synthetic-sciences/openscience
59 skills
$npx skills add synthetic-sciences/openscienceSkillInstalls
admet-predictionADMET property prediction for drug candidates. Full pharmacokinetic panel (Caco-2, PPB, clearance, CYP), toxicity (hERG, AMES, DILI), drug-likeness (Lipinski,…admet-reasoningInterpretable ADMET analysis with mechanistic reasoning. Maps liabilities to structural causes and biological pathways.anndataData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem.benchling-integrationBenchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for…binding-affinityHybrid ML + physics binding affinity prediction. Empirical scoring, MM/GBSA rescoring, multi-method consensus, and batch virtual screening for protein-ligand…bioimage-analysisMicroscopy image analysis for cell biology. Cell segmentation (Cellpose, watershed), object tracking (trackpy), morphology quantification, colony counting,…biopythonComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access…bioservicesUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with…bun-file-ioUse this when you are working on file operations like reading, writing, scanning, or deleting files.cancer-genomics-analysisComputational cancer genomics workflows. Somatic mutation detection and annotation, structural variation characterization, copy number analysis, tumor…clinical-decision-supportGenerate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses…clinical-imagingClinical and physiological imaging analysis. Diffusion MRI ADC maps, micro-CT bone morphometry, hemodynamic parameter analysis, circadian rhythm cosinor…clinical-reportsWrite comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3,…cobrapyConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.curated-bio-datasetsGuide to accessing curated biological datasets for computational biology.datamolPythonic wrapper around RDKit with simplified interface and sensible defaults.deepchemMolecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive…deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq…denovo-designDe novo molecule generation for drug discovery. Scaffold-based analog enumeration, fragment growing/linking, structure-based design, multi-objective…diffdockDiffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.dnanexus-integrationDNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline…drug-designEnd-to-end drug discovery pipeline orchestration. Deterministic Python script that auto-chains structure prediction, pocket detection, de novo design, docking,…esmComprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C…etetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for…flow-cytometry-analysisComplete flow cytometry analysis pipeline. FCS file handling, compensation, manual/automated gating, immunophenotyping, CFSE proliferation analysis, cell cycle…flowioParse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data…ggetFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis.glycobiologyGlycosylation site prediction and glycobiology analysis. N-glycosylation motif finding, O-glycosylation hotspot prediction, glycan structure resources.histolabLightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images.hypogenicAutomated LLM-driven hypothesis generation and testing on tabular datasets.immunology-assaysComputational analysis of immunology experimental data. ATAC-seq differential accessibility, immune cell tracking from microscopy, ELISA data processing with…lamindbThis skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR.latchbio-integrationLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir,…matchmsSpectral similarity and compound identification for metabolomics.medchemMedicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and…microbial-dynamicsMicrobial population dynamics modeling and analysis. Bacterial growth curve fitting (logistic, Gompertz, Baranyi), Lotka-Volterra community dynamics, Gillespie…molecular-cloningMolecular cloning simulation and design. PCR amplicon prediction, restriction enzyme digestion, Golden Gate and Gibson assembly simulation, primer design,…molecular-dockingEnd-to-end molecular docking pipeline. Target preparation, pocket detection, protein-ligand docking (DiffDock/Vina), scoring, interaction analysis, and pose…molecular-optimizationIterative lead optimization with analyze-reason-generate-verify-evaluate loop. Paper-backed (MT-Mol, DrugR, MultiMol).molecular-ragRetrieve structurally similar compounds with known properties from ChEMBL/ZINC to ground predictions and inform optimization. Based on MolRAG (Xian 2025, ACL).molecule-visualizationPublication-quality molecular visualization. 2D structure drawings (PNG/SVG), molecule grids with property annotations, scaffold highlighting, protein-ligand…neurokit2Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals.neuropixels-analysisNeuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL…omero-integrationMicroscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content…opentrons-integrationOfficial Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2…pathmlFull-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation,…pharmacology-wetlabComputational analysis of pharmacology wet-lab experiments. Western blot densitometry, xenograft tumor growth inhibition, pharmaceutical stability modeling…protocolsio-integrationIntegration with protocols.io API for managing scientific protocols.pydeseq2Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq…pydicomPython library for working with DICOM (Digital Imaging and Communications in Medicine) files.pyhealthComprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data.pylabrobotVendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified…pysamGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing…scanpyStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and…scikit-bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick…scikit-survivalComprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival.scvi-toolsDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with…synthetic-biologySynthetic biology design and simulation tools. Codon optimization, gene circuit ODE modeling with growth feedback, SBML model creation, bifurcation analysis,…treatment-plansGenerate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties.