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Compare a project .bib against a Paperpile project/topic folder to find uncited papers or unfiled entries. Use when the user asks to compare a project .bib against a Paperpile project/topic folder to …
turn a single-image bioimage workflow into a reproducible batch pipeline for folders of microscopy images. use when the task involves processing many tiff, ome-tiff, png, jpeg, czi, nd2, or lif files …
Design and implementation of reproducible bioinformatics and ML pipelines using workflow managers (Snakemake, Nextflow), containers (Singularity/Apptainer, Docker), conda environments with lock files,…
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downl…
Vision-language pre-training framework bridging frozen image encoders and LLMs. Use when you need image captioning, visual question answering, image-text retrieval, or multimodal chat with state-of-th…
Guides researchers through structured ideation frameworks to discover high-impact research directions. Use when exploring new problem spaces, pivoting between projects, or seeking novel angles on exis…
Design or audit the identification strategy for an observational study. Use when the task concerns estimands, causal assumptions, threats to identification, or defensible research design rather than m…
Use when creating, reading, or updating workflow checkpoint files (workflow-state.json, progress.log, init.sh) — the file-centric state system for cross-session computational workflows
Extract citations from a PDF and generate a validated .bib file. Use when the user asks to extract citations from a PDF and generate a validated .bib file. Reads the PDF, identifies referenced works, …
detect, inspect, and load common bioimage files into python and napari with a tiff-first workflow. use when a task starts from microscopy image files or folders, especially tiff or ome-tiff, but also …
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biome…
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analys…
Autonomous VTI sourcing. Discovers popular repositories that depend on a target SDK, fans out a fleet of subagents to scout each one for silent footguns, proves every candidate RED→GREEN, auto-promote…
Review branch changes against `master` using a diff-to-master workflow that emphasizes correctness, regressions, API breaks, side effects, and missing tests. Use when the user asks to review a branch …
run cellpose-based segmentation for common bioimage analysis tasks in python, cli, or gui workflows, including 2d, 3d, batch processing, model selection, parameter tuning, result export, and optional …
Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.
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measure segmented bioimage objects, generate qc summaries, and export tables, plots, scripts, and notebooks for microscopy analysis. use when labels or masks already exist or when a segmentation resul…
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, cu…
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Sends an agent on a scouting mission to find real-world coding traps (footguns in popular SDKs/protocols), synthesize the finding into a proven brainblast rule pack, and submit it to the pack registry…
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level cou…
Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summa…
Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.