Agent Skills catalog · page 64
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synthetic-sciences/openscience
imaging-data-commons
Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
synthetic-sciences/openscience
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
synthetic-sciences/openscience
benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
synthetic-sciences/openscience
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug develo
synthetic-sciences/openscience
dask
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.
synthetic-sciences/openscience
ml-paper-writing
Write publication-ready ML/AI papers for NeurIPS, ICML, ICLR, ACL, AAAI, COLM. Use when drafting papers from research repos, structuring arguments, verifying citations, or preparing camera-ready submissions. Includes LaTeX templates, reviewer guidelines, and citation verification workflows.
synthetic-sciences/openscience
molecular-cloning
Molecular cloning simulation and design. PCR amplicon prediction, restriction enzyme digestion, Golden Gate and Gibson assembly simulation, primer design, CRISPR sgRNA design, and plasmid annotation. For protein-level sequence analysis use biopython or esm; for database lookups use gene-database or ensembl-database.
synthetic-sciences/openscience
opentargets-database
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
synthetic-sciences/openscience
shap
Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analyzing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model
synthetic-sciences/openscience
bioimage-analysis
Microscopy image analysis for cell biology. Cell segmentation (Cellpose, watershed), object tracking (trackpy), morphology quantification, colony counting, colocalization analysis, and cytoskeleton characterization. For pathology WSI use pathml; for flow cytometry use flow-cytometry-analysis.
synthetic-sciences/openscience
exploratory-data-analysis
Analyze scientific data files across 200+ formats at the depth the user requests. Detect file type, assess structure, quality, and statistics, and create reports or visualizations only when they are requested or materially needed. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
synthetic-sciences/openscience
hugging-face-model-trainer
This skill should be used when users want to train or fine-tune language models using TRL (Transformer Reinforcement Learning) on Hugging Face Jobs infrastructure. Covers SFT, DPO, GRPO and reward modeling training methods, plus GGUF conversion for local deployment. Includes guidance on the TRL Jobs package, UV scripts with PEP 723 format, dataset preparation and validation, hardware selection, cost estimation, Trackio monitoring, Hub authentication, and model persistence. Should be invoked for
synthetic-sciences/openscience
instructor
Extract structured data from LLM responses with Pydantic validation, retry failed extractions automatically, parse complex JSON with type safety, and stream partial results with Instructor - battle-tested structured output library
synthetic-sciences/openscience
latchbio-integration
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
synthetic-sciences/openscience
market-research-reports
Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter's Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix.
synthetic-sciences/openscience
prime-intellect-lab
Expert guidance for hosted RL post-training with Prime Intellect Lab — environments, verifiers, GEPA prompt optimization, and agentic training
synthetic-sciences/openscience
synthetic-biology
Synthetic biology design and simulation tools. Codon optimization, gene circuit ODE modeling with growth feedback, SBML model creation, bifurcation analysis, barcode sequencing fitness analysis, and therapeutic genome engineering. For metabolic modeling use cobrapy; for sequence tools use biopython.
synthetic-sciences/openscience
deepspeed
Expert guidance for distributed training with DeepSpeed - ZeRO optimization stages, pipeline parallelism, FP16/BF16/FP8, 1-bit Adam, sparse attention
synthetic-sciences/openscience
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
synthetic-sciences/openscience
flow-cytometry-analysis
Complete flow cytometry analysis pipeline. FCS file handling, compensation, manual/automated gating, immunophenotyping, CFSE proliferation analysis, cell cycle analysis (Dean-Jett-Fox), and apoptosis assays. Extends flowio with analytical workflows. For raw FCS parsing only use flowio.
synthetic-sciences/openscience
gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
synthetic-sciences/openscience
hugging-face-jobs
This skill should be used when users want to run any workload on Hugging Face Jobs infrastructure. Covers UV scripts, Docker-based jobs, hardware selection, cost estimation, authentication with tokens, secrets management, timeout configuration, and result persistence. Designed for general-purpose compute workloads including data processing, inference, experiments, batch jobs, and any Python-based tasks. Should be invoked for tasks involving cloud compute, GPU workloads, or when users mention run
synthetic-sciences/openscience
hugging-face-paper-publisher
Publish and manage research papers on Hugging Face Hub. Supports creating paper pages, linking papers to models/datasets, claiming authorship, and generating professional markdown-based research articles.
synthetic-sciences/openscience
immunology-assays
Computational analysis of immunology experimental data. ATAC-seq differential accessibility, immune cell tracking from microscopy, ELISA data processing with 4-parameter logistic fitting, immunohistochemistry quantification, antibody titer analysis, and cell cycle phase duration estimation. For flow cytometry use flow-cytometry-analysis; for scRNA-seq use scanpy.