Software

This page lists open source software. Beyond what is listed, I have created and contributed to unpublished software in industry (machine learning, data science & engineering, photovoltaics simulations) and academic research (computational physics, causal inference) since 2009.

Initial conception & development

• lamindb: A data framework for biology
• Scanpy: Single-cell analysis in Python
• anndata: Annotated data
• PAGA: Mapping out the global connectivity structure of manifolds

Supervision of lead developer

• scvelo: Dynamic model for RNA velocity for single cells
• scgen: Generative modeling of single-cell perturbation response

Major contributions

• Data Science Bowl 2017: major contributions to 7th prize (out of 2400 participating teams) winning deep learning pipeline in highest endowed ($1M prize money) machine learning competition 2017