samuell/scicommander

The Bioinformatician’s Interactive Lab Notebook (BILN) is a smart, dynamic system for tracking experiments, datasets, and workflows. Designed for bioinformaticians, it ensures reproducibility, structured logging, and AI-readiness. Export logs, collaborate seamlessly, and let BILN become your interactive companion in computational biology.

Local-first CLI for reproducible biological analysis, with provenance tracked on every step.

Wrap Python functions and shell commands as content-addressed transformations. Cache results, run them locally or on a cluster, and share them by checksum.

A lightweight Python CLI for batch experiments: auto-generate tasks from configs, run in parallel, and track results with real-time monitoring.

Local natural-language-to-shell command generator. A 941 MB fine-tuned Qwen2.5-Coder-1.5B running on CPU in ~1s.

LocalOps Copilot

Visualize your shell usage with Highcharts!

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Run reproducible scientific workflows anywhere (laptop, remote, or HPC cluster) from a single YAML file. The open-source runtime behind Temple Compute.