Florian Finkernagel
Bioinformatician
Marburg, Hesse, Germany
Summary
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RockstarFlorian Finkernagel is a bioinformatician based in Marburg, Germany, with 16 years of experience building robust tools for genomic analysis and visualization. He contributes to core bioinformatics infrastructure—most notably improving pysam’s alignment and coverage APIs—demonstrating deep familiarity with SAM/BAM/VCF data models and HTSlib internals. Florian also brings strong data-science sensibilities, enhancing plotnine’s visualization primitives to make complex genomic results more interpretable. His work on static site tooling and code-quality improvements shows an attention to reproducible documentation and developer ergonomics beyond pure research code. Colleagues benefit from his blend of backend engineering rigor and practical visualization skills, applied to challenging domains like ovarian carcinoma research.
16 years of coding experience
Github Skills (19)
python10
image-processing10
pandas10
plot10
graphic10
grammar10
grammars10
htslib10
static-site10
cython10
bioinformatics10
data-analysis10
api-design9
lxml9
data-structures8
Programming languages (19)
Github contributions (5)
has2k1/plotnine
Sep 2018 - Sep 2021
A Grammar of Graphics for Python
Role in this project:
Data Scientist
Data ScientistContributions:21 commits, 25 PRs, 171 comments in 3 years
Contributions summary:Florian primarily contributed to enhancing the functionality of the `plotnine` library, which focuses on data visualization. The commits demonstrate a focus on improving existing plotting elements like `geom_label` and `geom_spoke`, adding new features like `annotation_logticks`, and refactoring existing code to enhance performance. These changes reflect the user's involvement in extending the library's capabilities for creating more complex and informative visualizations, indicative of a data science focus.
data-analysispythongrammar-of-graphicsgrammarplotting
pysam-developers/pysam
Mar 2015 - Aug 2016
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
Role in this project:Back-end Developer
Back-end DeveloperContributions:10 commits, 10 PRs, 11 comments in 1 year 4 months
Contributions summary:Florian contributed significantly to the pysam project, focusing on improving the `get_aligned_pairs` and `count_coverage` methods within the `AlignmentFile` class. They added support for various CIGAR entries in `get_aligned_pairs` and introduced a new `count_coverage` function with multiple filtering options. Furthermore, the user made adjustments to the documentation, enhancing the clarity of the API for `PileupRead` objects. These changes indicate a focus on core functionality and usability within the bioinformatics library.
bcftoolsapipythonbcfpowers
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