Daniel H. Huson

Scientific Software Engineering

Design and implementation of research-grade software systems for bioinformatics, phylogenetics, and scientific visualization.

Areas include Java and JavaFX systems, cross-platform deployment, mobile scientific applications, software architecture, visualization design, and modernization of legacy software.

Algorithm Implementation

Implementation and visualization of advanced algorithms from computational biology and related fields.

This includes prototype systems, interactive interfaces, deployment workflows, and integration into larger software platforms.

Mini Projects and Software Modernization

Short focused collaborations to transform research prototypes into usable software systems.

Typical projects include: graphical interfaces, packaging and installers, GitHub workflows, macOS notarization, cross-platform deployment, and interactive visualization systems.

Workshops and Visiting Engagements

Available for workshops, block courses, visiting collaborations, and scientific software mentoring.

Topics include: advanced Java, scientific visualization, AI-assisted software engineering, algorithms in bioinformatics, and research software architecture.

Example Collaboration: PICL

Collaboration with Prof. Laura Kubatko at The Ohio State University on the PICL phylogenetics system.

The original PICL C implementation is available at github.com/lkubatko/PICL .

The modernized JavaFX-based graphical system, deployment infrastructure, and cross-platform installers are available as https://github.com/husonlab/jpicl .

Work included GUI design, native-code integration, GitHub Actions workflows, cross-platform installers, and macOS notarization.

This project illustrates a focused scientific software modernization collaboration: transforming advanced computational methods into polished and deployable research software systems.