CV
Work experience
- 01/11/2020 - Present: Bioinformatician at European Molecular Biology Laboratory (EMBL), Heidelberg
- Development and maintenance of bioinformatics software for different research projects
- Adaptation of existing code and pipelines
- Providing programming and statistics support to the group members
- 01/01/2020 - 31/10/2020: Research software engineer at Institute for Computational Biomedicine, Germany
- Improvement of existing software tools for parallelised high performance computing
- Development of computational pipelines for benchmarking
- 01/10/2019 - 31/12/2020: Assistant programmer at European Molecular Biology Laboratory (EMBL) Heidelberg
- Developed analysis pipelines to use machine learning approaches to improve compound identification using Docker and Singularity container technology and Snakemake workflow manager
- Compared simulated data with experimental data generated on-site through different statistical methods
- Led the statistical analysis of several experimental data sets in collaboration with experimentalists
- 01/10/2016 - 31/09/2019: Demonstrator at Doctoral Training Center, University of Oxford
- Worked with students one-on-one to clarify concepts presented in lectures and marked students’ work
- Courses: essential maths, high performance computing, introduction to C++, computational biology, mathematical biology, introduction to programming
- 01/10/2016 - 31/09/2019: Teaching Assistant at Mathematical Institute, University of Oxford
- Courses: stochastic differential equations, stochastic modelling of biological processes, further mathematical biology
Education
- 11/10/2015 - 08/05/2021: PhD in Applied Mathematics, University of Oxford
- Thesis title: Efficient methods for simulating stochastic reaction-diffusion models on evolving domains
- Supervisor: Prof. Ruth Baker
- Implemented and analysed different stochastic models of reaction-diffusion systems
- Developed open-source packages for stochastic simulations and generation of non-uniform meshes
- Communicated scientific results in both oral presentations at international conferences and in scientific publications
- 03/10/2011 - 25/06/2015: Masters degree in Mathematics (Integrated), Durham University
- Joint undergraduate and masters degree in mathematics (MMath)
- Key subjects: PDEs, ODEs, Statistics, Complex Analysis, Numerical analysis
- Grade: 1st
Technical skills
- C++ (6 years): OpenMP, MPI, Boost, Pybind11, Chaste, C++98, C++11 and C++17 standards
- Python (7 years): Numpy, Matplotlib, Scipy and Pandas
- Container (2 years): Docker and Singularity
- Worflow management system (2 years): Snakemake and Nextflow
- Version control (6 years): Git and Subversion
- Bash shell (6 years)
- Matlab (1 year)
- LaTeX (5 years)
- HTML (2 years)
Publications
- Bartmanski, B. J., and Baker, R. E. (2019). “Effects of different discretisations of the Laplacian upon stochastic simulations of reaction-diffusion systems on both static and growing domains.” arXiv preprint arXiv:1911.11645.
- Bobadilla, A. V. P., Bartmanski, B. J., Grima, R., and Othmer, H. G. (2020). “The status of the QSSA approximation in stochastic simulations of reaction networks.” In 2018 MATRIX Annals (pp. 137-147). Springer, Cham.
- Bartmanski, B. J., and Baker, R. E. (2020). “StoSpa2: A C++ software package for stochastic simulations of spatially extended systems.” Journal of Open Source Software, 5(50), 2293.
Awards
- 11/10/2015: Engineering and Physical Sciences Research Council (EPSRC) Systems Biology PhD grant
- 01/07/2018: Oxford University Travel funding
- 01/02/2018: Winner of G-Research competition at University of Oxford
- 01/10/2018 - 31/09/2019: Mentor in ‘buddying’ scheme for incoming DPhil students at the Mathematical Institute, University of Oxford
- 16/06/2017 - 21/06/2017: Contributed interactive visualisations of heart development to a developmental biology group in the Oxford Science Festival 2017
Languages
- English - bilingual
- Polish - bilingual
- German - basic
- Spanish - intermediate
