This skill bridges a conversational interface and a scientific execution environment covering RNA-seq, single-cell RNA-seq, variant calling, molecular docking, virtual screening, ADMET prediction, survival analysis, clinical trial search, proteomics, metabolomics, pathway enrichment, DICOM processing, digital pathology, literature review and scientific writing. It identifies the task type, locates input data under a workspace data folder (asking the user if no path is given), and sets up a live dashboard by copying a dashboard template into a per-task folder with output and dashboard subfolders.
Long tasks with several stages, such as literature search, outline, body text, figures and PDF compilation, are split into separate Claude Code sessions, each doing one stage, because a single session running past about ten minutes tends to stall. Each session's prompt names the exact scientific skill file to read first, the input and output paths, and the dashboard state file to update after each step, with table data referenced by file path rather than inlined and image paths given as absolute paths.
Execution runs through the Claude Code CLI, preferably in stream-json mode with hooks, and progress is checked through the hooks' progress file, restarting a run if it stalls for more than five minutes.