz Institute); Gatersleben, GER; [download]
2013MayMartin Scharm: BudHat: Version Control for Computational Models. (Conference Talk) HARMONY 2013; Farmington, CT, USA; [download]
2013MarchMartin Scharm: BiVeS & BudHat: Version Control for Computational Models. (Conference Talk) 7th international CellML Workshop; Waiheke Island, Auckland, NZ; [download]
2013MarchMartin Scharm: BudHat: Version Control for Computational Models. (Software Demo) International Symposium on Integrative Bioinformatics (IB); Gatersleben, GER
2012NovemberMartin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer: BiVeS & BudHat — Version Control for Computational Models. (Invited Talk) Sysmo-PALs meeting; Heidelberg, GER; [download]
2012SeptemberSchmelzer 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
2011SeptemberSchmelzer 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
2015NovemberMartin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Diving into open Model Repositories: Investigating the Evolution of Computational Models. ICSB 2015; Singapore
2015OctoberMartin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: COMODI - because computational models differ. COMBINE 2015; Salt Lake City, US; [download]
2015MarchGary Mirams, Martin Scharm, Jonathan Cooper: A Web Lab for Cardiac Electrophysiology. Gordon Research Conference on Cardiac Arrhythmia Mechanisms; Lucca (Barga), IT; [download]
2015MarchMartin Scharm, Vivek Garg, Srijana Kayastha, Martin Peters, Dagmar Waltemath: Improving the Management of Simulation Studies in Computational Biology. WholeCell Summer School; Rostock, GER; [download]
2015MarchMartin 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]
2014DecemberMartin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: SEMS: Managing simulation models in systems biology. DAAD Science Tour 2014: Modelling the Future; Rostock, GER; [download]
2014DecemberMartin 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]
2014DecemberMartin 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]
2014DecemberMartin 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]
2014SeptemberMartin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Identifying, Interpreting, and Communicating Changes in XML-encoded Models of Biological Systems. e:Bio Statusseminar; Berlin, GER; [download]
2014JulyMartin 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]
2014AprilMartin Peters, Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: Combining model management tools developed in SEMS. HARMONY 2014; Manchester, UK; [download]
2014AprilMartin 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]
2014AprilRon Henkel, Martin Scharm, Dagmar Waltemath, Olaf Wolkenhauer: The SEMS Project: Managing Simulation Models. HARMONY 2014; Manchester, UK; [download]
2013SeptemberMartin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: Disentangling the Evolution of Computational Models. COMBINE 2013; Paris, Fr; [download]
2013MayMartin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: Disentangling the Evolution of Computational Models. HARMONY 2013; Farmington, CT, USA; [download]
2013MayDagmar 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]
2013MarchMartin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: Disentangling the Evolution of Computational Models. International Symposium on Integrative Bioinformatics (IB); Gatersleben, GER; [download]
2013MarchDagmar 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]
2011NovemberScharm M, Jung MC, Heinz A, Neubert RHH, Schmelzer CEH: IonHunter - Rapid Biomarker Discovery. Mass Spec Europe; Dublin, IRL
2011JulyJung 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
Reviews
2014MarchMartin Scharm, Dagmar Waltemath: for Data Integration in the Life Sciences (DILS)
2012DecemberUlf Liebal, Martin Scharm: for Evolutionary Bioinformatics
Teaching and Supervision
2016AutumnSupervision 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.
2015SummerProjektstudium 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 - nowSupervision 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 - nowSupervision of Student Assistants at University of Rostock:
Among others: Development of web-based platforms and libraries, integration heterogeneous software solutions, development of an ontology.

Curriculum vitae:CV of Martin Scharm