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marimo-notebook
Write a marimo notebook in a Python file in the right format.
saving-codeacts
Save executed Python code as reusable tools in the gentools package. Use when preserving successful code executions for later reuse. Covers creating package structure (api.py, impl.py), defining Pydantic output models, and implementing the run() interface.
synthetic-data-generation
Generate synthetic data using sdg_hub with composable blocks and YAML flows. Use when the user wants to create training datasets, generate QA pairs, run data generation pipelines, build custom flows, produce synthetic data from documents, use agent frameworks for data generation, or distill MCP tool-use traces. Supports pre-built flows, custom Python scripts, and YAML flow authoring with 20+ blocks, agent connectors (Langflow, LangGraph), MCP tool-use, and 100+ LLM providers via LiteLLM.
code-runner
在线代码执行：支持 Python、JavaScript、TypeScript、Go、Rust、Java、C/C++、Ruby、PHP 等语言的沙箱运行。
python-code-injection
Exploit Python eval(), exec(), and compile() injection in web applications. Distinct from OS command injection (shell operators) and SSTI (template engines) — this targets direct Python code evaluation of user input.
meta-forest-model-plot
Generate forest plots for meta-analysis of survival data. Input is a CSV file containing study names, HR and 95% confidence intervals, output forest plot PNG and data table CSV. Supports both R and Python scripts.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.
biopython-entrez
Use Bio.Entrez to access NCBI databases (e.g., PubMed/GenBank) for searching, fetching summaries, and downloading records when your workflow needs to call the NCBI E-utilities API over the network.
volcano-plot-script
Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expression data, p-value vs fold-change scatter plots, publication-ready figures for bioinformatics analysis.
biopython-sequence-io
Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O, lightweight sequence manipulation, or scalable processing of large sequence datasets.
biopython-alignment
Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.
biopython-phylo
Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.
biopython-advanced
Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.
scikit-bio
A Python bioinformatics toolkit for sequence, phylogeny, and microbiome/community-ecology analysis; use it when you need to compute diversity/ordination/statistics from biological data and standard formats (FASTA/FASTQ/Newick/BIOM).