TrendBio

#27 · Tools & infrastructure

Software tools for reproducible, interactive, and scalable computational biology

1 preprint · 3 published
Items per day, last 8 weekstoday: 4

The dominant thread is software infrastructure that makes computational biology models, analyses, and testing more accessible, reproducible, or scalable, rather than reporting new biological results. DeskIridium and WebIridium provide desktop and browser simulators for SBML and Antimony models, with real-time parameter exploration aimed at experimental biologists. hpci links CI platforms (GitHub Actions, GitLab CI) to HPC schedulers (Slurm, PBS) to automate testing of research code. COCOA.jl is a multithreaded Julia package for identifying concordant and kinetic modules in genome-scale biochemical networks, and PhyloZoo is a Python framework covering data structures, algorithms, visualization, and I/O for phylogenetic networks. Across these items, standard model formats, interactive or automated execution, and high-performance implementations each address a different step of the research workflow, which is the new element relative to prior tooling in this set.

Published papers

Preprints

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