Marco Masera

Marco Masera, Riccardo Smeriglio, Roberta Bardini et al.

We present PhysiBench, an open resource for developing and evaluating computational methods in systems biology including a benchmark suite of 612 executable intracellular Boolean regulatory network variants and a dataset of 120,000 time-resolved multiscale stochastic simulations. The benchmark models are derived from seven published Boolean networks spanning cell-cycle control, developmental patterning, cancer signaling, immune response, and cell-fate decisions, and are executable in the PhysiBoSS/PhysiCell multiscale simulation framework. Model variants are generated through mutation-based model construction, online behavioral filtering, and offline sensitivity evaluation. The simulation dataset is produced from 60 selected models under systematically sampled stimulation protocols and fixed model-level initial configurations. Each trajectory is linked to its model identifier, input-parameter file, stochastic seed, and cell-level output file. PhysiBench supports direct simulation, surrogate modeling, data-driven inference, simulation-based optimization, and comparative benchmarking. Technical validation includes file-integrity and executability checks, graph-based structural diversity analyses, and behavioral heterogeneity assessment from multiscale simulation outputs.

Marco Masera, Alessandro Leone, Johannes Köster et al.

Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces Snakemaker, a tool that leverages generative AI to facilitate researchers build sustainable data analysis pipelines by converting unstructured code into well-defined Snakemake workflows. Snakemaker non-invasively tracks the work performed in the terminal by the researcher, analyzes execution patterns, and generates Snakemake workflows that can be integrated into existing pipelines. Snakemaker also supports the transformation of monolithic Ipython Notebooks into modular Snakemake pipelines, resolving the global state of the notebook into discrete, file-based interactions between rules. An integrated chat assistant provides users with fine-grained control through natural language instructions. Snakemaker generates high-quality Snakemake workflows by adhering to the best practices, including Conda environment tracking, generic rule generation and loop unrolling. By lowering the barrier between prototype and production-quality code, Snakemaker addresses a critical gap in computational reproducibility for bioinformatics research.