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Development of a Biostatistical Software Framework

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Master Thesis Project at the Brandenburg University of Technology Cottbus–Senftenberg

Proposed Project Title:
“Development of a Biostatistical Software Framework for the Analysis of Amplification Curve Data, Melting Curve Data and digital PCR Experiments”

The InnoProfile-Transfer research group “Imagebased assays” at the Brandenburg University of Technology Cottbus – Senftenberg (Campus Senftenberg) offers the opportunity to carry out a Master thesis projects as part of an interdisciplinary project with strong foundations in both basic and applied research. We have an intense collaboration with small and medium-sized businesses. Our group focuses on the development of novel an innovative multi-parameter assays for life sciences and diagnostics. The scope of our working group is deliberately broad covering:
  • Medical and environmental Microbiogy
  • Molecular biology
  • Nucleic acid detection technologies (Real-Time-PCR, Microbead-based PCR)
  • Multiparamter biomolecule detection (small nucleic acids, proteins, …),
  • Microbead-based assays,
  • Statistical Bioinformatics (digtial PCR, …),
The foundation of our work is a highly versatile microscope imaging technology platform for the multiplex real-time detection of biomolecules and autoimmune antibodies [1]. For more about the working group information please visit
The analysis of amplification curve data, melting curve data and digital PCR experiment data is of prime importance in life sciences and diagnostic applications. Numerous technological platforms have been developed, which can be used for the analysis. An example is our VideoScan technology, which is a highly versatile multi-parametric diagnostic tool [1]. The data analysis is often done with in-house made software or closed source software, which is hard to distribute among users. In particular, the statistical processing of the data is often done in software, which are not optimal for the given use case scenario. Therefore, we implemented several plug-ins for the RKWard [2] statistical software package. RKWard is a comprehensive GUI and IDE for R. Numerous R packages have been developed, which can be used to analyze amplification curve data and related data sets [3]. Recently we published a set of R packages (MBmca, chipPCR, dpcR, RDML), which specifically address further applications.

Your Scope:
  • Conduct a survey of steps required for an analysis of amplification curve data, melting curve data and digital PCR experiment
  • Sketch an efficient architecture
  • Implement import, export and report generation mechanisms for the VideoScan platform and related technologies
  • Use literate programming/WEB system developed by Don Knuth
  • Implement plug-ins for RKWard
  • Evaluate the user experience on empirical data
  • Evaluate the performance of the implementation for high-throughput applications
  • Evaluate the distribution of the software on different platforms (e. g., Linux, MS Windows, Mac OS)
  • Survey the applicability of the software for reproducible research
We expect that the software will result in a valuable tool for scientists working in the field. Therefore, we anticipate the outcome of the thesis will be submitted for publication in an international peer-reviewed journal.

Your qualification:
  • Keen interest in life sciences and applied statistical bioinformatics
  • Basic understanding of amplification curve data, melting curve data and digital PCR experiment
  • Completed Bachelor & ongoing Master curriculum in bio/informatics, engineering, natural sciences, biotechnology or related subject
  • Some experience in GUI design, (scripting) languages (R, ECMA Script, XML) and version control (preferably git)
  • Advanced understanding of statistical bioinformatics
  • Advanced knowledge of R and keen interest to learn independently new technologies
  • Ability to think and perform independently. Your work on your own, your advisor will only suggest a direction and the rest is up to you.
Further Reading:

[1] Rödiger, S. et al., 2013. A highly versatile microscope imaging technology platform for the multiplex real-time detection of biomolecules and autoimmune antibodies. Adv. Biochem. Eng. Biotechnol. 133, 35–74. doi:10.1007/10_2011_132

[2] Rödiger, S. et al., 2012. RKWard: A Comprehensive Graphical User Interface and Integrated Development Environment for Statistical Analysis with R. Journal of Statistical Software 49, 1–34.

[3] Pabinger, S., Rödiger, S., et al., 2014. A survey of tools for the analysis of quantitative PCR (qPCR) data. Biomolecular Detection and Quantification.


Art des Bewerbungszugangs
Kontakt für Bewerbungen
Dr. Stefan Rödiger
BTU Cottbus – Senftenberg
Campus Senftenberg
Faculty of Natural Sciences
Group Leader

Großenhainer Str. 57
01968 Senftenberg, Germany

Details der Stellenanzeige

Befristete Anstellung
Diplom- & Masterarbeit
Berufserfahrung nicht vorausgesetzt
Deutschland (Brandenburg)
01968 Senftenberg
Informatik, Biologie & Life Sciences, Healthcare & Gesundheitswesen, Biotechnologie, Elektrotechnik, Medizintechnik